Starting phenix.real_space_refine on Sun Aug 24 03:09:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xvb_38695/08_2025/8xvb_38695.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xvb_38695/08_2025/8xvb_38695.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xvb_38695/08_2025/8xvb_38695.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xvb_38695/08_2025/8xvb_38695.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xvb_38695/08_2025/8xvb_38695.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xvb_38695/08_2025/8xvb_38695.map" } resolution = 3.4 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 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= 0.005 sd= 0.016 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 72 5.49 5 S 72 5.16 5 C 10208 2.51 5 N 3104 2.21 5 O 3272 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16728 Number of models: 1 Model: "" Number of chains: 18 Chain: "I" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 504 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "A" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1937 Classifications: {'peptide': 246} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 237} Chain: "B" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1937 Classifications: {'peptide': 246} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 237} Chain: "C" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1937 Classifications: {'peptide': 246} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 237} Chain: "D" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1937 Classifications: {'peptide': 246} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 237} Chain: "E" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1937 Classifications: {'peptide': 246} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 237} Chain: "F" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1937 Classifications: {'peptide': 246} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 237} Chain: "G" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1937 Classifications: {'peptide': 246} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 237} Chain: "H" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1937 Classifications: {'peptide': 246} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 237} Chain: "J" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 480 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.76, per 1000 atoms: 0.22 Number of scatterers: 16728 At special positions: 0 Unit cell: (132.84, 136.94, 118.9, 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 72 16.00 P 72 15.00 O 3272 8.00 N 3104 7.00 C 10208 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.29 Conformation dependent library (CDL) restraints added in 821.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3680 Finding SS restraints... Secondary structure from input PDB file: 119 helices and 8 sheets defined 67.5% alpha, 9.0% beta 13 base pairs and 42 stacking pairs defined. Time for finding SS restraints: 1.96 Creating SS restraints... Processing helix chain 'A' and resid 76 through 93 Processing helix chain 'A' and resid 105 through 117 Processing helix chain 'A' and resid 126 through 130 removed outlier: 3.715A pdb=" N ALA A 130 " --> pdb=" O PRO A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 144 Processing helix chain 'A' and resid 151 through 164 Processing helix chain 'A' and resid 174 through 178 Processing helix chain 'A' and resid 179 through 194 Processing helix chain 'A' and resid 203 through 208 Processing helix chain 'A' and resid 213 through 218 Processing helix chain 'A' and resid 218 through 225 Processing helix chain 'A' and resid 235 through 246 Processing helix chain 'A' and resid 250 through 262 Processing helix chain 'A' and resid 265 through 285 Processing helix chain 'A' and resid 289 through 299 Processing helix chain 'A' and resid 305 through 310 removed outlier: 3.918A pdb=" N LEU A 310 " --> pdb=" O ILE A 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 93 Processing helix chain 'B' and resid 105 through 117 Processing helix chain 'B' and resid 126 through 130 removed outlier: 3.705A pdb=" N ALA B 130 " --> pdb=" O PRO B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 144 Processing helix chain 'B' and resid 151 through 164 Processing helix chain 'B' and resid 174 through 178 Processing helix chain 'B' and resid 179 through 194 Processing helix chain 'B' and resid 203 through 208 Processing helix chain 'B' and resid 213 through 218 Processing helix chain 'B' and resid 218 through 225 Processing helix chain 'B' and resid 235 through 246 Processing helix chain 'B' and resid 250 through 262 Processing helix chain 'B' and resid 265 through 285 Processing helix chain 'B' and resid 289 through 299 Processing helix chain 'B' and resid 305 through 310 removed outlier: 3.776A pdb=" N LEU B 310 " --> pdb=" O ILE B 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 93 Processing helix chain 'C' and resid 106 through 117 Processing helix chain 'C' and resid 126 through 130 removed outlier: 3.729A pdb=" N ALA C 130 " --> pdb=" O PRO C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 144 Processing helix chain 'C' and resid 151 through 164 Processing helix chain 'C' and resid 174 through 178 Processing helix chain 'C' and resid 179 through 194 Processing helix chain 'C' and resid 203 through 208 Processing helix chain 'C' and resid 213 through 218 Processing helix chain 'C' and resid 218 through 224 Processing helix chain 'C' and resid 235 through 246 Processing helix chain 'C' and resid 250 through 262 Processing helix chain 'C' and resid 265 through 285 Processing helix chain 'C' and resid 289 through 299 Processing helix chain 'C' and resid 305 through 310 removed outlier: 4.004A pdb=" N LEU C 310 " --> pdb=" O ILE C 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 93 Processing helix chain 'D' and resid 105 through 117 Processing helix chain 'D' and resid 131 through 144 Processing helix