Starting phenix.real_space_refine on Sat Sep 12 14:55:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xvb_38695/09_2026/8xvb_38695.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xvb_38695/09_2026/8xvb_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8xvb_38695/09_2026/8xvb_38695.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xvb_38695/09_2026/8xvb_38695.map" model { file = "/net/cci-nas-00/data/ceres_data/8xvb_38695/09_2026/8xvb_38695.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xvb_38695/09_2026/8xvb_38695.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 3.68, 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: 1.40 Conformation dependent library (CDL) restraints added in 827.3 milliseconds 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: 1.92 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: 2.76 Time building geometry restraints manager: 1.90 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 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.37e+01 bond pdb=" C3' DT J 22 " pdb=" C2' DT J 22 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.25e+01 bond pdb=" C3' DT J 7 " pdb=" C2' DT J 7 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.02e+01 bond pdb=" C3' DT J 4 " pdb=" C2' DT J 4 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.52e+00 bond pdb=" C3' DT J 14 " pdb=" C2' DT J 14 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.08e+00 ... (remaining 17065 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.03: 22183 1.03 - 2.07: 770 2.07 - 3.10: 294 3.10 - 4.13: 48 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=" N3 DT J 14 " pdb=" C4 DT J 14 " pdb=" O4 DT J 14 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 angle pdb=" N3 DT J 4 " pdb=" C4 DT J 4 " pdb=" O4 DT J 4 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT J 2 " pdb=" C4 DT J 2 " pdb=" O4 DT J 2 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" N3 DT J 23 " pdb=" C4 DT J 23 " pdb=" O4 DT J 23 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 ... (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: 1824 0.030 - 0.059: 556 0.059 - 0.089: 180 0.089 - 0.119: 103 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: 2.560 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: 0.310 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 17.180 Find NCS groups from input model: 0.340 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 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 : 0.003 0.039 17070 Z= 0.206 Angle : 0.521 5.163 23312 Z= 0.356 Chirality : 0.037 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 are 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/Z covalent geometry : bond 0.00289 / 0.21 (17070) covalent geometry : angle 0.52078 / 0.36 (23312) hydrogen bonds : bond 0.14697 / 14.84 ( 924) hydrogen bonds : angle 5.88866 / 5.75 ( 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 : 0.613 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: 0.1475 time to fit residues: 53.3890 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 : 0.660 ------------------------------------------------------------------------------- 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: 50.0000 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 6.9990 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: 5.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 146 ASN H 262 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.056029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.042667 restraints weight = 79681.433| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 3.58 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 17070 Z= 0.236 Angle : 0.636 6.755 23312 Z= 0.339 Chirality : 0.040 0.197 2672 Planarity : 0.005 0.047 2824 Dihedral : 17.944 170.028 3026 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.36 % Allowed : 10.14 % Favored : 89.49 % 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 are not related in a simple way. whole: 1.62 (0.20), residues: 1952 helix: 1.61 (0.15), residues: 1184 sheet: -0.06 (0.42), residues: 216 loop : 0.60 (0.29), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 311 TYR 0.007 0.001 TYR H 206 PHE 0.013 0.001 PHE D 297 TRP 0.016 