Starting phenix.real_space_refine on Mon Mar 11 08:51:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vx3_21428/03_2024/6vx3_21428_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vx3_21428/03_2024/6vx3_21428.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vx3_21428/03_2024/6vx3_21428.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vx3_21428/03_2024/6vx3_21428.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vx3_21428/03_2024/6vx3_21428_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vx3_21428/03_2024/6vx3_21428_neut_updated.pdb" } resolution = 3.7 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 24 5.16 5 C 5336 2.51 5 N 1188 2.21 5 O 1224 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 23": "NH1" <-> "NH2" Residue "C PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 51": "OD1" <-> "OD2" Residue "C PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 60": "OD1" <-> "OD2" Residue "C GLU 70": "OE1" <-> "OE2" Residue "C PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 86": "NH1" <-> "NH2" Residue "C PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 132": "NH1" <-> "NH2" Residue "C ASP 135": "OD1" <-> "OD2" Residue "C TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 23": "NH1" <-> "NH2" Residue "A PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 51": "OD1" <-> "OD2" Residue "A PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 60": "OD1" <-> "OD2" Residue "A GLU 70": "OE1" <-> "OE2" Residue "A PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 86": "NH1" <-> "NH2" Residue "A PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 132": "NH1" <-> "NH2" Residue "A ASP 135": "OD1" <-> "OD2" Residue "A TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 23": "NH1" <-> "NH2" Residue "B PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 51": "OD1" <-> "OD2" Residue "B PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 60": "OD1" <-> "OD2" Residue "B GLU 70": "OE1" <-> "OE2" Residue "B PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 86": "NH1" <-> "NH2" Residue "B PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 132": "NH1" <-> "NH2" Residue "B ASP 135": "OD1" <-> "OD2" Residue "B TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 23": "NH1" <-> "NH2" Residue "D PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 51": "OD1" <-> "OD2" Residue "D PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 60": "OD1" <-> "OD2" Residue "D GLU 70": "OE1" <-> "OE2" Residue "D PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 86": "NH1" <-> "NH2" Residue "D PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 132": "NH1" <-> "NH2" Residue "D ASP 135": "OD1" <-> "OD2" Residue "D TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7780 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 1841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1841 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "A" Number of atoms: 1841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1841 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "B" Number of atoms: 1841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1841 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "D" Number of atoms: 1841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1841 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "C" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 104 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 104 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 104 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 104 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.56, per 1000 atoms: 0.59 Number of scatterers: 7780 At special positions: 0 Unit cell: (125.882, 125.882, 65.726, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 24 16.00 P 8 15.00 O 1224 8.00 N 1188 7.00 C 5336 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.14 Conformation dependent library (CDL) restraints added in 1.3 seconds 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1728 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 0 sheets defined 65.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'C' and resid 25 through 44 removed outlier: 3.554A pdb=" N ILE C 42 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THR C 44 " --> pdb=" O VAL C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 51 Processing helix chain 'C' and resid 53 through 75 removed outlier: 4.310A pdb=" N ARG C 58 " --> pdb=" O TRP C 54 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE C 69 " --> pdb=" O TRP C 65 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU C 70 " --> pdb=" O ILE C 66 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG C 74 " --> pdb=" O GLU C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 105 removed outlier: 3.794A pdb=" N ALA C 104 " --> pdb=" O GLY C 100 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N GLY C 105 " --> pdb=" O HIS C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 124 removed outlier: 4.377A pdb=" N VAL C 120 " --> pdb=" O ARG C 116 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N LEU C 121 " --> pdb=" O VAL C 117 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ARG C 122 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ALA C 123 " --> pdb=" O ARG C 119 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ILE C 124 " --> pdb=" O VAL C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 139 Processing helix chain 'C' and resid 147 through 165 removed outlier: 3.860A pdb=" N PHE C 155 " --> pdb=" O MET C 151 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N PHE C 158 " --> pdb=" O PHE C 154 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N THR C 163 " --> pdb=" O ALA C 159 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N MET C 164 " --> pdb=" O VAL C 160 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU C 165 " --> pdb=" O ILE C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 174 No H-bonds generated for 'chain 'C' and resid 171 through 174' Processing helix chain 'C' and resid 177 through 186 removed outlier: 4.181A pdb=" N LEU C 182 " --> pdb=" O GLN C 178 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N THR C 183 " --> pdb=" O LEU C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 202 Processing helix chain 'C' and resid 206 through 212 removed outlier: 4.388A pdb=" N TRP C 209 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU C 210 " --> pdb=" O TRP C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 236 removed outlier: 3.576A pdb=" N PHE C 227 " --> pdb=" O ILE C 223 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN C 233 " --> pdb=" O GLY C 229 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASN C 234 " --> pdb=" O VAL C 230 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL C 235 " --> pdb=" O ILE C 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 