chain 'D' and resid 151 through 164 Processing helix chain 'D' and resid 174 through 178 Processing helix chain 'D' and resid 179 through 194 Processing helix chain 'D' and resid 203 through 208 Processing helix chain 'D' and resid 213 through 218 Processing helix chain 'D' and resid 218 through 225 removed outlier: 3.528A pdb=" N ILE D 225 " --> pdb=" O LEU D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 246 Processing helix chain 'D' and resid 250 through 262 removed outlier: 3.574A pdb=" N GLN D 262 " --> pdb=" O GLN D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 285 Processing helix chain 'D' and resid 289 through 299 Processing helix chain 'D' and resid 300 through 302 No H-bonds generated for 'chain 'D' and resid 300 through 302' Processing helix chain 'E' and resid 76 through 93 Processing helix chain 'E' and resid 105 through 117 Processing helix chain 'E' and resid 131 through 143 Processing helix chain 'E' and resid 151 through 164 Processing helix chain 'E' and resid 174 through 178 Processing helix chain 'E' and resid 179 through 194 Processing helix chain 'E' and resid 203 through 208 removed outlier: 3.570A pdb=" N SER E 207 " --> pdb=" O HIS E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 218 Processing helix chain 'E' and resid 218 through 225 Processing helix chain 'E' and resid 235 through 246 Processing helix chain 'E' and resid 250 through 262 Processing helix chain 'E' and resid 265 through 285 Processing helix chain 'E' and resid 289 through 299 Processing helix chain 'E' and resid 305 through 312 Processing helix chain 'F' and resid 76 through 93 Processing helix chain 'F' and resid 105 through 117 Processing helix chain 'F' and resid 131 through 143 Processing helix chain 'F' and resid 151 through 164 Processing helix chain 'F' and resid 174 through 178 Processing helix chain 'F' and resid 179 through 194 Processing helix chain 'F' and resid 203 through 208 Processing helix chain 'F' and resid 213 through 218 Processing helix chain 'F' and resid 218 through 224 Processing helix chain 'F' and resid 235 through 246 Processing helix chain 'F' and resid 250 through 262 Processing helix chain 'F' and resid 265 through 285 Processing helix chain 'F' and resid 289 through 299 Processing helix chain 'F' and resid 300 through 302 No H-bonds generated for 'chain 'F' and resid 300 through 302' Processing helix chain 'F' and resid 305 through 310 removed outlier: 3.919A pdb=" N LEU F 310 " --> pdb=" O ILE F 306 " (cutoff:3.500A) Processing helix chain 'G' and resid 76 through 93 Processing helix chain 'G' and resid 106 through 117 Processing helix chain 'G' and resid 126 through 130 removed outlier: 3.683A pdb=" N ALA G 130 " --> pdb=" O PRO G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 144 Processing helix chain 'G' and resid 151 through 164 Processing helix chain 'G' and resid 174 through 178 Processing helix chain 'G' and resid 179 through 194 Processing helix chain 'G' and resid 203 through 208 Processing helix chain 'G' and resid 213 through 218 Processing helix chain 'G' and resid 218 through 224 Processing helix chain 'G' and resid 235 through 246 Processing helix chain 'G' and resid 250 through 262 Processing helix chain 'G' and resid 265 through 285 Processing helix chain 'G' and resid 289 through 299 Processing helix chain 'G' and resid 300 through 302 No H-bonds generated for 'chain 'G' and resid 300 through 302' Processing helix chain 'G' and resid 305 through 310 removed outlier: 3.902A pdb=" N LEU G 310 " --> pdb=" O ILE G 306 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 93 Processing helix chain 'H' and resid 105 through 117 removed outlier: 3.595A pdb=" N ALA H 109 " --> pdb=" O GLY H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 130 removed outlier: 3.767A pdb=" N ALA H 130 " --> pdb=" O PRO H 127 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 144 Processing helix chain 'H' and resid 151 through 164 Processing helix chain 'H' and resid 174 through 178 removed outlier: 3.620A pdb=" N HIS H 177 " --> pdb=" O GLU H 174 " (cutoff:3.500A) Processing helix chain 'H' and resid 179 through 194 Processing helix chain 'H' and resid 203 through 208 Processing helix chain 'H' and resid 213 through 218 Processing helix chain 'H' and resid 218 through 224 Processing helix chain 'H' and resid 235 through 246 Processing helix chain 'H' and resid 250 through 262 Processing helix chain 'H' and resid 265 through 285 Processing helix chain 'H' and resid 289 through 299 Processing helix chain 'H' and resid 305 through 312 removed outlier: 3.508A pdb=" N LEU H 310 " --> pdb=" O ILE H 306 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG H 311 " --> pdb=" O SER H 307 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 120 through 124 removed outlier: 6.952A pdb=" N TRP A 121 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N ASP A 173 " --> pdb=" O TRP A 121 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE A 123 " --> pdb=" O ASP A 173 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY A 201 " --> pdb=" O VAL A 98 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL A 97 " --> pdb=" O THR A 229 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ILE A 231 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N CYS A 99 " --> pdb=" O ILE A 231 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 120 through 124 removed outlier: 6.782A pdb=" N TRP B 121 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ASP B 173 " --> pdb=" O TRP B 121 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE B 123 " --> pdb=" O ASP B 173 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLY B 201 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY B 100 " --> pdb=" O GLY B 201 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL B 97 " --> pdb=" O THR B 229 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N ILE B 231 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N CYS B 99 " --> pdb=" O ILE B 231 