0.001 TRP C 121 HIS 0.009 0.001 HIS G 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.24 (17070) covalent geometry : angle 0.63639 / 0.34 (23312) hydrogen bonds : bond 0.03653 / 3.73 ( 924) hydrogen bonds : angle 4.89657 / 4.92 ( 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 140 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 134 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 305 ASP cc_start: 0.8950 (t0) cc_final: 0.8707 (t70) REVERT: B 305 ASP cc_start: 0.8933 (t0) cc_final: 0.8671 (t0) REVERT: C 305 ASP cc_start: 0.9044 (t0) cc_final: 0.8775 (t0) REVERT: E 305 ASP cc_start: 0.9076 (t0) cc_final: 0.8815 (t0) REVERT: F 305 ASP cc_start: 0.8906 (t0) cc_final: 0.8684 (t0) REVERT: G 259 GLN cc_start: 0.9475 (mt0) cc_final: 0.9266 (mp10) outliers start: 6 outliers final: 3 residues processed: 137 average time/residue: 0.1261 time to fit residues: 27.4969 Evaluate side-chains 122 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 119 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 13 optimal weight: 5.9990 chunk 180 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 12 optimal weight: 0.9980 chunk 85 optimal weight: 0.3980 chunk 25 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 158 optimal weight: 9.9990 chunk 194 optimal weight: 50.0000 chunk 7 optimal weight: 8.9990 chunk 39 optimal weight: 0.8980 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 259 GLN C 259 GLN D 259 GLN E 259 GLN F 259 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.055203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.041332 restraints weight = 81004.428| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 3.80 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17070 Z= 0.140 Angle : 0.544 5.975 23312 Z= 0.292 Chirality : 0.038 0.209 2672 Planarity : 0.004 0.042 2824 Dihedral : 17.856 171.316 3026 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.48 % Allowed : 11.29 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.20), residues: 1952 helix: 1.70 (0.15), residues: 1192 sheet: -0.24 (0.41), residues: 216 loop : 0.80 (0.30), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 187 TYR 0.007 0.001 TYR H 206 PHE 0.007 0.001 PHE D 297 TRP 0.008 0.001 TRP D 121 HIS 0.008 0.001 HIS G 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (17070) covalent geometry : angle 0.54420 / 0.29 (23312) hydrogen bonds : bond 0.03060 / 3.11 ( 924) hydrogen bonds : angle 4.57557 / 4.62 ( 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 133 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 125 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 305 ASP cc_start: 0.8970 (t0) cc_final: 0.8663 (t70) REVERT: B 305 ASP cc_start: 0.8973 (t0) cc_final: 0.8627 (t0) REVERT: C 122 MET cc_start: 0.8895 (ttt) cc_final: 0.8664 (ttp) REVERT: C 259 GLN cc_start: 0.9316 (mt0) cc_final: 0.9084 (mp10) REVERT: C 305 ASP cc_start: 0.9072 (t0) cc_final: 0.8738 (t0) REVERT: E 305 ASP cc_start: 0.9102 (t0) cc_final: 0.8703 (t0) REVERT: F 305 ASP cc_start: 0.8973 (t0) cc_final: 0.8689 (t0) REVERT: G 259 GLN cc_start: 0.9437 (mt0) cc_final: 0.9208 (mp10) outliers start: 8 outliers final: 2 residues processed: 128 average time/residue: 0.1138 time to fit residues: 24.1721 Evaluate side-chains 120 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 118 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 35 optimal weight: 4.9990 chunk 191 optimal weight: 20.0000 chunk 38 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 141 optimal weight: 7.9990 chunk 162 optimal weight: 20.0000 chunk 7 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 chunk 76 optimal weight: 7.