44 removed outlier: 3.554A pdb=" N ILE A 42 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THR A 44 " --> pdb=" O VAL A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 51 Processing helix chain 'A' and resid 53 through 75 removed outlier: 4.311A pdb=" N ARG A 58 " --> pdb=" O TRP A 54 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE A 69 " --> pdb=" O TRP A 65 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU A 70 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG A 74 " --> pdb=" O GLU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 105 removed outlier: 3.795A pdb=" N ALA A 104 " --> pdb=" O GLY A 100 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N GLY A 105 " --> pdb=" O HIS A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 124 removed outlier: 4.377A pdb=" N VAL A 120 " --> pdb=" O ARG A 116 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N LEU A 121 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ARG A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ALA A 123 " --> pdb=" O ARG A 119 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ILE A 124 " --> pdb=" O VAL A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 139 Processing helix chain 'A' and resid 147 through 165 removed outlier: 3.860A pdb=" N PHE A 155 " --> pdb=" O MET A 151 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N PHE A 158 " --> pdb=" O PHE A 154 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N THR A 163 " --> pdb=" O ALA A 159 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N MET A 164 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A 165 " --> pdb=" O ILE A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 174 No H-bonds generated for 'chain 'A' and resid 171 through 174' Processing helix chain 'A' and resid 177 through 186 removed outlier: 4.182A pdb=" N LEU A 182 " --> pdb=" O GLN A 178 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR A 183 " --> pdb=" O LEU A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 202 Processing helix chain 'A' and resid 206 through 212 removed outlier: 4.388A pdb=" N TRP A 209 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU A 210 " --> pdb=" O TRP A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 236 removed outlier: 3.576A pdb=" N PHE A 227 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN A 233 " --> pdb=" O GLY A 229 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASN A 234 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL A 235 " --> pdb=" O ILE A 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 44 removed outlier: 3.553A pdb=" N ILE B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR B 44 " --> pdb=" O VAL B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 51 Processing helix chain 'B' and resid 53 through 75 removed outlier: 4.310A pdb=" N ARG B 58 " --> pdb=" O TRP B 54 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE B 59 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE B 69 " --> pdb=" O TRP B 65 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU B 70 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG B 74 " --> pdb=" O GLU B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 105 removed outlier: 3.794A pdb=" N ALA B 104 " --> pdb=" O GLY B 100 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N GLY B 105 " --> pdb=" O HIS B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 124 removed outlier: 4.376A pdb=" N VAL B 120 " --> pdb=" O ARG B 116 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N LEU B 121 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ARG B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N ALA B 123 " --> pdb=" O ARG B 119 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ILE B 124 " --> pdb=" O VAL B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 139 Processing helix chain 'B' and resid 147 through 165 removed outlier: 3.861A pdb=" N PHE B 155 " --> pdb=" O MET B 151 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N PHE B 158 " --> pdb=" O PHE B 154 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N THR B 163 " --> pdb=" O ALA B 159 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N MET B 164 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 165 " --> pdb=" O ILE B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 174 No H-bonds generated for 'chain 'B' and resid 171 through 174' Processing helix chain 'B' and resid 177 through 186 removed outlier: 4.182A pdb=" N LEU B 182 " --> pdb=" O GLN B 178 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N THR B 183 " --> pdb=" O LEU B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 202 Processing helix chain 'B' and resid 206 through 212 removed outlier: 4.388A pdb=" N TRP B 209 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU B 210 " --> pdb=" O TRP B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 236 removed outlier: 3.577A pdb=" N PHE B 227 " --> pdb=" O ILE B 223 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN B 233 " --> pdb=" O GLY B 229 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASN B 234 " --> pdb=" O VAL B 230 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL B 235 " --> pdb=" O ILE B 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 44 removed outlier: 3.553A pdb=" N ILE D 42 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR D 44 " --> pdb=" O VAL D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 51 Processing helix chain 'D' and resid 53 through 75 removed outlier: 4.310A pdb=" N ARG D 58 " --> pdb=" O TRP D 54 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE D 59 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE D 69 " --> pdb=" O TRP D 65 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU D 70 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG D 74 " --> pdb=" O GLU D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 105 removed outlier: 3.794A pdb=" N ALA D 104 " --> pdb=" O GLY D 100 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N GLY D 105 " --> pdb=" O HIS D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 124 removed outlier: 4.377A pdb=" N VAL D 120 " --> pdb=" O ARG D 116 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N LEU D 121 " --> pdb=" O VAL D 117 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ARG D 122 " --> pdb=" O LEU D 118 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N ALA D 123 " --> pdb=" O ARG D 119 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ILE D 124 " --> pdb=" O VAL D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 139 Processing helix chain 'D' and resid 147 through 165 removed outlier: 3.860A pdb=" N PHE D 155 " --> pdb=" O MET D 151 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N PHE D 158 " --> pdb=" O PHE D 154 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N THR D 163 " --> pdb=" O