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 120 through 124 removed outlier: 7.007A pdb=" N TRP C 121 " --> pdb=" O ILE C 171 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N ASP C 173 " --> pdb=" O TRP C 121 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE C 123 " --> pdb=" O ASP C 173 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ILE C 95 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ARG C 228 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL C 97 " --> pdb=" O ARG C 228 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N ALA C 230 " --> pdb=" O VAL C 97 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N CYS C 99 " --> pdb=" O ALA C 230 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 120 through 124 removed outlier: 6.869A pdb=" N TRP D 121 " --> pdb=" O ILE D 171 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ASP D 173 " --> pdb=" O TRP D 121 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE D 123 " --> pdb=" O ASP D 173 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL D 170 " --> pdb=" O VAL D 198 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N MET D 200 " --> pdb=" O VAL D 170 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ILE D 172 " --> pdb=" O MET D 200 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY D 201 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL D 97 " --> pdb=" O THR D 229 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N ILE D 231 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N CYS D 99 " --> pdb=" O ILE D 231 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 120 through 124 removed outlier: 6.959A pdb=" N TRP E 121 " --> pdb=" O ILE E 171 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N ASP E 173 " --> pdb=" O TRP E 121 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE E 123 " --> pdb=" O ASP E 173 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL E 170 " --> pdb=" O VAL E 198 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N MET E 200 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ILE E 172 " --> pdb=" O MET E 200 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY E 201 " --> pdb=" O VAL E 98 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N VAL E 97 " --> pdb=" O THR E 229 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N ILE E 231 " --> pdb=" O VAL E 97 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N CYS E 99 " --> pdb=" O ILE E 231 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 120 through 124 removed outlier: 6.948A pdb=" N TRP F 121 " --> pdb=" O ILE F 171 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N ASP F 173 " --> pdb=" O TRP F 121 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE F 123 " --> pdb=" O ASP F 173 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL F 170 " --> pdb=" O VAL F 198 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N MET F 200 " --> pdb=" O VAL F 170 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE F 172 " --> pdb=" O MET F 200 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ILE F 95 " --> pdb=" O ALA F 226 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ARG F 228 " --> pdb=" O ILE F 95 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL F 97 " --> pdb=" O ARG F 228 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N ALA F 230 " --> pdb=" O VAL F 97 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N CYS F 99 " --> pdb=" O ALA F 230 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 120 through 124 removed outlier: 6.980A pdb=" N TRP G 121 " --> pdb=" O ILE G 171 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N ASP G 173 " --> pdb=" O TRP G 121 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ILE G 123 " --> pdb=" O ASP G 173 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL G 170 " --> pdb=" O VAL G 198 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N MET G 200 " --> pdb=" O VAL G 170 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ILE G 172 " --> pdb=" O MET G 200 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ILE G 95 " --> pdb=" O ALA G 226 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ARG G 228 " --> pdb=" O ILE G 95 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL G 97 " --> pdb=" O ARG G 228 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N ALA G 230 " --> pdb=" O VAL G 97 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N CYS G 99 " --> pdb=" O ALA G 230 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 120 through 124 removed outlier: 6.824A pdb=" N TRP H 121 " --> pdb=" O ILE H 171 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ASP H 173 " --> pdb=" O TRP H 121 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE H 123 " --> pdb=" O ASP H 173 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL H 170 " --> pdb=" O VAL H 198 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N MET H 200 " --> pdb=" O VAL H 170 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ILE H 172 " --> pdb=" O MET H 200 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ILE H 95 " --> pdb=" O ALA H 226 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ARG H 228 " --> pdb=" O ILE H 95 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL H 97 " --> pdb=" O ARG H 228 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ALA H 230 " --> pdb=" O VAL H 97 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N CYS H 99 " --> pdb=" O ALA H 230 " (cutoff:3.500A) 898 hydrogen bonds defined for protein. 2622 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 26 hydrogen bonds 52 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 42 stacking parallelities Total time for adding SS restraints: 2.70 Time building geometry restraints manager: 1.