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN D 117 ASN D 259 GLN E 259 GLN G 117 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.056110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.042967 restraints weight = 79883.462| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 3.50 r_work: 0.2849 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.2268 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= 0.194 Angle : 0.569 8.383 23312 Z= 0.301 Chirality : 0.039 0.207 2672 Planarity : 0.004 0.041 2824 Dihedral : 17.825 170.310 3026 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.60 % Allowed : 12.74 % 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 are not related in a simple way. whole: 1.95 (0.20), residues: 1952 helix: 1.79 (0.15), residues: 1200 sheet: -0.39 (0.36), residues: 264 loop : 1.34 (0.33), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 268 TYR 0.009 0.001 TYR H 206 PHE 0.009 0.001 PHE D 297 TRP 0.011 0.001 TRP D 121 HIS 0.004 0.001 HIS B 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.19 (17070) covalent geometry : angle 0.56856 / 0.30 (23312) hydrogen bonds : bond 0.02930 / 2.96 ( 924) hydrogen bonds : angle 4.47057 / 4.50 ( 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 125 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 0.588 Fit side-chains revert: symmetry clash REVERT: A 305 ASP cc_start: 0.9031 (t0) cc_final: 0.8682 (t0) REVERT: B 200 MET cc_start: 0.9071 (mtm) cc_final: 0.8770 (mtp) REVERT: B 305 ASP cc_start: 0.9064 (t0) cc_final: 0.8716 (t0) REVERT: C 259 GLN cc_start: 0.9380 (mt0) cc_final: 0.9143 (mp10) REVERT: C 305 ASP cc_start: 0.9110 (t0) cc_final: 0.8753 (t0) REVERT: D 305 ASP cc_start: 0.9320 (t0) cc_final: 0.9053 (t0) REVERT: D 308 THR cc_start: 0.9092 (OUTLIER) cc_final: 0.8776 (t) REVERT: E 181 GLU cc_start: 0.7222 (tp30) cc_final: 0.7021 (tp30) REVERT: E 305 ASP cc_start: 0.9175 (t0) cc_final: 0.8762 (t0) REVERT: F 200 MET cc_start: 0.9033 (ttm) cc_final: 0.8699 (mtp) REVERT: F 259 GLN cc_start: 0.9485 (mt0) cc_final: 0.9259 (mp10) REVERT: F 305 ASP cc_start: 0.9005 (t0) cc_final: 0.8712 (t0) REVERT: G 259 GLN cc_start: 0.9458 (mt0) cc_final: 0.9235 (mp10) REVERT: H 200 MET cc_start: 0.9003 (tpp) cc_final: 0.8595 (ttt) outliers start: 10 outliers final: 4 residues processed: 122 average time/residue: 0.1159 time to fit residues: 23.1691 Evaluate side-chains 117 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 112 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain H residue 92 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 2.9990 chunk 125 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 113 optimal weight: 0.9990 chunk 174 optimal weight: 4.9990 chunk 58 optimal weight: 9.9990 chunk 149 optimal weight: 10.0000 chunk 133 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 186 optimal weight: 3.9990 chunk 2 optimal weight: 0.0050 overall best weight: 2.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN D 259 GLN E 259 GLN ** H 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.072935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.059684 restraints weight = 103265.138| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 3.39 r_work: 0.2842 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17070 Z= 0.137 Angle : 0.526 7.546 23312 Z= 0.282 Chirality : 0.038 0.211 2672 Planarity : 0.004 0.043 2824 Dihedral : 17.807 170.708 3026 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.72 % Allowed : 13.53 % Favored : 85.75 % 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 are not related in a simple way. whole: 2.02 (0.20), residues: 1952 helix: 1.84 (0.15), residues: 1200 sheet: -0.47 (0.35), residues: 264 loop : 1.44 (0.33), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 224 TYR 0.008 0.001 TYR H 206 PHE 0.006 0.001 PHE D 297 TRP 0.009 0.001 TRP D 121 HIS 0.002 0.000 HIS G 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (17070) covalent geometry : angle 0.52552 / 0.28 (23312) hydrogen bonds : bond 0.02694 / 2.73 ( 924) hydrogen bonds : angle 4.33448 / 4.35 ( 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 133 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 305 ASP cc_start: 0.9031 (t0) cc_final: 0.8641 (t0) REVERT: B 305 ASP cc_start: 0.9081 (t0) cc_final: 0.8712 (t0) REVERT: C 259 GLN cc_start: 0.9376 (mt0) cc_final: 0.9138 (mp10) REVERT: C 305 ASP cc_start: 0.9113 (t0) cc_final: 0.8728 (t0) REVERT: D 305 ASP cc_start: 0.9342 (t0) cc_final: 0.8999 (t0) REVERT: D 308 THR cc_start: 0.9160 (OUTLIER) cc_final: 0.8932 (t) REVERT: E 181 GLU cc_start: 0.7201 (tp30) cc_final: 0.6956 (tp30) REVERT: E 305 ASP cc_start: 0.9182 (t0) cc_final: 0.8742 (t0) REVERT: E 311 ARG cc_start: 0.8293 (ttp-110) cc_final: 0.8039 (ptp-170) REVERT: F 200 MET cc_start: 0.8983 (ttm) cc_final: 0.8614 (mtp) REVERT: F 259 