ALA D 159 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N MET D 164 " --> pdb=" O VAL D 160 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU D 165 " --> pdb=" O ILE D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 174 No H-bonds generated for 'chain 'D' and resid 171 through 174' Processing helix chain 'D' and resid 177 through 186 removed outlier: 4.181A pdb=" N LEU D 182 " --> pdb=" O GLN D 178 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR D 183 " --> pdb=" O LEU D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 202 Processing helix chain 'D' and resid 206 through 212 removed outlier: 4.388A pdb=" N TRP D 209 " --> pdb=" O PRO D 206 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU D 210 " --> pdb=" O TRP D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 236 removed outlier: 3.577A pdb=" N PHE D 227 " --> pdb=" O ILE D 223 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN D 233 " --> pdb=" O GLY D 229 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASN D 234 " --> pdb=" O VAL D 230 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL D 235 " --> pdb=" O ILE D 231 " (cutoff:3.500A) 292 hydrogen bonds defined for protein. 852 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: 1.84 Time building geometry restraints manager: 3.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1914 1.33 - 1.45: 1531 1.45 - 1.57: 4479 1.57 - 1.69: 16 1.69 - 1.80: 48 Bond restraints: 7988 Sorted by residual: bond pdb=" C31 POV A 301 " pdb=" O31 POV A 301 " ideal model delta sigma weight residual 1.327 1.454 -0.127 2.00e-02 2.50e+03 4.02e+01 bond pdb=" C31 POV C 301 " pdb=" O31 POV C 301 " ideal model delta sigma weight residual 1.327 1.453 -0.126 2.00e-02 2.50e+03 3.99e+01 bond pdb=" C31 POV B 301 " pdb=" O31 POV B 301 " ideal model delta sigma weight residual 1.327 1.453 -0.126 2.00e-02 2.50e+03 3.98e+01 bond pdb=" C31 POV D 301 " pdb=" O31 POV D 301 " ideal model delta sigma weight residual 1.327 1.453 -0.126 2.00e-02 2.50e+03 3.97e+01 bond pdb=" C31 POV A 302 " pdb=" O31 POV A 302 " ideal model delta sigma weight residual 1.327 1.451 -0.124 2.00e-02 2.50e+03 3.81e+01 ... (remaining 7983 not shown) Histogram of bond angle deviations from ideal: 100.14 - 106.92: 188 106.92 - 113.71: 4700 113.71 - 120.49: 3136 120.49 - 127.28: 2680 127.28 - 134.06: 100 Bond angle restraints: 10804 Sorted by residual: angle pdb=" C PHE D 67 " pdb=" N THR D 68 " pdb=" CA THR D 68 " ideal model delta sigma weight residual 120.82 127.73 -6.91 1.50e+00 4.44e-01 2.12e+01 angle pdb=" C PHE A 67 " pdb=" N THR A 68 " pdb=" CA THR A 68 " ideal model delta sigma weight residual 120.82 127.70 -6.88 1.50e+00 4.44e-01 2.10e+01 angle pdb=" C PHE C 67 " pdb=" N THR C 68 " pdb=" CA THR C 68 " ideal model delta sigma weight residual 120.82 127.69 -6.87 1.50e+00 4.44e-01 2.10e+01 angle pdb=" N ILE D 59 " pdb=" CA ILE D 59 " pdb=" C ILE D 59 " ideal model delta sigma weight residual 110.72 115.33 -4.61 1.01e+00 9.80e-01 2.08e+01 angle pdb=" C PHE B 67 " pdb=" N THR B 68 " pdb=" CA THR B 68 " ideal model delta sigma weight residual 120.82 127.66 -6.84 1.50e+00 4.44e-01 2.08e+01 ... (remaining 10799 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.06: 4112 22.06 - 44.12: 436 44.12 - 66.18: 84 66.18 - 88.23: 28 88.23 - 110.29: 8 Dihedral angle restraints: 4668 sinusoidal: 2020 harmonic: 2648 Sorted by residual: dihedral pdb=" C29 POV C 301 " pdb="C210 POV C 301 " pdb="C211 POV C 301 " pdb="C212 POV C 301 " ideal model delta sinusoidal sigma weight residual 112.25 -137.46 -110.29 1 3.00e+01 1.11e-03 1.44e+01 dihedral pdb=" C29 POV A 301 " pdb="C210 POV A 301 " pdb="C211 POV A 301 " pdb="C212 POV A 301 " ideal model delta sinusoidal sigma weight residual 112.25 -137.46 -110.29 1 3.00e+01 1.11e-03 1.44e+01 dihedral pdb=" C29 POV D 301 " pdb="C210 POV D 301 " pdb="C211 POV D 301 " pdb="C212 POV D 301 " ideal model delta sinusoidal sigma weight residual 112.25 -137.47 -110.28 1 3.00e+01 1.11e-03 1.44e+01 ... (remaining 4665 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 691 0.036 - 0.072: 381 0.072 - 0.108: 127 0.108 - 0.145: 21 0.145 - 0.181: 12 Chirality restraints: 1232 Sorted by residual: chirality pdb=" CA LEU A 177 " pdb=" N LEU A 177 " pdb=" C LEU A 177 " pdb=" CB LEU A 177 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.17e-01 chirality pdb=" CA LEU C 177 " pdb=" N LEU C 177 " pdb=" C LEU C 177 " pdb=" CB LEU C 177 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.07e-01 chirality pdb=" CA LEU B 177 " pdb=" N LEU B 177 " pdb=" C LEU B 177 " pdb=" CB LEU B 177 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.95e-01 ... (remaining 1229 not shown) Planarity restraints: 1256 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 64 " 0.015 2.00e-02 2.50e+03 2.96e-02 8.73e+00 pdb=" C LEU B 64 " -0.051 2.00e-02 2.50e+03 pdb=" O LEU B 64 " 0.019 2.00e-02 2.50e+03 pdb=" N TRP B 65 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 64 " 0.015 2.00e-02 2.50e+03 2.94e-02 8.66e+00 pdb=" C LEU D 64 " -0.051 2.00e-02 2.50e+03 pdb=" O LEU D 64 " 0.019 2.00e-02 2.50e+03 pdb=" N TRP D 65 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 64 " -0.015 2.00e-02 2.50e+03 2.94e-02 8.64e+00 pdb=" C LEU C 64 " 0.051 2.00e-02 2.50e+03 pdb=" O LEU C 64 " -0.019 2.00e-02 2.50e+03 pdb=" N TRP C 65 " -0.017 2.00e-02 2.50e+03 ... (remaining 1253 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 48 2.44 - 3.06: 5589 3.06 - 3.67: 10815 3.67 - 4.29: 16073 4.29 - 4.90: 26183 Nonbonded interactions: 58708 Sorted by model distance: nonbonded pdb=" OD2 ASP D 60 " pdb=" NH2 ARG D 116 " model vdw 1.829 2.520 nonbonded pdb=" OD2 ASP A 60 " pdb=" NH2 ARG A 116 " model vdw 1.829 2.520 nonbonded pdb=" OD2 ASP C 60 " pdb=" NH2 ARG C 116 " model vdw 1.829 2.520 nonbonded pdb=" OD2 ASP B 60 " pdb=" NH2 ARG B 116 " model vdw 1.830 2.520 nonbonded pdb=" O GLN D 178 " pdb=" O32 POV D 302 " model vdw 2.014 3.040 ... (remaining 58703 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' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.900 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: 0.010 Extract box with map and model: 3.400 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 25.020 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 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 : 0.009 0.127 7988 Z= 0.533 Angle : 1.110 10.264 10804 Z= 0.573 Chirality : 0.049 0.181 1232 Planarity : 0.004 0.030 1256 Dihedral : 19.669 110.293 2940 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 25.