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5174 1.34 - 1.45: 2236 1.45 - 1.57: 9406 1.57 - 1.69: 134 1.69 - 1.81: 120 Bond restraints: 17070 Sorted by residual: bond pdb=" C3' DT J 10 " pdb=" C2' DT J 10 " ideal model delta sigma weight residual 1.525 1.546 -0.021 2.00e-02 2.50e+03 1.06e+00 bond pdb=" C3' DT J 22 " pdb=" C2' DT J 22 " ideal model delta sigma weight residual 1.525 1.544 -0.019 2.00e-02 2.50e+03 9.25e-01 bond pdb=" CG ARG E 268 " pdb=" CD ARG E 268 " ideal model delta sigma weight residual 1.520 1.492 0.028 3.00e-02 1.11e+03 8.85e-01 bond pdb=" C3' DT J 7 " pdb=" O3' DT J 7 " ideal model delta sigma weight residual 1.422 1.450 -0.028 3.00e-02 1.11e+03 8.78e-01 bond pdb=" CG ARG B 161 " pdb=" CD ARG B 161 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 8.05e-01 ... (remaining 17065 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.03: 22356 1.03 - 2.07: 669 2.07 - 3.10: 226 3.10 - 4.13: 44 4.13 - 5.16: 17 Bond angle restraints: 23312 Sorted by residual: angle pdb=" N VAL B 216 " pdb=" CA VAL B 216 " pdb=" C VAL B 216 " ideal model delta sigma weight residual 112.96 108.77 4.19 1.00e+00 1.00e+00 1.75e+01 angle pdb=" C GLY B 265 " pdb=" N ALA B 266 " pdb=" CA ALA B 266 " ideal model delta sigma weight residual 120.79 124.31 -3.52 1.39e+00 5.18e-01 6.40e+00 angle pdb=" N ALA B 266 " pdb=" CA ALA B 266 " pdb=" C ALA B 266 " ideal model delta sigma weight residual 111.02 114.09 -3.07 1.22e+00 6.72e-01 6.32e+00 angle pdb=" N ILE G 306 " pdb=" CA ILE G 306 " pdb=" C ILE G 306 " ideal model delta sigma weight residual 113.00 109.94 3.06 1.30e+00 5.92e-01 5.54e+00 angle pdb=" N GLU D 299 " pdb=" CA GLU D 299 " pdb=" C GLU D 299 " ideal model delta sigma weight residual 110.19 107.28 2.91 1.24e+00 6.50e-01 5.51e+00 ... (remaining 23307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.98: 9971 34.98 - 69.96: 557 69.96 - 104.94: 33 104.94 - 139.92: 0 139.92 - 174.89: 1 Dihedral angle restraints: 10562 sinusoidal: 4898 harmonic: 5664 Sorted by residual: dihedral pdb=" C4' DT J 7 " pdb=" C3' DT J 7 " pdb=" O3' DT J 7 " pdb=" P DT J 8 " ideal model delta sinusoidal sigma weight residual -140.00 34.89 -174.89 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" CG ARG B 311 " pdb=" CD ARG B 311 " pdb=" NE ARG B 311 " pdb=" CZ ARG B 311 " ideal model delta sinusoidal sigma weight residual -180.00 -135.45 -44.55 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CG ARG C 204 " pdb=" CD ARG C 204 " pdb=" NE ARG C 204 " pdb=" CZ ARG C 204 " ideal model delta sinusoidal sigma weight residual 90.00 133.89 -43.89 2 1.50e+01 4.44e-03 1.03e+01 ... (remaining 10559 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1882 0.030 - 0.059: 524 0.059 - 0.089: 160 0.089 - 0.119: 97 0.119 - 0.149: 9 Chirality restraints: 2672 Sorted by residual: chirality pdb=" CA ILE A 171 " pdb=" N ILE A 171 " pdb=" C ILE A 171 " pdb=" CB ILE A 171 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.53e-01 chirality pdb=" CG LEU A 267 " pdb=" CB LEU A 267 " pdb=" CD1 LEU A 267 " pdb=" CD2 LEU A 267 " both_signs ideal model delta sigma weight residual False -2.59 -2.74 0.15 2.00e-01 2.50e+01 5.47e-01 chirality pdb=" CG LEU F 267 " pdb=" CB LEU F 267 " pdb=" CD1 LEU F 267 " pdb=" CD2 LEU F 267 " both_signs ideal model delta sigma weight residual False -2.59 -2.73 0.14 2.00e-01 2.50e+01 5.00e-01 ... (remaining 2669 not shown) Planarity restraints: 2824 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN G 101 " -0.042 5.00e-02 4.00e+02 6.26e-02 6.27e+00 pdb=" N PRO G 102 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO G 102 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO G 102 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 263 " -0.033 5.00e-02 4.00e+02 5.02e-02 4.03e+00 pdb=" N PRO D 264 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO D 264 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 264 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY H 153 " -0.025 5.00e-02 4.00e+02 3.82e-02 2.33e+00 pdb=" N PRO H 154 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO H 154 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO H 154 " -0.021 5.00e-02 4.00e+02 ... (remaining 2821 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3125 2.78 - 3.31: 16546 3.31 - 3.84: 29228 3.84 - 4.37: 33407 4.37 - 4.90: 57434 Nonbonded interactions: 139740 Sorted by model distance: nonbonded pdb=" OE1 GLU G 191 " pdb=" NH2 ARG G 224 " model vdw 2.248 3.120 nonbonded pdb=" O LEU H 189 " pdb=" OG1 THR H 193 " model vdw 2.251 3.040 nonbonded pdb=" ND2 ASN B 232 " pdb=" O ASN C 312 " model vdw 2.252 3.120 nonbonded pdb=" OE1 GLU A 191 " pdb=" NH2 ARG B 268 " model vdw 2.255 3.120 nonbonded pdb=" O ASN A 312 " pdb=" ND2 ASN F 232 " model vdw 2.256 3.120 ... (remaining 139735 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.830 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6777 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17070 Z= 0.109 Angle : 0.489 5.163 23312 Z= 0.266 Chirality : 0.036 0.149 2672 Planarity : 0.004 0.063 2824 Dihedral : 18.531 174.895 6882 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.66 (0.20), residues: 1952 helix: 1.65 (0.16), residues: 1160 sheet: -0.15 (0.39), residues: 240 loop : 0.74 (0.31), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 224 TYR 0.011 0.001 TYR G 206 PHE 0.006 0.001 PHE C 218 TRP 0.006 0.001 TRP B 121 HIS 0.010 0.001 HIS B 177 Details of bonding type rmsd covalent geometry : bond 0.00242 (17070) covalent geometry : angle 0.48892 (23312) hydrogen bonds : bond 0.14697 ( 924) hydrogen bonds : angle 5.88866 ( 2674) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.1389 time to fit residues: 49.8926 Evaluate side-chains 128 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 20.0000 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 30.0000 chunk 91 optimal weight: 0.0970 overall best weight: 5.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 GLN G 262 GLN H 146 ASN H 262 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.055157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.041771 restraints weight = 79833.418| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 3.62 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 17070 Z= 0.227 Angle : 0.616 7.015 23312 Z= 0.326 Chirality : 0.039 0.135 2672 Planarity : 0.005 0.045 2824 Dihedral : 17.732 173.768 3026 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.30 % Allowed : 9.60 % Favored : 90.