GLN cc_start: 0.9496 (mt0) cc_final: 0.9270 (mp10) REVERT: F 305 ASP cc_start: 0.9039 (t0) cc_final: 0.8675 (t0) REVERT: G 122 MET cc_start: 0.9261 (ttt) cc_final: 0.9031 (ttp) REVERT: G 259 GLN cc_start: 0.9443 (mt0) cc_final: 0.9218 (mp10) REVERT: H 200 MET cc_start: 0.8922 (tpp) cc_final: 0.8454 (ttt) outliers start: 12 outliers final: 4 residues processed: 130 average time/residue: 0.1256 time to fit residues: 26.3847 Evaluate side-chains 118 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 113 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain H residue 92 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 190 optimal weight: 0.9990 chunk 71 optimal weight: 8.9990 chunk 133 optimal weight: 0.9990 chunk 96 optimal weight: 5.9990 chunk 192 optimal weight: 9.9990 chunk 154 optimal weight: 0.9990 chunk 164 optimal weight: 0.9990 chunk 151 optimal weight: 4.9990 chunk 0 optimal weight: 50.0000 chunk 111 optimal weight: 9.9990 chunk 64 optimal weight: 8.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 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 = 0.3423 r_free = 0.3423 target = 0.054678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.041450 restraints weight = 79812.169| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 3.66 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17070 Z= 0.127 Angle : 0.532 8.432 23312 Z= 0.285 Chirality : 0.037 0.213 2672 Planarity : 0.004 0.041 2824 Dihedral : 17.774 170.437 3026 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.48 % Allowed : 14.79 % Favored : 84.72 % 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 are not related in a simple way. whole: 1.99 (0.20), residues: 1952 helix: 1.85 (0.15), residues: 1200 sheet: -0.62 (0.37), residues: 248 loop : 1.36 (0.32), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 275 TYR 0.008 0.001 TYR H 206 PHE 0.010 0.001 PHE D 297 TRP 0.008 0.001 TRP D 121 HIS 0.002 0.000 HIS G 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (17070) covalent geometry : angle 0.53189 / 0.28 (23312) hydrogen bonds : bond 0.02589 / 2.59 ( 924) hydrogen bonds : angle 4.27854 / 4.30 ( 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 126 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 305 ASP cc_start: 0.9024 (t0) cc_final: 0.8617 (t0) REVERT: B 200 MET cc_start: 0.8625 (mtm) cc_final: 0.8413 (mtp) REVERT: B 305 ASP cc_start: 0.9012 (t0) cc_final: 0.8611 (t0) REVERT: C 259 GLN cc_start: 0.9283 (mt0) cc_final: 0.9016 (mp10) REVERT: C 305 ASP cc_start: 0.9104 (t0) cc_final: 0.8694 (t0) REVERT: D 305 ASP cc_start: 0.9344 (t0) cc_final: 0.9126 (t0) REVERT: E 305 ASP cc_start: 0.9095 (t0) cc_final: 0.8643 (t0) REVERT: E 311 ARG cc_start: 0.8302 (ttp-110) cc_final: 0.8085 (ptp90) REVERT: F 200 MET cc_start: 0.8736 (ttm) cc_final: 0.8353 (mtp) REVERT: F 259 GLN cc_start: 0.9438 (mt0) cc_final: 0.9217 (mp10) REVERT: F 305 ASP cc_start: 0.9010 (t0) cc_final: 0.8633 (t0) REVERT: G 122 MET cc_start: 0.9069 (ttt) cc_final: 0.8761 (ttp) REVERT: G 259 GLN cc_start: 0.9402 (mt0) cc_final: 0.9174 (mp10) REVERT: H 200 MET cc_start: 0.8561 (tpp) cc_final: 0.8260 (ttt) outliers start: 8 outliers final: 5 residues processed: 123 average time/residue: 0.1148 time to fit residues: 22.9996 Evaluate side-chains 120 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 115 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain H residue 92 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 138 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 158 optimal weight: 9.9990 chunk 103 optimal weight: 9.9990 chunk 94 optimal weight: 5.9990 chunk 114 optimal weight: 20.0000 chunk 39 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 190 optimal weight: 8.9990 chunk 113 optimal weight: 3.9990 chunk 49 optimal weight: 20.