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 4.02 % Allowed : 10.55 % Favored : 85.43 % 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: -4.21 (0.24), residues: 892 helix: -2.22 (0.18), residues: 580 sheet: None (None), residues: 0 loop : -3.72 (0.30), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 91 HIS 0.003 0.001 HIS D 22 PHE 0.023 0.002 PHE D 155 TYR 0.008 0.001 TYR C 173 ARG 0.001 0.000 ARG B 74 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 200 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 48 ILE cc_start: 0.8702 (OUTLIER) cc_final: 0.8310 (mm) REVERT: C 57 TYR cc_start: 0.6466 (OUTLIER) cc_final: 0.5184 (t80) REVERT: C 191 GLU cc_start: 0.8749 (tm-30) cc_final: 0.8352 (tm-30) REVERT: C 224 PHE cc_start: 0.7177 (t80) cc_final: 0.6607 (t80) REVERT: C 234 ASN cc_start: 0.8423 (t0) cc_final: 0.8048 (t0) REVERT: A 48 ILE cc_start: 0.8701 (OUTLIER) cc_final: 0.8334 (mm) REVERT: A 57 TYR cc_start: 0.6508 (OUTLIER) cc_final: 0.5307 (t80) REVERT: A 191 GLU cc_start: 0.8716 (tm-30) cc_final: 0.8357 (tm-30) REVERT: A 224 PHE cc_start: 0.7025 (t80) cc_final: 0.6623 (t80) REVERT: B 48 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8348 (mm) REVERT: B 57 TYR cc_start: 0.6634 (OUTLIER) cc_final: 0.5536 (t80) REVERT: B 63 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8594 (mm) REVERT: B 191 GLU cc_start: 0.8723 (tm-30) cc_final: 0.8063 (tm-30) REVERT: D 48 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8320 (mm) REVERT: D 57 TYR cc_start: 0.6457 (OUTLIER) cc_final: 0.5180 (t80) REVERT: D 191 GLU cc_start: 0.8750 (tm-30) cc_final: 0.8144 (tm-30) REVERT: D 224 PHE cc_start: 0.7133 (t80) cc_final: 0.6883 (t80) outliers start: 32 outliers final: 14 residues processed: 220 average time/residue: 0.1358 time to fit residues: 44.1059 Evaluate side-chains 177 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 154 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 65 TRP Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 57 TYR Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 57 TYR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 65 TRP Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 65 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 chunk 37 optimal weight: 0.6980 chunk 22 optimal weight: 20.0000 chunk 44 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 41 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 79 optimal weight: 0.0170 overall best weight: 0.9220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 ASN ** C 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 79 ASN ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 ASN ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 ASN ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7988 Z= 0.219 Angle : 0.601 8.787 10804 Z= 0.299 Chirality : 0.041 0.109 1232 Planarity : 0.003 0.023 1256 Dihedral : 20.401 111.796 1358 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 4.52 % Allowed : 21.61 % Favored : 73.87 % 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: -3.36 (0.25), residues: 892 helix: -1.61 (0.19), residues: 632 sheet: None (None), residues: 0 loop : -3.49 (0.32), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 54 HIS 0.005 0.002 HIS B 101 PHE 0.014 0.001 PHE B 224 TYR 0.006 0.001 TYR C 156 ARG 0.002 0.000 ARG B 116 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 181 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 35 PHE cc_start: 0.8828 (t80) cc_final: 0.8484 (t80) REVERT: C 57 TYR cc_start: 0.7022 (OUTLIER) cc_final: 0.5876 (t80) REVERT: C 65 TRP cc_start: 0.5836 (OUTLIER) cc_final: 0.4335 (t60) REVERT: C 139 MET cc_start: 0.8198 (tpp) cc_final: 0.7772 (tpp) REVERT: C 191 GLU cc_start: 0.8588 (tm-30) cc_final: 0.8210 (tm-30) REVERT: C 201 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8614 (mt) REVERT: A 35 PHE cc_start: 0.8767 (t80) cc_final: 0.8387 (t80) REVERT: A 57 TYR cc_start: 0.7019 (OUTLIER) cc_final: 0.5885 (t80) REVERT: A 65 TRP cc_start: 0.5805 (OUTLIER) cc_final: 0.4309 (t60) REVERT: A 139 MET cc_start: 0.8286 (tpp) cc_final: 0.7853 (tpp) REVERT: A 191 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8161 (tm-30) REVERT: A 201 ILE cc_start: 0.8873 (OUTLIER) cc_final: 0.8620 (mt) REVERT: B 35 PHE cc_start: 0.8738 (t80) cc_final: 0.8338 (t80) REVERT: B 57 TYR cc_start: 0.6899 (OUTLIER) cc_final: 0.5725 (t80) REVERT: B 65 TRP cc_start: 0.5769 (OUTLIER) cc_final: 0.4287 (t60) REVERT: B 191 GLU cc_start: 0.8575 (tm-30) cc_final: 0.7926 (tm-30) REVERT: B 201 ILE cc_start: 0.8880 (OUTLIER) cc_final: 0.8633 (mt) REVERT: D 35 PHE cc_start: 0.8784 (t80) cc_final: 0.8389 (t80) REVERT: D 57 TYR cc_start: 0.6954 (OUTLIER) cc_final: 0.5664 (t80) REVERT: D 65 TRP cc_start: 0.5752 (OUTLIER) cc_final: 0.4247 (t60) REVERT: D 191 GLU cc_start: 0.8580 (tm-30) cc_final: 0.7996 (tm-30) REVERT: D 201 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8611 (mt) outliers start: 36 outliers final: 17 residues processed: 197 average time/residue: 0.1437 time to fit residues: 41.3615 Evaluate side-chains 192 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 163 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 MET Chi-restraints excluded: chain C residue 27 PHE Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain C residue 65 TRP Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 57 TYR Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 57 TYR Chi-restraints excluded: chain B residue 65 TRP Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain D residue 65 TRP Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 230 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 66 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 64 optimal weight: 0.4980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 101 HIS C 146 ASN A 101 HIS A 146 ASN B 101 HIS B 146 ASN D 101 HIS D 146 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7988 Z= 0.285 Angle : 0.574 6.169 10804 Z= 0.291 Chirality : 0.041 0.110 1232 Planarity : 0.003 0.024 1256 Dihedral : 19.103 109.925 1328 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 7.16 % Allowed : 23.24 % Favored : 69.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.26), residues: 892 helix: -1.20 (0.20), residues: 624 sheet: None (None), residues: 0 loop : -3.09 (0.33), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 54 HIS 0.002 0.001 HIS B 101 PHE 0.016 0.001 PHE D 224 TYR 0.005 0.001 TYR D 173 ARG 0.002 0.000 ARG B 58 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 180 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 35 PHE cc_start: 0.8749 (t80) cc_final: 0.8254 (t80) REVERT: C 57 TYR cc_start: 0.6932 (OUTLIER) cc_final: 0.5663 (t80) REVERT: C 139 MET cc_start: 0.8386 (tpp) cc_final: 0.8011 (tpp) REVERT: C 191 GLU cc_start: 0.8631 (tm-30) cc_final: 0.8240 (tm-30) REVERT: A 57 TYR cc_start: 0.7020 (OUTLIER) cc_final: 0.5824 (t80) REVERT: A 59 ILE cc_start: 0.8604 (tp) cc_final: 0.8355 (tp) REVERT: A 63 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8947 (mm) REVERT: A 65 TRP cc_start: 0.6435 (OUTLIER) cc_final: 0.4518 (t60) REVERT: A 139 MET cc_start: 0.8520 (tpp) cc_final: 0.8065 (tpp) REVERT: A 191 GLU cc_start: 0.8617 (tm-30) cc_final: 0.8146 (tm-30) REVERT: B 57 TYR cc_start: 0.6966 (OUTLIER) cc_final: 0.5682 (t80) REVERT: B 59 ILE cc_start: 0.8552 (tp) cc_final: 0.8253 (tp) REVERT: B 63 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8822 (mm) REVERT: B 191 GLU cc_start: 0.8630 (tm-30) cc_final: 0.7931 (tm-30) REVERT: D 35 PHE cc_start: 0.8783 (t80) cc_final: 0.8268 (t80) REVERT: D 57 TYR cc_start: 0.7022 (OUTLIER) cc_final: 0.5801 (t80) REVERT: D 59 ILE cc_start: 0.8589 (tp) cc_final: 0.8353 (tp) REVERT: D 63 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8828 (mm) REVERT: D 139 MET cc_start: 0.8410 (tpp) cc_final: 0.8015 (tpp) REVERT: D 191 GLU cc_start: 0.8646 (tm-30) cc_final: 0.8011 (tm-30) outliers start: 57 outliers final: 36 residues processed: 210 average time/residue: 0.1333 time to fit residues: 42.3634 Evaluate side-chains 218 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 174 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 MET Chi-restraints excluded: chain C residue 27 PHE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain C residue 65 TRP Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 168 HIS Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 57 TYR Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 57 TYR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 65 TRP Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 65 TRP Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 168 HIS Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 230 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 41 optimal weight: 0.0170 chunk 8 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 85 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 22 optimal weight: 20.0000 chunk 70 optimal weight: 0.9980 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 101 HIS A 101 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7988 Z= 0.170 Angle : 0.545 7.386 10804 Z= 0.266 Chirality : 0.040 0.128 1232 Planarity : 0.003 0.023 1256 Dihedral : 18.194 104.519 1328 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 5.15 % Allowed : 27.64 % Favored : 67.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.27), residues: 892 helix: -1.03 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -3.07 (0.32), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 54 HIS 0.001 0.001 HIS D 52 PHE 0.015 0.001 PHE D 85 TYR 0.014 0.001 TYR C 49 ARG 0.002 0.000 ARG C 116 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 192 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 35 PHE cc_start: 0.8768 (t80) cc_final: 0.8420 (t80) REVERT: C 57 TYR cc_start: 0.7150 (OUTLIER) cc_final: 0.5972 (t80) REVERT: C 65 TRP cc_start: 0.6789 (OUTLIER) cc_final: 0.4755 (t60) REVERT: C 139 MET cc_start: 0.8339 (tpp) cc_final: 0.8041 (tpp) REVERT: C 191 GLU cc_start: 0.8568 (tm-30) cc_final: 0.8059 (tm-30) REVERT: C 224 PHE cc_start: 0.6319 (t80) cc_final: 0.5638 (t80) REVERT: A 57 TYR cc_start: 0.7088 (OUTLIER) cc_final: 0.5981 (t80) REVERT: A 59 ILE cc_start: 0.8279 (tp) cc_final: 0.7929 (tp) REVERT: A 63 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8841 (mm) REVERT: A 65 TRP cc_start: 0.6700 (OUTLIER) cc_final: 0.4676 (t60) REVERT: A 139 MET cc_start: 0.8524 (tpp) cc_final: 0.8110 (tpp) REVERT: A 191 GLU cc_start: 0.8535 (tm-30) cc_final: 0.7932 (tm-30) REVERT: A 224 PHE cc_start: 0.6080 (t80) cc_final: 0.5582 (t80) REVERT: B 57 TYR cc_start: 0.7015 (OUTLIER) cc_final: 0.5851 (t80) REVERT: B 59 ILE cc_start: 0.8503 (tp) cc_final: 0.8148 (tp) REVERT: B 63 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8733 (mm) REVERT: B 65 TRP cc_start: 0.6684 (OUTLIER) cc_final: 0.4666 (t60) REVERT: B 139 MET cc_start: 0.8307 (tpp) cc_final: 0.8073 (tpp) REVERT: B 191 GLU cc_start: 0.8567 (tm-30) cc_final: 0.7696 (tm-30) REVERT: B 224 PHE cc_start: 0.6185 (t80) cc_final: 0.5576 (t80) REVERT: B 230 VAL cc_start: 0.9165 (OUTLIER) cc_final: 0.8851 (p) REVERT: D 35 PHE cc_start: 0.8711 (t80) cc_final: 0.8295 (t80) REVERT: D 57 TYR cc_start: 0.7081 (OUTLIER) cc_final: 0.5925 (t80) REVERT: D 59 ILE cc_start: 0.8506 (tp) cc_final: 0.8213 (tp) REVERT: D 63 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8812 (mm) REVERT: D 65 TRP cc_start: 0.6728 (OUTLIER) cc_final: 0.4676 (t60) REVERT: D 139 MET cc_start: 0.8456 (tpp) cc_final: 0.8084 (tpp) REVERT: D 191 GLU cc_start: 0.8598 (tm-30) cc_final: 0.7918 (tm-30) REVERT: D 224 PHE cc_start: 0.6271 (t80) cc_final: 0.5672 (t80) REVERT: D 230 VAL cc_start: 0.9139 (OUTLIER) cc_final: 0.8771 (p) outliers start: 41 outliers final: 25 residues processed: 207 average time/residue: 0.1540 time to fit residues: 45.3777 Evaluate side-chains 211 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 173 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 MET Chi-restraints excluded: chain C residue 27 PHE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain C residue 65 TRP Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 168 HIS Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 57 TYR Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 57 TYR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 65 TRP Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 65 TRP Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 230 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 0.8980 chunk 1 optimal weight: 0.0020 chunk 63 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 72 optimal weight: 0.0770 chunk 58 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 43 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.5546 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 ASN ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 HIS ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 HIS ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7988 Z= 0.160 Angle : 0.541 8.213 10804 Z= 0.263 Chirality : 0.039 0.118 1232 Planarity : 0.003 0.025 1256 Dihedral : 17.157 90.152 1328 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 6.53 % Allowed : 27.01 % Favored : 66.