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.76 (0.20), residues: 1952 helix: 1.68 (0.15), residues: 1184 sheet: -0.19 (0.38), residues: 240 loop : 0.91 (0.31), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 311 TYR 0.008 0.001 TYR D 292 PHE 0.011 0.001 PHE D 297 TRP 0.016 0.002 TRP C 121 HIS 0.009 0.001 HIS G 282 Details of bonding type rmsd covalent geometry : bond 0.00501 (17070) covalent geometry : angle 0.61630 (23312) hydrogen bonds : bond 0.03407 ( 924) hydrogen bonds : angle 4.73427 ( 2674) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 131 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 305 ASP cc_start: 0.8947 (t0) cc_final: 0.8719 (t0) REVERT: B 305 ASP cc_start: 0.9015 (t0) cc_final: 0.8766 (t0) REVERT: C 305 ASP cc_start: 0.9117 (t0) cc_final: 0.8792 (t0) REVERT: E 305 ASP cc_start: 0.9081 (t0) cc_final: 0.8831 (t0) REVERT: F 259 GLN cc_start: 0.9502 (mt0) cc_final: 0.9296 (mp10) REVERT: F 305 ASP cc_start: 0.8979 (t0) cc_final: 0.8762 (t0) outliers start: 5 outliers final: 4 residues processed: 134 average time/residue: 0.1178 time to fit residues: 24.8955 Evaluate side-chains 115 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 111 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain E residue 122 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 13 optimal weight: 5.9990 chunk 180 optimal weight: 8.9990 chunk 94 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 25 optimal weight: 9.9990 chunk 52 optimal weight: 7.9990 chunk 158 optimal weight: 2.9990 chunk 194 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN C 259 GLN D 117 ASN D 259 GLN E 259 GLN G 117 ASN G 259 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.056810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.043383 restraints weight = 81375.415| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 3.60 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 17070 Z= 0.177 Angle : 0.542 6.825 23312 Z= 0.288 Chirality : 0.037 0.132 2672 Planarity : 0.004 0.041 2824 Dihedral : 17.634 174.226 3026 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.54 % Allowed : 10.63 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.98 (0.20), residues: 1952 helix: 1.76 (0.15), residues: 1200 sheet: -0.40 (0.36), residues: 264 loop : 1.49 (0.33), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 224 TYR 0.009 0.001 TYR H 206 PHE 0.014 0.001 PHE D 297 TRP 0.011 0.001 TRP D 121 HIS 0.009 0.001 HIS G 282 Details of bonding type rmsd covalent geometry : bond 0.00390 (17070) covalent geometry : angle 0.54170 (23312) hydrogen bonds : bond 0.02958 ( 924) hydrogen bonds : angle 4.44726 ( 2674) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 119 time to evaluate : 0.645 Fit side-chains revert: symmetry clash REVERT: A 122 MET cc_start: 0.8864 (ttt) cc_final: 0.8645 (ttp) REVERT: A 305 ASP cc_start: 0.9032 (t0) cc_final: 0.8705 (t0) REVERT: B 305 ASP cc_start: 0.9024 (t0) cc_final: 0.8681 (t0) REVERT: C 305 ASP cc_start: 0.9155 (t0) cc_final: 0.8816 (t0) REVERT: D 122 MET cc_start: 0.8881 (ttt) cc_final: 0.8479 (ttp) REVERT: E 305 ASP cc_start: 0.9052 (t0) cc_final: 0.8651 (t0) REVERT: F 305 ASP cc_start: 0.9021 (t0) cc_final: 0.8743 (t0) REVERT: G 122 MET cc_start: 0.8994 (ttt) cc_final: 0.8714 (ttp) outliers start: 9 outliers final: 4 residues processed: 122 average time/residue: 0.1165 time to fit residues: 22.8701 Evaluate side-chains 111 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 107 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain E residue 122 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 105 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 191 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 141 optimal weight: 6.9990 chunk 162 optimal weight: 20.0000 chunk 7 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 76 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 259 GLN D 259 GLN E 259 GLN G 259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.053830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.040723 restraints weight = 80872.948| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 3.48 r_work: 0.2779 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 17070 Z= 0.210 Angle : 0.573 10.020 23312 Z= 0.300 Chirality : 0.038 0.134 2672 Planarity : 0.004 0.044 2824 Dihedral : 17.622 172.574 3026 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.03 % Allowed : 12.32 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.01 (0.20), residues: 1952 helix: 1.85 (0.15), residues: 1200 sheet: -0.67 (0.34), residues: 280 loop : 1.61 (0.33), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 311 TYR 0.010 0.001 TYR A 206 PHE 0.010 0.001 PHE B 297 TRP 0.012 0.001 TRP A 121 HIS 0.003 0.001 HIS B 177 Details of bonding type rmsd covalent geometry : bond 0.00465 (17070) covalent geometry : angle 0.57272 (23312) hydrogen bonds : bond 0.02929 ( 924) hydrogen bonds : angle 4.38315 ( 2674) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 ASP cc_start: 0.9059 (t0) cc_final: 0.8688 (t70) REVERT: B 305 ASP cc_start: 0.9109 (t0) cc_final: 0.8755 (t0) REVERT: C 305 ASP cc_start: 0.9105 (t0) cc_final: 0.8733 (t0) REVERT: D 122 MET cc_start: 0.9332 (ttt) cc_final: 0.9075 (ttp) REVERT: E 181 GLU cc_start: 0.6814 (tp30) cc_final: 0.6533 (tp30) REVERT: E 305 ASP cc_start: 0.9126 (t0) cc_final: 0.8701 (t0) REVERT: F 305 ASP cc_start: 0.9066 (t0) cc_final: 0.8754 (t0) REVERT: G 122 MET cc_start: 0.9392 (ttt) cc_final: 0.9184 (ttp) REVERT: H 167 GLN cc_start: 0.8553 (mm-40) cc_final: 0.8028 (mm-40) REVERT: H 200 MET cc_start: 0.8980 (tpp) cc_final: 0.8646 (ttt) REVERT: H 305 ASP cc_start: 0.9085 (t70) cc_final: 0.8802 (t0) outliers start: 17 outliers final: 8 residues processed: 123 average time/residue: 0.1181 time to fit residues: 23.6421 Evaluate side-chains 117 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain H residue 259 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 0.9980 chunk 125 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 chunk 174 optimal weight: 6.9990 chunk 58 optimal weight: 8.9990 chunk 149 optimal weight: 4.9990 chunk 133 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 186 optimal weight: 20.0000 chunk 2 optimal weight: 9.