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN ** H 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 = 0.3456 r_free = 0.3456 target = 0.054664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.041366 restraints weight = 79811.722| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 3.59 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17070 Z= 0.157 Angle : 0.537 8.166 23312 Z= 0.285 Chirality : 0.038 0.211 2672 Planarity : 0.004 0.040 2824 Dihedral : 17.759 169.486 3026 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.85 % Allowed : 14.86 % Favored : 84.30 % 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 are not related in a simple way. whole: 2.14 (0.20), residues: 1952 helix: 1.93 (0.15), residues: 1200 sheet: -0.45 (0.35), residues: 264 loop : 1.53 (0.33), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 311 TYR 0.008 0.001 TYR H 206 PHE 0.009 0.001 PHE D 297 TRP 0.010 0.001 TRP D 121 HIS 0.002 0.001 HIS B 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 (17070) covalent geometry : angle 0.53681 / 0.28 (23312) hydrogen bonds : bond 0.02587 / 2.60 ( 924) hydrogen bonds : angle 4.23125 / 4.26 ( 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 131 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.8946 (ttt) cc_final: 0.8690 (ttp) REVERT: A 305 ASP cc_start: 0.9052 (t0) cc_final: 0.8646 (t0) REVERT: B 305 ASP cc_start: 0.9017 (t0) cc_final: 0.8607 (t0) REVERT: C 259 GLN cc_start: 0.9296 (mt0) cc_final: 0.9020 (mp10) REVERT: C 305 ASP cc_start: 0.9104 (t0) cc_final: 0.8683 (t0) REVERT: D 122 MET cc_start: 0.9033 (ttt) cc_final: 0.8742 (ttp) REVERT: D 305 ASP cc_start: 0.9400 (t0) cc_final: 0.9018 (t0) REVERT: E 305 ASP cc_start: 0.9118 (t0) cc_final: 0.8671 (t0) REVERT: F 200 MET cc_start: 0.8800 (ttm) cc_final: 0.8454 (mtp) REVERT: F 259 GLN cc_start: 0.9402 (mt0) cc_final: 0.9182 (mp10) REVERT: F 305 ASP cc_start: 0.9026 (t0) cc_final: 0.8641 (t0) REVERT: G 122 MET cc_start: 0.9087 (ttt) cc_final: 0.8750 (ttp) REVERT: G 200 MET cc_start: 0.8875 (mmm) cc_final: 0.8596 (mmm) REVERT: H 200 MET cc_start: 0.8527 (tpp) cc_final: 0.8269 (ttt) outliers start: 14 outliers final: 7 residues processed: 125 average time/residue: 0.1071 time to fit residues: 21.7964 Evaluate side-chains 120 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 113 time to evaluate : 0.586 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 1.9990 chunk 192 optimal weight: 8.9990 chunk 36 optimal weight: 9.9990 chunk 135 optimal weight: 3.9990 chunk 42 optimal weight: 20.0000 chunk 80 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 174 optimal weight: 9.9990 chunk 185 optimal weight: 8.9990 chunk 126 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 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 = 0.3385 r_free = 0.3385 target = 0.053496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.040041 restraints weight = 83239.956| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 3.81 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17070 Z= 0.167 Angle : 0.566 13.281 23312 Z= 0.298 Chirality : 0.038 0.211 2672 Planarity : 0.004 0.041 2824 Dihedral : 17.768 169.262 3026 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.85 % Allowed : 15.34 % Favored : 83.82 % 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 are not related in a simple way. whole: 2.16 (0.20), residues: 1952 helix: 1.94 (0.15), residues: 1200 sheet: -0.44 (0.35), residues: 264 loop : 1.56 (0.33), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 311 TYR 0.008 0.001 TYR H 206 PHE 0.007 0.001 PHE D 297 TRP 0.009 0.001 TRP D 121 HIS 0.002 0.000 HIS B 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 (17070) covalent geometry : angle 0.56566 / 0.30 (23312) hydrogen bonds : bond 0.02629 / 2.61 ( 924) hydrogen bonds : angle 4.22351 / 4.23 ( 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 128 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.8933 (ttt) cc_final: 0.8707 (ttp) REVERT: A 200 MET cc_start: 0.8521 (tpp) cc_final: 0.8185 (mtp) REVERT: A 305 ASP cc_start: 0.9054 (t0) cc_final: 0.8647 (t0) REVERT: B 305 ASP cc_start: 0.9042 (t0) cc_final: 0.8627 (t0) REVERT: C 305 ASP cc_start: 0.9121 (t0) cc_final: 0.8694 (t0) REVERT: D 122 MET cc_start: 0.8978 (ttt) cc_final: 0.8730 (ttp) REVERT: E 305 ASP cc_start: 0.9160 (t0) cc_final: 0.8690 (t0) REVERT: E 311 ARG cc_start: 0.8296 (ttp-110) cc_final: 0.8066 (ptp90) REVERT: F 92 THR cc_start: 0.9604 (OUTLIER) cc_final: 0.9351 (p) REVERT: F 305 ASP cc_start: 0.9032 (t0) cc_final: 0.8640 (t0) REVERT: G 86 MET cc_start: 0.9254 (mmm) cc_final: 0.8632 (mtm) REVERT: G 122 MET cc_start: 0.9034 (ttt) cc_final: 0.8775 (ttp) REVERT: G 200 MET