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.28), residues: 892 helix: -0.79 (0.21), residues: 644 sheet: None (None), residues: 0 loop : -2.92 (0.35), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 54 HIS 0.001 0.000 HIS D 22 PHE 0.017 0.001 PHE B 215 TYR 0.010 0.001 TYR C 49 ARG 0.012 0.001 ARG D 74 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 188 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 35 PHE cc_start: 0.8725 (t80) cc_final: 0.8431 (t80) REVERT: C 57 TYR cc_start: 0.7114 (OUTLIER) cc_final: 0.5913 (t80) REVERT: C 138 VAL cc_start: 0.9452 (p) cc_final: 0.9225 (m) REVERT: C 139 MET cc_start: 0.7959 (tpp) cc_final: 0.7566 (tpp) REVERT: C 191 GLU cc_start: 0.8533 (tm-30) cc_final: 0.8205 (tm-30) REVERT: C 224 PHE cc_start: 0.6293 (t80) cc_final: 0.5657 (t80) REVERT: A 57 TYR cc_start: 0.7003 (OUTLIER) cc_final: 0.5863 (t80) REVERT: A 138 VAL cc_start: 0.9481 (p) cc_final: 0.9248 (m) REVERT: A 139 MET cc_start: 0.8437 (tpp) cc_final: 0.8009 (tpp) REVERT: A 190 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7663 (mm) REVERT: A 191 GLU cc_start: 0.8524 (tm-30) cc_final: 0.8268 (tm-30) REVERT: A 217 LEU cc_start: 0.9033 (mt) cc_final: 0.8833 (mt) REVERT: A 224 PHE cc_start: 0.6021 (t80) cc_final: 0.5521 (t80) REVERT: B 57 TYR cc_start: 0.6913 (OUTLIER) cc_final: 0.5764 (t80) REVERT: B 63 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8860 (mm) REVERT: B 138 VAL cc_start: 0.9498 (p) cc_final: 0.9224 (m) REVERT: B 139 MET cc_start: 0.8417 (tpp) cc_final: 0.8108 (tpp) REVERT: B 191 GLU cc_start: 0.8377 (tm-30) cc_final: 0.7720 (tm-30) REVERT: B 217 LEU cc_start: 0.9064 (mt) cc_final: 0.8859 (mt) REVERT: B 224 PHE cc_start: 0.6054 (t80) cc_final: 0.5477 (t80) REVERT: D 35 PHE cc_start: 0.8706 (t80) cc_final: 0.8465 (t80) REVERT: D 57 TYR cc_start: 0.7036 (OUTLIER) cc_final: 0.5874 (t80) REVERT: D 59 ILE cc_start: 0.8181 (tp) cc_final: 0.7798 (tp) REVERT: D 63 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8773 (mm) REVERT: D 138 VAL cc_start: 0.9466 (p) cc_final: 0.9225 (m) REVERT: D 139 MET cc_start: 0.8390 (tpp) cc_final: 0.8038 (tpp) REVERT: D 191 GLU cc_start: 0.8400 (tm-30) cc_final: 0.7863 (tm-30) REVERT: D 224 PHE cc_start: 0.6189 (t80) cc_final: 0.5634 (t80) REVERT: D 230 VAL cc_start: 0.9098 (OUTLIER) cc_final: 0.8637 (p) outliers start: 52 outliers final: 39 residues processed: 207 average time/residue: 0.1294 time to fit residues: 40.3920 Evaluate side-chains 225 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 178 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 MET Chi-restraints excluded: chain C residue 27 PHE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 168 HIS Chi-restraints excluded: chain C residue 178 GLN Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 57 TYR Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 57 TYR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 168 HIS Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 230 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 82 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 ASN A 225 ASN B 101 HIS ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 ASN D 101 HIS ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 7988 Z= 0.295 Angle : 0.614 7.272 10804 Z= 0.296 Chirality : 0.043 0.157 1232 Planarity : 0.003 0.029 1256 Dihedral : 16.840 87.907 1320 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 9.42 % Allowed : 26.13 % Favored : 64.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.27), residues: 892 helix: -0.89 (0.21), residues: 640 sheet: None (None), residues: 0 loop : -2.79 (0.35), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 54 HIS 0.001 0.001 HIS C 22 PHE 0.018 0.001 PHE B 215 TYR 0.011 0.001 TYR D 49 ARG 0.007 0.000 ARG B 74 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 176 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 19 ILE cc_start: 0.4217 (OUTLIER) cc_final: 0.3436 (mm) REVERT: C 35 PHE cc_start: 0.8758 (t80) cc_final: 0.8323 (t80) REVERT: C 57 TYR cc_start: 0.7180 (OUTLIER) cc_final: 0.6003 (t80) REVERT: C 138 VAL cc_start: 0.9533 (p) cc_final: 0.9260 (m) REVERT: C 139 MET cc_start: 0.8010 (tpp) cc_final: 0.7620 (tpp) REVERT: C 191 GLU cc_start: 0.8635 (tm-30) cc_final: 0.8203 (tm-30) REVERT: C 224 PHE cc_start: 0.6308 (t80) cc_final: 0.6043 (m-80) REVERT: A 19 ILE cc_start: 0.4254 (OUTLIER) cc_final: 0.3504 (mm) REVERT: A 57 TYR cc_start: 0.7182 (OUTLIER) cc_final: 0.5967 (t80) REVERT: A 138 VAL cc_start: 0.9498 (p) cc_final: 0.9249 (m) REVERT: A 139 MET cc_start: 0.8494 (tpp) cc_final: 0.8082 (tpp) REVERT: A 191 GLU cc_start: 0.8566 (tm-30) cc_final: 0.8360 (tm-30) REVERT: A 224 PHE cc_start: 0.6121 (t80) cc_final: 0.5497 (t80) REVERT: B 19 ILE cc_start: 0.4364 (OUTLIER) cc_final: 0.3597 (mm) REVERT: B 57 TYR cc_start: 0.7078 (OUTLIER) cc_final: 0.5829 (t80) REVERT: B 63 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8953 (mm) REVERT: B 138 VAL cc_start: 0.9503 (p) cc_final: 0.9214 (m) REVERT: B 139 MET cc_start: 0.8451 (tpp) cc_final: 0.8160 (tpp) REVERT: B 191 GLU cc_start: 0.8552 (tm-30) cc_final: 0.8017 (tm-30) REVERT: B 224 PHE cc_start: 0.6165 (t80) cc_final: 0.5561 (t80) REVERT: D 19 ILE cc_start: 0.4193 (OUTLIER) cc_final: 0.3399 (mm) REVERT: D 57 TYR cc_start: 0.7180 (OUTLIER) cc_final: 0.5936 (t80) REVERT: D 59 ILE cc_start: 0.8231 (tp) cc_final: 0.7882 (tp) REVERT: D 63 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8908 (mm) REVERT: D 138 VAL cc_start: 0.9525 (p) cc_final: 0.9252 (m) REVERT: D 139 MET cc_start: 0.8445 (tpp) cc_final: 0.8126 (tpp) REVERT: D 191 GLU cc_start: 0.8573 (tm-30) cc_final: 0.8178 (tm-30) outliers start: 75 outliers final: 37 residues processed: 212 average time/residue: 0.1343 time to fit residues: 42.1072 Evaluate side-chains 221 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 174 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 MET Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 27 PHE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 168 HIS Chi-restraints excluded: chain C residue 178 GLN Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 57 TYR Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 57 TYR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 168 HIS Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 230 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 62 optimal weight: 0.0970 chunk 71 optimal weight: 0.2980 chunk 47 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 39 optimal weight: 0.0970 chunk 52 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 ASN A 225 ASN ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 ASN ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7988 Z= 0.148 Angle : 0.546 7.541 10804 Z= 0.265 Chirality : 0.040 0.130 1232 Planarity : 0.003 0.023 1256 Dihedral : 16.051 89.753 1320 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 7.16 % Allowed : 28.14 % Favored : 64.70 % 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: -1.94 (0.27), residues: 892 helix: -0.55 (0.21), residues: 616 sheet: None (None), residues: 0 loop : -2.87 (0.31), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 54 HIS 0.001 0.000 HIS D 52 PHE 0.020 0.001 PHE D 215 TYR 0.009 0.001 TYR B 49 ARG 0.006 0.000 ARG B 74 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 185 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 19 ILE cc_start: 0.4308 (OUTLIER) cc_final: 0.3607 (mm) REVERT: C 35 PHE cc_start: 0.8691 (t80) cc_final: 0.8406 (t80) REVERT: C 57 TYR cc_start: 0.7199 (OUTLIER) cc_final: 0.6020 (t80) REVERT: C 138 VAL cc_start: 0.9523 (p) cc_final: 0.9283 (m) REVERT: C 139 MET cc_start: 0.7961 (tpp) cc_final: 0.7582 (tpp) REVERT: C 191 GLU cc_start: 0.8623 (tm-30) cc_final: 0.8254 (tm-30) REVERT: C 217 LEU