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 259 GLN D 259 GLN E 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.052523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.039349 restraints weight = 81056.784| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 3.66 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17070 Z= 0.184 Angle : 0.548 10.044 23312 Z= 0.290 Chirality : 0.037 0.161 2672 Planarity : 0.004 0.045 2824 Dihedral : 17.626 172.675 3026 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.85 % Allowed : 13.83 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.10 (0.20), residues: 1952 helix: 1.91 (0.15), residues: 1200 sheet: -0.69 (0.34), residues: 280 loop : 1.71 (0.34), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 311 TYR 0.011 0.001 TYR A 206 PHE 0.007 0.001 PHE B 297 TRP 0.009 0.001 TRP A 121 HIS 0.002 0.001 HIS E 272 Details of bonding type rmsd covalent geometry : bond 0.00410 (17070) covalent geometry : angle 0.54845 (23312) hydrogen bonds : bond 0.02799 ( 924) hydrogen bonds : angle 4.32411 ( 2674) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 ASP cc_start: 0.9054 (t0) cc_final: 0.8646 (t70) REVERT: B 305 ASP cc_start: 0.9058 (t0) cc_final: 0.8682 (t0) REVERT: C 122 MET cc_start: 0.9038 (ttt) cc_final: 0.8826 (ttp) REVERT: C 305 ASP cc_start: 0.9121 (t0) cc_final: 0.8706 (t0) REVERT: E 305 ASP cc_start: 0.9062 (t0) cc_final: 0.8576 (t0) REVERT: F 305 ASP cc_start: 0.9074 (t0) cc_final: 0.8702 (t0) REVERT: G 122 MET cc_start: 0.9041 (ttt) cc_final: 0.8771 (ttp) REVERT: H 167 GLN cc_start: 0.8383 (mm-40) cc_final: 0.7888 (mm-40) REVERT: H 200 MET cc_start: 0.8650 (tpp) cc_final: 0.8335 (ttt) REVERT: H 305 ASP cc_start: 0.9083 (t70) cc_final: 0.8780 (t0) outliers start: 14 outliers final: 9 residues processed: 121 average time/residue: 0.1197 time to fit residues: 23.6547 Evaluate side-chains 115 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain H residue 259 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 190 optimal weight: 9.9990 chunk 71 optimal weight: 6.9990 chunk 133 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 192 optimal weight: 10.0000 chunk 154 optimal weight: 6.9990 chunk 164 optimal weight: 0.7980 chunk 151 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 111 optimal weight: 4.9990 chunk 64 optimal weight: 8.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 259 GLN E 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.052040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.038887 restraints weight = 81277.095| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 3.67 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17070 Z= 0.201 Angle : 0.565 11.986 23312 Z= 0.297 Chirality : 0.038 0.170 2672 Planarity : 0.004 0.045 2824 Dihedral : 17.653 171.866 3026 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.51 % Allowed : 13.89 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.16 (0.20), residues: 1952 helix: 1.96 (0.15), residues: 1200 sheet: -0.66 (0.34), residues: 280 loop : 1.73 (0.34), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 311 TYR 0.011 0.001 TYR A 206 PHE 0.013 0.001 PHE D 297 TRP 0.009 0.001 TRP D 121 HIS 0.002 0.001 HIS B 177 Details of bonding type rmsd covalent geometry : bond 0.00445 (17070) covalent geometry : angle 0.56480 (23312) hydrogen bonds : bond 0.02842 ( 924) hydrogen bonds : angle 4.31662 ( 2674) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 MET cc_start: 0.8576 (tpp) cc_final: 0.8210 (mtp) REVERT: A 305 ASP cc_start: 0.9098 (t0) cc_final: 0.8717 (t70) REVERT: B 305 ASP cc_start: 0.9068 (t0) cc_final: 0.8692 (t0) REVERT: C 305 ASP cc_start: 0.9122 (t0) cc_final: 0.8705 (t0) REVERT: D 122 MET cc_start: 0.9091 (ttt) cc_final: 0.8718 (ttp) REVERT: D 305 ASP cc_start: 0.9394 (t0) cc_final: 0.9137 (t0) REVERT: E 305 ASP cc_start: 0.9129 (t0) cc_final: 0.8730 (t0) REVERT: F 92 THR cc_start: 0.9610 (OUTLIER) cc_final: 0.9358 (t) REVERT: F 305 ASP cc_start: 0.9057 (t0) cc_final: 0.8692 (t0) REVERT: G 86 MET cc_start: 0.9193 (mmm) cc_final: 0.8823 (mmm) REVERT: G 122 MET cc_start: 0.9212 (ttt) cc_final: 0.8902 (ttp) REVERT: H 167 GLN cc_start: 0.8518 (mm-40) cc_final: 0.7951 (mm-40) REVERT: H 305 ASP cc_start: 0.9093 (t70) cc_final: 0.8771 (t0) outliers start: 25 outliers final: 12 residues processed: 129 average time/residue: 0.1112 time to fit residues: 23.3739 Evaluate side-chains 116 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain E residue 291 ASP Chi-restraints excluded: chain E residue 306 ILE Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 301 ASP Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain H residue 259 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 138 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 158 optimal weight: 7.9990 chunk 103 optimal weight: 10.0000 chunk 94 optimal weight: 5.9990 chunk 114 optimal weight: 20.0000 chunk 39 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 190 optimal weight: 9.9990 chunk 113 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.052101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.038827 restraints weight = 81101.861| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 3.66 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17070 Z= 0.179 Angle : 0.553 12.132 23312 Z= 0.291 Chirality : 0.037 0.181 2672 Planarity : 0.004 0.044 2824 Dihedral : 17.668 171.798 3026 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.39 % Allowed : 14.73 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.25 (0.20), residues: 1952 helix: 