cc_start: 0.8886 (mmm) cc_final: 0.8282 (mmm) REVERT: H 167 GLN cc_start: 0.8184 (mm-40) cc_final: 0.7730 (mm-40) outliers start: 14 outliers final: 10 residues processed: 123 average time/residue: 0.1103 time to fit residues: 22.7915 Evaluate side-chains 124 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 113 time to evaluate : 0.622 ------------------------------------------------------------------------------- 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 259 GLN Chi-restraints excluded: chain D residue 267 LEU 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 H residue 92 THR Chi-restraints excluded: chain H residue 145 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 154 optimal weight: 3.9990 chunk 87 optimal weight: 9.9990 chunk 65 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 190 optimal weight: 6.9990 chunk 172 optimal weight: 6.9990 chunk 1 optimal weight: 50.0000 chunk 152 optimal weight: 2.9990 chunk 50 optimal weight: 0.0060 chunk 173 optimal weight: 5.9990 chunk 121 optimal weight: 20.0000 overall best weight: 1.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 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 = 0.3401 r_free = 0.3401 target = 0.053933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.040276 restraints weight = 81003.373| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 3.78 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17070 Z= 0.126 Angle : 0.549 12.187 23312 Z= 0.293 Chirality : 0.038 0.214 2672 Planarity : 0.004 0.040 2824 Dihedral : 17.763 169.415 3026 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.09 % Allowed : 15.34 % Favored : 83.57 % 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 are not related in a simple way. whole: 2.13 (0.20), residues: 1952 helix: 1.89 (0.15), residues: 1200 sheet: -0.48 (0.35), residues: 264 loop : 1.63 (0.33), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 311 TYR 0.007 0.001 TYR A 206 PHE 0.014 0.001 PHE D 297 TRP 0.008 0.001 TRP D 121 HIS 0.001 0.000 HIS D 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 (17070) covalent geometry : angle 0.54893 / 0.29 (23312) hydrogen bonds : bond 0.02537 / 2.54 ( 924) hydrogen bonds : angle 4.21331 / 4.25 ( 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 134 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 THR cc_start: 0.9537 (OUTLIER) cc_final: 0.9316 (t) REVERT: A 122 MET cc_start: 0.8939 (ttt) cc_final: 0.8718 (ttp) REVERT: A 200 MET cc_start: 0.8530 (tpp) cc_final: 0.8170 (mtp) REVERT: A 305 ASP cc_start: 0.9052 (t0) cc_final: 0.8638 (t0) REVERT: B 305 ASP cc_start: 0.9031 (t0) cc_final: 0.8611 (t0) REVERT: C 305 ASP cc_start: 0.9105 (t0) cc_final: 0.8668 (t0) REVERT: D 215 THR cc_start: 0.9660 (OUTLIER) cc_final: 0.9415 (p) REVERT: E 305 ASP cc_start: 0.9118 (t0) cc_final: 0.8645 (t0) REVERT: F 92 THR cc_start: 0.9601 (OUTLIER) cc_final: 0.9351 (p) REVERT: F 200 MET cc_start: 0.8607 (ttm) cc_final: 0.8193 (mtp) REVERT: F 305 ASP cc_start: 0.9048 (t0) cc_final: 0.8657 (t0) REVERT: G 86 MET cc_start: 0.9253 (mmm) cc_final: 0.8632 (mtm) REVERT: G 92 THR cc_start: 0.9591 (OUTLIER) cc_final: 0.9321 (p) REVERT: G 200 MET cc_start: 0.8857 (mmm) cc_final: 0.8328 (mmm) REVERT: H 167 GLN cc_start: 0.8194 (mm-40) cc_final: 0.7730 (mm-40) outliers start: 18 outliers final: 9 residues processed: 129 average time/residue: 0.1096 time to fit residues: 23.7167 Evaluate side-chains 124 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR 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 215 THR Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 259 GLN Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain E residue 122 MET 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 133 optimal weight: 3.9990 chunk 143 optimal weight: 10.0000 chunk 165 optimal weight: 8.9990 chunk 91 optimal weight: 10.0000 chunk 161 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 177 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 194 optimal weight: 50.0000 chunk 67 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 259 GLN D 259 GLN ** H 259 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 = 0.3813 r_free = 0.3813 target = 0.071623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.058346 