Starting phenix.real_space_refine (version: dev) on Sat Feb 18 08:49:41 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vx3_21428/02_2023/6vx3_21428_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vx3_21428/02_2023/6vx3_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_21428/02_2023/6vx3_21428.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vx3_21428/02_2023/6vx3_21428.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vx3_21428/02_2023/6vx3_21428_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vx3_21428/02_2023/6vx3_21428_neut_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 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-4877/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: 4.78, per 1000 atoms: 0.61 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: 3.47 Conformation dependent library (CDL) restraints added in 1.1 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: 0.55 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: 1.78 Time building geometry restraints manager: 3.65 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: 4080 22.06 - 44.12: 428 44.12 - 66.18: 76 66.18 - 88.23: 28 88.23 - 110.29: 8 Dihedral angle restraints: 4620 sinusoidal: 1972 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 4617 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 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. 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.850 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: 4.050 Check model and map are aligned: 0.120 Process input model: 22.950 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.070 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 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 : 19.480 110.293 2892 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 % 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 *********************** 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 : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 14 residues processed: 220 average time/residue: 0.1408 time to fit residues: 45.4472 Evaluate side-chains 164 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 150 time to evaluate : 0.905 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0799 time to fit residues: 3.1280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 1.9990 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: 0.7980 chunk 41 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 79 optimal weight: 0.0170 overall best weight: 0.8820 ------------------------------------------------------------------------------- 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** C 234 ASN 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1839 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= 0.209 Angle : 0.596 8.626 10804 Z= 0.299 Chirality : 0.041 0.118 1232 Planarity : 0.003 0.023 1256 Dihedral : 19.200 112.275 1264 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer Outliers : 3.52 % 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: -3.40 (0.25), residues: 892 helix: -1.65 (0.18), residues: 632 sheet: None (None), residues: 0 loop : -3.49 (0.33), residues: 260 *********************** 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 212 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 184 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 16 residues processed: 196 average time/residue: 0.1430 time to fit residues: 41.2298 Evaluate side-chains 183 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 167 time to evaluate : 0.886 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.0782 time to fit residues: 3.3686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 22 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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: 0.8061 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 7988 Z= 0.267 Angle : 0.572 6.211 10804 Z= 0.290 Chirality : 0.041 0.118 1232 Planarity : 0.003 0.025 1256 Dihedral : 17.854 110.445 1264 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer Outliers : 3.52 % 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: -2.78 (0.26), residues: 892 helix: -1.22 (0.20), residues: 624 sheet: None (None), residues: 0 loop : -3.10 (0.32), residues: 268 *********************** 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 207 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 179 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 15 residues processed: 196 average time/residue: 0.1349 time to fit residues: 39.8305 Evaluate side-chains 179 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 164 time to evaluate : 0.836 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0729 time to fit residues: 3.1667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 80 optimal weight: 0.6980 chunk 85 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 22 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 7988 Z= 0.206 Angle : 0.552 5.324 10804 Z= 0.277 Chirality : 0.040 0.117 1232 Planarity : 0.003 0.024 1256 Dihedral : 16.904 104.391 1264 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer Outliers : 3.02 % 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: -1.08 (0.20), residues: 624 sheet: None (None), residues: 0 loop : -2.86 (0.33), residues: 268 *********************** 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 192 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 168 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 13 residues processed: 179 average time/residue: 0.1761 time to fit residues: 44.7866 Evaluate side-chains 166 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 153 time to evaluate : 0.741 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0732 time to fit residues: 2.9765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 63 optimal weight: 0.1980 chunk 35 optimal weight: 0.0010 chunk 72 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 0 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 overall best weight: 0.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 146 ASN C 225 ASN ** 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 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.021 7988 Z= 0.149 Angle : 0.557 8.034 10804 Z= 0.272 Chirality : 0.039 0.122 1232 Planarity : 0.003 0.026 1256 Dihedral : 15.800 93.327 1264 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer Outliers : 1.26 % 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: -2.29 (0.27), residues: 892 helix: -0.93 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -2.76 (0.34), residues: 256 *********************** 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 181 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 171 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 2 residues processed: 179 average time/residue: 0.1387 time to fit residues: 37.4340 Evaluate side-chains 151 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 149 time to evaluate : 0.925 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0747 time to fit residues: 1.4611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 49 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 39 optimal weight: 0.3980 chunk 7 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 44 optimal weight: 10.0000 chunk 82 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.8042 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 7988 Z= 0.253 Angle : 0.585 7.429 10804 Z= 0.288 Chirality : 0.042 0.134 1232 Planarity : 0.003 0.028 1256 Dihedral : 15.552 86.704 1264 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer Outliers : 4.15 % 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: -2.25 (0.27), residues: 892 helix: -0.91 (0.21), residues: 624 sheet: None (None), residues: 0 loop : -2.67 (0.33), residues: 268 *********************** 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 195 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 162 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 12 residues processed: 184 average time/residue: 0.1494 time to fit residues: 40.8003 Evaluate side-chains 167 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 155 time to evaluate : 0.848 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0829 time to fit residues: 2.8725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 62 optimal weight: 0.2980 chunk 71 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 53 optimal weight: 0.0070 chunk 51 optimal weight: 0.0170 chunk 39 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 33 optimal weight: 0.0670 overall best weight: 0.4776 ------------------------------------------------------------------------------- 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** B 101 HIS ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 ASN ** 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: 0.7972 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 7988 Z= 0.163 Angle : 0.566 7.615 10804 Z= 0.280 Chirality : 0.041 0.153 1232 Planarity : 0.003 0.022 1256 Dihedral : 14.801 88.079 1264 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer Outliers : 2.76 % 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: -2.14 (0.27), residues: 892 helix: -0.72 (0.21), residues: 620 sheet: None (None), residues: 0 loop : -2.89 (0.30), residues: 272 *********************** 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 189 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 167 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 6 residues processed: 179 average time/residue: 0.1423 time to fit residues: 37.6401 Evaluate side-chains 149 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 143 time to evaluate : 0.882 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0712 time to fit residues: 1.9800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 7.9990 chunk 25 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 57 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 7 optimal weight: 0.0060 chunk 66 optimal weight: 10.0000 chunk 77 optimal weight: 0.0270 chunk 81 optimal weight: 1.9990 chunk 74 optimal weight: 0.3980 overall best weight: 0.3854 ------------------------------------------------------------------------------- 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** ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 7988 Z= 0.153 Angle : 0.576 7.852 10804 Z= 0.282 Chirality : 0.042 0.168 1232 Planarity : 0.003 0.022 1256 Dihedral : 14.247 87.911 1264 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer Outliers : 1.63 % 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: -1.77 (0.26), residues: 892 helix: -0.24 (0.22), residues: 576 sheet: None (None), residues: 0 loop : -2.93 (0.27), residues: 316 *********************** 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 177 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 164 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 169 average time/residue: 0.1495 time to fit residues: 37.3137 Evaluate side-chains 150 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 144 time to evaluate : 0.987 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0788 time to fit residues: 2.0541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 78 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 7988 Z= 0.194 Angle : 0.621 11.042 10804 Z= 0.299 Chirality : 0.045 0.239 1232 Planarity : 0.003 0.021 1256 Dihedral : 14.294 87.153 1264 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer Outliers : 1.88 % 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: -1.90 (0.27), residues: 892 helix: -0.48 (0.21), residues: 612 sheet: None (None), residues: 0 loop : -2.91 (0.29), residues: 280 *********************** 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 168 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 153 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 12 residues processed: 160 average time/residue: 0.1609 time to fit residues: 37.2768 Evaluate side-chains 161 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 149 time to evaluate : 0.811 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0819 time to fit residues: 2.8112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 0.9990 chunk 39 optimal weight: 0.0970 chunk 58 optimal weight: 0.7980 chunk 87 optimal weight: 0.7980 chunk 80 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 7 optimal weight: 0.0000 chunk 53 optimal weight: 7.9990 chunk 42 optimal weight: 0.0270 chunk 55 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 overall best weight: 0.3040 ------------------------------------------------------------------------------- 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** ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.4143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 7988 Z= 0.156 Angle : 0.617 8.021 10804 Z= 0.299 Chirality : 0.045 0.214 1232 Planarity : 0.003 0.024 1256 Dihedral : 14.045 87.752 1264 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer Outliers : 0.13 % 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: -1.84 (0.27), residues: 892 helix: -0.42 (0.21), residues: 612 sheet: None (None), residues: 0 loop : -2.95 (0.28), residues: 280 ********************** 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 168 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 167 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 168 average time/residue: 0.1554 time to fit residues: 37.7871 Evaluate side-chains 155 residues out of total 796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 0.814 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 10 optimal weight: 0.1980 chunk 19 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 61 optimal weight: 0.4980 chunk 3 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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** ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 ASN ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.155400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.117893 restraints weight = 11548.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.121108 restraints weight = 6915.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.123252 restraints weight = 5020.735| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 7988 Z= 0.176 Angle : 0.621 8.330 10804 Z= 0.303 Chirality : 0.045 0.229 1232 Planarity : 0.003 0.034 1256 Dihedral : 13.965 87.247 1264 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer Outliers : 0.50 % 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: -1.77 (0.27), residues: 892 helix: -0.37 (0.21), residues: 612 sheet: None (None), residues: 0 loop : -2.92 (0.28), residues: 280 =============================================================================== Job complete usr+sys time: 1653.09 seconds wall clock time: 30 minutes 56.53 seconds (1856.53 seconds total)