2.04 (0.15), residues: 1192 sheet: -0.63 (0.33), residues: 280 loop : 1.73 (0.34), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 311 TYR 0.011 0.001 TYR A 206 PHE 0.007 0.001 PHE D 297 TRP 0.009 0.001 TRP D 121 HIS 0.002 0.000 HIS A 203 Details of bonding type rmsd covalent geometry : bond 0.00398 (17070) covalent geometry : angle 0.55263 (23312) hydrogen bonds : bond 0.02746 ( 924) hydrogen bonds : angle 4.25232 ( 2674) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 THR cc_start: 0.9554 (OUTLIER) cc_final: 0.9345 (t) REVERT: A 200 MET cc_start: 0.8445 (tpp) cc_final: 0.8207 (mtp) REVERT: A 305 ASP cc_start: 0.9096 (t0) cc_final: 0.8695 (t70) REVERT: B 200 MET cc_start: 0.8544 (ttm) cc_final: 0.8263 (mtp) REVERT: B 305 ASP cc_start: 0.9078 (t0) cc_final: 0.8680 (t0) REVERT: C 122 MET cc_start: 0.9128 (ttt) cc_final: 0.8896 (ttp) REVERT: C 305 ASP cc_start: 0.9134 (t0) cc_final: 0.8712 (t0) REVERT: D 122 MET cc_start: 0.9006 (ttt) cc_final: 0.8680 (ttp) REVERT: E 305 ASP cc_start: 0.9090 (t0) cc_final: 0.8641 (t0) REVERT: F 92 THR cc_start: 0.9601 (OUTLIER) cc_final: 0.9364 (t) REVERT: F 305 ASP cc_start: 0.9086 (t0) cc_final: 0.8700 (t0) REVERT: G 86 MET cc_start: 0.9205 (mmm) cc_final: 0.8643 (mtm) REVERT: G 92 THR cc_start: 0.9615 (OUTLIER) cc_final: 0.9357 (p) REVERT: G 122 MET cc_start: 0.9090 (ttt) cc_final: 0.8842 (ttp) REVERT: H 167 GLN cc_start: 0.8490 (mm-40) cc_final: 0.7953 (mm-40) REVERT: H 305 ASP cc_start: 0.9145 (t70) cc_final: 0.8818 (t0) outliers start: 23 outliers final: 12 residues processed: 124 average time/residue: 0.1084 time to fit residues: 22.4089 Evaluate side-chains 117 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain C residue 291 ASP Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 259 GLN Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain E residue 291 ASP Chi-restraints excluded: chain E residue 306 ILE Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain H residue 259 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 2.9990 chunk 192 optimal weight: 8.9990 chunk 36 optimal weight: 10.0000 chunk 135 optimal weight: 2.9990 chunk 42 optimal weight: 9.9990 chunk 80 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 174 optimal weight: 6.9990 chunk 185 optimal weight: 0.8980 chunk 126 optimal weight: 0.9980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 167 GLN D 259 GLN E 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.070521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.057225 restraints weight = 104891.687| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 3.46 r_work: 0.2775 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17070 Z= 0.137 Angle : 0.543 11.771 23312 Z= 0.290 Chirality : 0.037 0.178 2672 Planarity : 0.004 0.041 2824 Dihedral : 17.648 171.880 3026 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.21 % Allowed : 15.16 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.33 (0.20), residues: 1952 helix: 2.03 (0.15), residues: 1192 sheet: -0.35 (0.35), residues: 264 loop : 1.76 (0.33), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 311 TYR 0.010 0.001 TYR A 206 PHE 0.006 0.001 PHE F 218 TRP 0.008 0.001 TRP D 121 HIS 0.001 0.000 HIS A 203 Details of bonding type rmsd covalent geometry : bond 0.00307 (17070) covalent geometry : angle 0.54301 (23312) hydrogen bonds : bond 0.02647 ( 924) hydrogen bonds : angle 4.19898 ( 2674) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 305 ASP cc_start: 0.9090 (t0) cc_final: 0.8677 (t0) REVERT: B 305 ASP cc_start: 0.9114 (t0) cc_final: 0.8727 (t0) REVERT: C 305 ASP cc_start: 0.9119 (t0) cc_final: 0.8691 (t0) REVERT: D 122 MET cc_start: 0.9281 (ttt) cc_final: 0.8980 (ttp) REVERT: E 305 ASP cc_start: 0.9111 (t0) cc_final: 0.8661 (t0) REVERT: F 92 THR cc_start: 0.9630 (OUTLIER) cc_final: 0.9426 (t) REVERT: F 305 ASP cc_start: 0.9105 (t0) cc_final: 0.8740 (t0) REVERT: G 86 MET cc_start: 0.9387 (mmm) cc_final: 0.8875 (mtm) REVERT: G 92 THR cc_start: 0.9625 (OUTLIER) cc_final: 0.9390 (p) REVERT: G 122 MET cc_start: 0.9364 (ttt) cc_final: 0.9154 (ttp) REVERT: H 92 THR cc_start: 0.9612 (OUTLIER) cc_final: 0.9352 (t) REVERT: H 167 GLN cc_start: 0.8725 (mm-40) cc_final: 0.8175 (mm-40) REVERT: H 305 ASP cc_start: 0.9144 (t70) cc_final: 0.8794 (t0) outliers start: 20 outliers final: 12 residues processed: 125 average time/residue: 0.1077 time to fit residues: 22.8274 Evaluate side-chains 122 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain C residue 291 ASP Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain E residue 259 GLN Chi-restraints excluded: chain E residue 306 ILE Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain G residue 259 GLN Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain H residue 259 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 154 optimal weight: 8.9990 chunk 87 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 190 optimal weight: 9.9990 chunk 172 optimal weight: 6.9990 chunk 1 optimal weight: 20.0000 chunk 152 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 173 optimal weight: 9.9990 chunk 121 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 259 GLN E 259 GLN ** G 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.051953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.038858 restraints weight = 81800.427| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 3.56 r_work: 0.2765 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 17070 Z= 0.238 Angle : 0.619 12.560 23312 Z= 0.324 Chirality : 0.039 0.175 2672 Planarity : 0.004 0.048 2824 Dihedral : 17.717 170.726 3026 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.21 % Allowed : 16.18 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.26 (0.21), residues: 1952 helix: 2.03 (0.15), residues: 1192 sheet: -0.55 (0.34), residues: 280 loop : 1.73 (0.34), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 268 TYR 0.012 0.001 TYR G 206 PHE 0.009 0.001 PHE D 297 TRP 0.010 0.001 TRP D 121 HIS 0.002 0.001 HIS D 177 Details of