restraints weight = 103774.241| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 3.44 r_work: 0.2810 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17070 Z= 0.151 Angle : 0.575 11.345 23312 Z= 0.308 Chirality : 0.038 0.213 2672 Planarity : 0.004 0.056 2824 Dihedral : 17.757 169.002 3026 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.97 % Allowed : 15.52 % Favored : 83.51 % 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 are not related in a simple way. whole: 2.16 (0.20), residues: 1952 helix: 1.92 (0.15), residues: 1200 sheet: -0.47 (0.35), residues: 264 loop : 1.63 (0.33), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 311 TYR 0.008 0.001 TYR A 206 PHE 0.006 0.001 PHE B 297 TRP 0.008 0.001 TRP A 121 HIS 0.001 0.000 HIS B 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (17070) covalent geometry : angle 0.57508 / 0.31 (23312) hydrogen bonds : bond 0.02604 / 2.60 ( 924) hydrogen bonds : angle 4.24713 / 4.26 ( 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 127 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 MET cc_start: 0.8852 (tpp) cc_final: 0.8538 (mtp) REVERT: A 305 ASP cc_start: 0.9071 (t0) cc_final: 0.8658 (t0) REVERT: B 305 ASP cc_start: 0.9084 (t0) cc_final: 0.8677 (t0) REVERT: C 305 ASP cc_start: 0.9122 (t0) cc_final: 0.8699 (t0) REVERT: D 122 MET cc_start: 0.9180 (ttt) cc_final: 0.8948 (ttp) REVERT: D 215 THR cc_start: 0.9648 (OUTLIER) cc_final: 0.9419 (p) REVERT: E 181 GLU cc_start: 0.6632 (tp30) cc_final: 0.6390 (tp30) REVERT: E 305 ASP cc_start: 0.9189 (t0) cc_final: 0.8739 (t0) REVERT: F 92 THR cc_start: 0.9616 (OUTLIER) cc_final: 0.9403 (p) REVERT: F 200 MET cc_start: 0.8965 (ttm) cc_final: 0.8593 (mtp) REVERT: F 305 ASP cc_start: 0.9082 (t0) cc_final: 0.8692 (t0) REVERT: G 86 MET cc_start: 0.9352 (mmm) cc_final: 0.8813 (mtm) REVERT: G 92 THR cc_start: 0.9616 (OUTLIER) cc_final: 0.9380 (p) REVERT: G 200 MET cc_start: 0.9123 (mmm) cc_final: 0.8694 (mmm) REVERT: H 167 GLN cc_start: 0.8393 (mm-40) cc_final: 0.7934 (mm-40) REVERT: H 200 MET cc_start: 0.9129 (tpp) cc_final: 0.8544 (ttt) outliers start: 16 outliers final: 11 residues processed: 123 average time/residue: 0.1038 time to fit residues: 21.3432 Evaluate side-chains 124 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.432 ------------------------------------------------------------------------------- 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 B residue 259 GLN Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 259 GLN Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain E residue 122 MET 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 161 optimal weight: 10.0000 chunk 162 optimal weight: 9.9990 chunk 190 optimal weight: 5.9990 chunk 176 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 chunk 103 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 42 optimal weight: 0.4980 overall best weight: 4.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 259 GLN D 259 GLN ** H 259 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 = 0.3792 r_free = 0.3792 target = 0.070472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.057367 restraints weight = 103203.510| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 3.44 r_work: 0.2785 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17070 Z= 0.199 Angle : 0.596 10.899 23312 Z= 0.316 Chirality : 0.039 0.210 2672 Planarity : 0.004 0.041 2824 Dihedral : 17.774 168.382 3026 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.85 % Allowed : 15.64 % Favored : 83.51 % 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 are not related in a simple way. whole: 2.13 (0.20), residues: 1952 helix: 1.96 (0.15), residues: 1200 sheet: -0.67 (0.34), residues: 280 loop : 1.63 (0.34), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 311 TYR 0.009 0.001 TYR A 206 PHE 0.016 0.001 PHE D 297 TRP 0.009 0.001 TRP A 121 HIS 0.002 0.000 HIS B 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.20 (17070) covalent geometry : angle 0.59620 / 0.32 (23312) hydrogen bonds : bond 0.02704 / 2.69 ( 924) hydrogen bonds : angle 4.28646 / 4.30 ( 2674) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2943.09 seconds wall clock time: 51 minutes 43.81 seconds (3103.81 seconds total)