cc_start: 0.9076 (mt) cc_final: 0.8835 (mt) REVERT: C 224 PHE cc_start: 0.6186 (t80) cc_final: 0.5588 (t80) REVERT: A 19 ILE cc_start: 0.4349 (OUTLIER) cc_final: 0.3658 (mm) REVERT: A 57 TYR cc_start: 0.7218 (OUTLIER) cc_final: 0.6012 (t80) REVERT: A 138 VAL cc_start: 0.9512 (p) cc_final: 0.9263 (m) REVERT: A 139 MET cc_start: 0.8282 (tpp) cc_final: 0.7873 (tpp) REVERT: A 190 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7588 (mm) REVERT: A 217 LEU cc_start: 0.9117 (mt) cc_final: 0.8889 (mt) REVERT: A 224 PHE cc_start: 0.5998 (t80) cc_final: 0.5427 (t80) REVERT: A 230 VAL cc_start: 0.9107 (OUTLIER) cc_final: 0.8680 (p) REVERT: B 19 ILE cc_start: 0.4295 (OUTLIER) cc_final: 0.3552 (mm) REVERT: B 57 TYR cc_start: 0.7197 (OUTLIER) cc_final: 0.5921 (t80) REVERT: B 63 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8853 (mm) REVERT: B 138 VAL cc_start: 0.9514 (p) cc_final: 0.9239 (m) REVERT: B 139 MET cc_start: 0.8444 (tpp) cc_final: 0.8171 (tpp) REVERT: B 191 GLU cc_start: 0.8362 (tm-30) cc_final: 0.7830 (tm-30) REVERT: B 217 LEU cc_start: 0.9142 (mt) cc_final: 0.8911 (mt) REVERT: B 224 PHE cc_start: 0.5989 (t80) cc_final: 0.5429 (t80) REVERT: B 230 VAL cc_start: 0.9112 (OUTLIER) cc_final: 0.8637 (p) REVERT: D 19 ILE cc_start: 0.4168 (OUTLIER) cc_final: 0.3419 (mm) REVERT: D 57 TYR cc_start: 0.7205 (OUTLIER) cc_final: 0.5921 (t80) REVERT: D 138 VAL cc_start: 0.9532 (p) cc_final: 0.9275 (m) REVERT: D 139 MET cc_start: 0.8200 (tpp) cc_final: 0.7848 (tpp) REVERT: D 191 GLU cc_start: 0.8409 (tm-30) cc_final: 0.8098 (tm-30) REVERT: D 217 LEU cc_start: 0.9048 (mt) cc_final: 0.8830 (mt) REVERT: D 230 VAL cc_start: 0.9076 (OUTLIER) cc_final: 0.8550 (p) outliers start: 57 outliers final: 34 residues processed: 209 average time/residue: 0.1404 time to fit residues: 43.2156 Evaluate side-chains 221 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 174 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 MET Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 27 PHE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 168 HIS Chi-restraints excluded: chain C residue 178 GLN Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 57 TYR Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 57 TYR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 168 HIS Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 230 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 57 optimal weight: 0.1980 chunk 41 optimal weight: 0.0470 chunk 7 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 chunk 77 optimal weight: 0.1980 chunk 81 optimal weight: 0.3980 chunk 74 optimal weight: 0.8980 overall best weight: 0.3078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 225 ASN ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 ASN D 101 HIS ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7988 Z= 0.139 Angle : 0.537 7.810 10804 Z= 0.261 Chirality : 0.040 0.123 1232 Planarity : 0.003 0.023 1256 Dihedral : 15.489 89.986 1320 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 6.28 % Allowed : 28.89 % Favored : 64.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.27), residues: 892 helix: -0.59 (0.21), residues: 640 sheet: None (None), residues: 0 loop : -3.29 (0.30), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 193 HIS 0.001 0.000 HIS A 22 PHE 0.018 0.001 PHE C 215 TYR 0.008 0.001 TYR D 49 ARG 0.005 0.000 ARG C 74 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 188 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 19 ILE cc_start: 0.4305 (OUTLIER) cc_final: 0.3604 (mm) REVERT: C 35 PHE cc_start: 0.8649 (t80) cc_final: 0.8400 (t80) REVERT: C 57 TYR cc_start: 0.7158 (OUTLIER) cc_final: 0.5947 (t80) REVERT: C 139 MET cc_start: 0.7967 (tpp) cc_final: 0.7598 (tpp) REVERT: C 191 GLU cc_start: 0.8608 (tm-30) cc_final: 0.8076 (tm-30) REVERT: C 224 PHE cc_start: 0.6143 (t80) cc_final: 0.5544 (t80) REVERT: A 19 ILE cc_start: 0.4353 (OUTLIER) cc_final: 0.3663 (mm) REVERT: A 57 TYR cc_start: 0.7173 (OUTLIER) cc_final: 0.5977 (t80) REVERT: A 138 VAL cc_start: 0.9471 (p) cc_final: 0.9256 (m) REVERT: A 139 MET cc_start: 0.8277 (tpp) cc_final: 0.7855 (tpp) REVERT: A 187 VAL cc_start: 0.9217 (OUTLIER) cc_final: 0.8935 (p) REVERT: A 217 LEU cc_start: 0.9085 (mt) cc_final: 0.8863 (mt) REVERT: A 224 PHE cc_start: 0.5846 (t80) cc_final: 0.5335 (t80) REVERT: A 230 VAL cc_start: 0.9096 (OUTLIER) cc_final: 0.8626 (p) REVERT: B 19 ILE cc_start: 0.4296 (OUTLIER) cc_final: 0.3551 (mm) REVERT: B 35 PHE cc_start: 0.8655 (t80) cc_final: 0.8389 (t80) REVERT: B 57 TYR cc_start: 0.7101 (OUTLIER) cc_final: 0.6051 (t80) REVERT: B 63 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8798 (mm) REVERT: B 138 VAL cc_start: 0.9503 (p) cc_final: 0.9289 (m) REVERT: B 139 MET cc_start: 0.8300 (tpp) cc_final: 0.8008 (tpp) REVERT: B 187 VAL cc_start: 0.9150 (OUTLIER) cc_final: 0.8853 (p) REVERT: B 191 GLU cc_start: 0.8356 (tm-30) cc_final: 0.7697 (tm-30) REVERT: B 217 LEU cc_start: 0.9048 (mt) cc_final: 0.8835 (mt) REVERT: B 224 PHE cc_start: 0.5990 (t80) cc_final: 0.5328 (t80) REVERT: B 230 VAL cc_start: 0.9082 (OUTLIER) cc_final: 0.8556 (p) REVERT: D 19 ILE cc_start: 0.4156 (OUTLIER) cc_final: 0.3415 (mm) REVERT: D 57 TYR cc_start: 0.7222 (OUTLIER) cc_final: 0.5922 (t80) REVERT: D 138 VAL cc_start: 0.9514 (p) cc_final: 0.9297 (m) REVERT: D 139 MET cc_start: 0.8169 (tpp) cc_final: 0.7820 (tpp) REVERT: D 191 GLU cc_start: 0.8439 (tm-30) cc_final: 0.7984 (tm-30) REVERT: D 230 VAL cc_start: 0.9053 (OUTLIER) cc_final: 0.8457 (p) outliers start: 50 outliers final: 28 residues processed: 212 average time/residue: 0.1515 time to fit residues: 47.1406 Evaluate side-chains 207 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 165 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 27 PHE Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 168 HIS Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 57 TYR Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 57 TYR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 168 HIS Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 230 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 ASN ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 HIS ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7988 Z= 0.213 Angle : 0.593 7.773 10804 Z= 0.285 Chirality : 0.044 0.219 1232 Planarity : 0.003 0.028 1256 Dihedral : 15.711 89.148 1320 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 6.53 % Allowed : 29.02 % Favored : 64.45 % 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: -1.81 (0.27), residues: 892 helix: -0.42 (0.21), residues: 616 sheet: None (None), residues: 0 loop : -2.89 (0.30), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 193 HIS 0.001 0.000 HIS D 101 PHE 0.019 0.001 PHE C 215 TYR 0.009 0.001 TYR B 49 ARG 0.007 0.000 ARG B 74 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 170 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 