bonding type rmsd covalent geometry : bond 0.00529 (17070) covalent geometry : angle 0.61935 (23312) hydrogen bonds : bond 0.02957 ( 924) hydrogen bonds : angle 4.32137 ( 2674) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 MET cc_start: 0.9150 (mtm) cc_final: 0.8948 (mtp) REVERT: A 305 ASP cc_start: 0.9140 (t0) cc_final: 0.8733 (t70) REVERT: B 305 ASP cc_start: 0.9147 (t0) cc_final: 0.8769 (t0) REVERT: C 305 ASP cc_start: 0.9144 (t0) cc_final: 0.8686 (t0) REVERT: D 122 MET cc_start: 0.9309 (ttt) cc_final: 0.9011 (ttp) REVERT: D 200 MET cc_start: 0.9066 (ttm) cc_final: 0.8777 (mtm) REVERT: E 181 GLU cc_start: 0.6893 (tp30) cc_final: 0.6651 (tp30) REVERT: E 305 ASP cc_start: 0.9153 (t0) cc_final: 0.8713 (t0) REVERT: F 92 THR cc_start: 0.9639 (OUTLIER) cc_final: 0.9407 (t) REVERT: F 305 ASP cc_start: 0.9123 (t0) cc_final: 0.8736 (t0) REVERT: G 92 THR cc_start: 0.9642 (OUTLIER) cc_final: 0.9395 (p) REVERT: H 167 GLN cc_start: 0.8721 (mm-40) cc_final: 0.8513 (mm-40) REVERT: H 305 ASP cc_start: 0.9164 (t70) cc_final: 0.8769 (t0) outliers start: 20 outliers final: 15 residues processed: 119 average time/residue: 0.1123 time to fit residues: 22.3072 Evaluate side-chains 120 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain C residue 259 GLN Chi-restraints excluded: chain C residue 291 ASP Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain E residue 259 GLN Chi-restraints excluded: chain E residue 291 ASP Chi-restraints excluded: chain E residue 306 ILE Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain G residue 259 GLN Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain H residue 259 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 133 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 165 optimal weight: 0.0000 chunk 91 optimal weight: 7.9990 chunk 161 optimal weight: 7.9990 chunk 183 optimal weight: 6.9990 chunk 178 optimal weight: 0.9980 chunk 177 optimal weight: 0.9990 chunk 61 optimal weight: 7.9990 chunk 194 optimal weight: 10.0000 chunk 67 optimal weight: 6.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 259 GLN E 259 GLN ** G 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.053150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.040047 restraints weight = 80720.749| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 3.57 r_work: 0.2804 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17070 Z= 0.135 Angle : 0.576 11.795 23312 Z= 0.308 Chirality : 0.037 0.190 2672 Planarity : 0.004 0.040 2824 Dihedral : 17.695 171.896 3026 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.03 % Allowed : 16.43 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.25 (0.21), residues: 1952 helix: 1.98 (0.15), residues: 1192 sheet: -0.55 (0.34), residues: 280 loop : 1.87 (0.34), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 311 TYR 0.029 0.001 TYR G 206 PHE 0.006 0.001 PHE D 218 TRP 0.007 0.001 TRP D 121 HIS 0.001 0.000 HIS D 282 Details of bonding type rmsd covalent geometry : bond 0.00303 (17070) covalent geometry : angle 0.57583 (23312) hydrogen bonds : bond 0.02691 ( 924) hydrogen bonds : angle 4.22366 ( 2674) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 MET cc_start: 0.9084 (mtm) cc_final: 0.8869 (mtp) REVERT: A 305 ASP cc_start: 0.9120 (t0) cc_final: 0.8709 (t0) REVERT: B 305 ASP cc_start: 0.9109 (t0) cc_final: 0.8721 (t0) REVERT: C 305 ASP cc_start: 0.9126 (t0) cc_final: 0.8689 (t0) REVERT: D 200 MET cc_start: 0.8991 (ttm) cc_final: 0.8734 (mtm) REVERT: E 181 GLU cc_start: 0.6797 (tp30) cc_final: 0.6560 (tp30) REVERT: E 305 ASP cc_start: 0.9126 (t0) cc_final: 0.8663 (t0) REVERT: F 200 MET cc_start: 0.9196 (tpp) cc_final: 0.8508 (mtp) REVERT: F 305 ASP cc_start: 0.9107 (t0) cc_final: 0.8710 (t0) REVERT: G 92 THR cc_start: 0.9629 (OUTLIER) cc_final: 0.9401 (p) REVERT: H 92 THR cc_start: 0.9620 (OUTLIER) cc_final: 0.9356 (t) REVERT: H 167 GLN cc_start: 0.8688 (mm-40) cc_final: 0.8131 (mm-40) REVERT: H 305 ASP cc_start: 0.9172 (t70) cc_final: 0.8778 (t0) outliers start: 17 outliers final: 13 residues processed: 123 average time/residue: 0.1072 time to fit residues: 22.2968 Evaluate side-chains 125 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain C residue 259 GLN Chi-restraints excluded: chain C residue 291 ASP Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain E residue 306 ILE Chi-restraints excluded: chain F residue 259 GLN Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain H residue 259 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 161 optimal weight: 6.9990 chunk 162 optimal weight: 9.9990 chunk 190 optimal weight: 10.0000 chunk 176 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 124 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 49 optimal weight: 0.2980 chunk 42 optimal weight: 9.9990 overall best weight: 4.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 259 GLN ** G 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.052267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.039151 restraints weight = 80864.563| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 3.56 r_work: 0.2771 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17070 Z= 0.196 Angle : 0.605 11.613 23312 Z= 0.323 Chirality : 0.038 0.197 2672 Planarity : 0.004 0.043 2824 Dihedral : 17.713 170.808 3026 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.09 % Allowed : 16.73 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.26 (0.20), residues: 1952 helix: 2.00 (0.15), residues: 1192 sheet: -0.50 (0.34), residues: 280 loop : 1.79 (0.34), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 268 TYR 0.030 0.001 TYR G 206 PHE 0.009 0.001 PHE D 297 TRP 0.009 0.001 TRP D 121 HIS 0.002 0.001 HIS D 177 Details of bonding type rmsd covalent geometry : bond 0.00439 (17070) covalent geometry : angle 0.60508 (23312) hydrogen bonds : bond 0.02852 ( 924) hydrogen bonds : angle 4.29537 ( 2674) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2990.79 seconds wall clock time: 52 minutes 38.23 seconds (3158.23 seconds total)