19 ILE cc_start: 0.4365 (OUTLIER) cc_final: 0.3650 (mm) REVERT: C 35 PHE cc_start: 0.8712 (t80) cc_final: 0.8394 (t80) REVERT: C 57 TYR cc_start: 0.7156 (OUTLIER) cc_final: 0.5957 (t80) REVERT: C 139 MET cc_start: 0.7921 (tpp) cc_final: 0.7656 (tpp) REVERT: C 191 GLU cc_start: 0.8591 (tm-30) cc_final: 0.8044 (tm-30) REVERT: C 224 PHE cc_start: 0.6205 (t80) cc_final: 0.5615 (t80) REVERT: A 19 ILE cc_start: 0.4400 (OUTLIER) cc_final: 0.3697 (mm) REVERT: A 57 TYR cc_start: 0.7250 (OUTLIER) cc_final: 0.6052 (t80) REVERT: A 138 VAL cc_start: 0.9468 (p) cc_final: 0.9235 (m) REVERT: A 139 MET cc_start: 0.8308 (tpp) cc_final: 0.7895 (tpp) REVERT: A 187 VAL cc_start: 0.9231 (OUTLIER) cc_final: 0.8970 (p) REVERT: A 224 PHE cc_start: 0.5912 (t80) cc_final: 0.5383 (t80) REVERT: B 19 ILE cc_start: 0.4349 (OUTLIER) cc_final: 0.3592 (mm) REVERT: B 35 PHE cc_start: 0.8705 (t80) cc_final: 0.8403 (t80) REVERT: B 57 TYR cc_start: 0.7065 (OUTLIER) cc_final: 0.5814 (t80) REVERT: B 63 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8868 (mm) REVERT: B 138 VAL cc_start: 0.9491 (p) cc_final: 0.9250 (m) REVERT: B 139 MET cc_start: 0.8368 (tpp) cc_final: 0.8100 (tpp) REVERT: B 191 GLU cc_start: 0.8467 (tm-30) cc_final: 0.7718 (tm-30) REVERT: B 217 LEU cc_start: 0.9122 (mt) cc_final: 0.8902 (mt) REVERT: B 224 PHE cc_start: 0.6005 (t80) cc_final: 0.5378 (t80) REVERT: D 19 ILE cc_start: 0.4187 (OUTLIER) cc_final: 0.3435 (mm) REVERT: D 57 TYR cc_start: 0.7184 (OUTLIER) cc_final: 0.5897 (t80) REVERT: D 138 VAL cc_start: 0.9503 (p) cc_final: 0.9268 (m) REVERT: D 139 MET cc_start: 0.8061 (tpp) cc_final: 0.7702 (tpp) REVERT: D 191 GLU cc_start: 0.8489 (tm-30) cc_final: 0.8068 (tm-30) outliers start: 52 outliers final: 38 residues processed: 194 average time/residue: 0.1338 time to fit residues: 38.1930 Evaluate side-chains 213 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 165 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 27 PHE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 168 HIS Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 57 TYR Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 57 TYR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 168 HIS Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 230 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 0.5980 chunk 39 optimal weight: 0.1980 chunk 58 optimal weight: 0.7980 chunk 87 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 7 optimal weight: 0.4980 chunk 53 optimal weight: 6.9990 chunk 42 optimal weight: 0.0770 chunk 55 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 HIS ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7988 Z= 0.152 Angle : 0.569 8.756 10804 Z= 0.271 Chirality : 0.042 0.261 1232 Planarity : 0.003 0.028 1256 Dihedral : 15.306 89.804 1320 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 5.65 % Allowed : 30.03 % Favored : 64.32 % 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: -1.72 (0.27), residues: 892 helix: -0.32 (0.22), residues: 612 sheet: None (None), residues: 0 loop : -2.90 (0.30), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 193 HIS 0.001 0.000 HIS A 22 PHE 0.013 0.001 PHE D 215 TYR 0.008 0.001 TYR B 49 ARG 0.007 0.000 ARG B 74 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 178 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 19 ILE cc_start: 0.4307 (OUTLIER) cc_final: 0.3602 (mm) REVERT: C 35 PHE cc_start: 0.8651 (t80) cc_final: 0.8383 (t80) REVERT: C 57 TYR cc_start: 0.7128 (OUTLIER) cc_final: 0.5978 (t80) REVERT: C 139 MET cc_start: 0.7892 (tpp) cc_final: 0.7628 (tpp) REVERT: C 191 GLU cc_start: 0.8611 (tm-30) cc_final: 0.8101 (tm-30) REVERT: C 224 PHE cc_start: 0.6131 (t80) cc_final: 0.5529 (t80) REVERT: A 19 ILE cc_start: 0.4344 (OUTLIER) cc_final: 0.3654 (mm) REVERT: A 57 TYR cc_start: 0.7192 (OUTLIER) cc_final: 0.6011 (t80) REVERT: A 138 VAL cc_start: 0.9442 (p) cc_final: 0.9235 (m) REVERT: A 139 MET cc_start: 0.8289 (tpp) cc_final: 0.7871 (tpp) REVERT: A 187 VAL cc_start: 0.9229 (OUTLIER) cc_final: 0.8953 (p) REVERT: A 217 LEU cc_start: 0.9094 (mt) cc_final: 0.8870 (mt) REVERT: A 224 PHE cc_start: 0.5816 (t80) cc_final: 0.5285 (t80) REVERT: A 230 VAL cc_start: 0.9079 (OUTLIER) cc_final: 0.8559 (p) REVERT: B 19 ILE cc_start: 0.4284 (OUTLIER) cc_final: 0.3545 (mm) REVERT: B 35 PHE cc_start: 0.8665 (t80) cc_final: 0.8387 (t80) REVERT: B 57 TYR cc_start: 0.7100 (OUTLIER) cc_final: 0.6090 (t80) REVERT: B 138 VAL cc_start: 0.9459 (p) cc_final: 0.9251 (m) REVERT: B 139 MET cc_start: 0.8220 (tpp) cc_final: 0.7946 (tpp) REVERT: B 191 GLU cc_start: 0.8337 (tm-30) cc_final: 0.7625 (tm-30) REVERT: B 217 LEU cc_start: 0.9041 (mt) cc_final: 0.8797 (mt) REVERT: B 230 VAL cc_start: 0.9066 (OUTLIER) cc_final: 0.8522 (p) REVERT: D 19 ILE cc_start: 0.4155 (OUTLIER) cc_final: 0.3417 (mm) REVERT: D 57 TYR cc_start: 0.7145 (OUTLIER) cc_final: 0.5895 (t80) REVERT: D 81 LYS cc_start: 0.5067 (mmtt) cc_final: 0.3935 (ptmt) REVERT: D 139 MET cc_start: 0.7962 (tpp) cc_final: 0.7572 (tpp) REVERT: D 191 GLU cc_start: 0.8365 (tm-30) cc_final: 0.7952 (tm-30) REVERT: D 230 VAL cc_start: 0.9072 (OUTLIER) cc_final: 0.8861 (p) outliers start: 45 outliers final: 31 residues processed: 198 average time/residue: 0.1588 time to fit residues: 46.0815 Evaluate side-chains 212 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 169 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 27 PHE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 168 HIS Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 57 TYR Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 57 TYR Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 168 HIS Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 230 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 29 optimal weight: 0.4980 chunk 71 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.151875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.113482 restraints weight = 11755.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.116557 restraints weight = 7166.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.118694 restraints weight = 5257.545| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7988 Z= 0.202 Angle : 0.593 9.878 10804 Z= 0.284 Chirality : 0.044 0.283 1232 Planarity : 0.003 0.026 1256 Dihedral : 15.398 89.049 1320 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 6.66 % Allowed : 29.65 % Favored : 63.69 % 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: -1.70 (0.27), residues: 892 helix: -0.32 (0.22), residues: 612 sheet: None (None), residues: 0 loop : -2.86 (0.30), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 193 HIS 0.001 0.000 HIS C 101 PHE 0.018 0.001 PHE C 215 TYR 0.008 0.001 TYR B 49 ARG 0.006 0.000 ARG B 74 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1812.95 seconds wall clock time: 33 minutes 25.79 seconds (2005.79 seconds total)