Starting phenix.real_space_refine on Fri Jul 3 22:08:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xvb_38695/07_2026/8xvb_38695.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xvb_38695/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/8xvb_38695/07_2026/8xvb_38695.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xvb_38695/07_2026/8xvb_38695.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xvb_38695/07_2026/8xvb_38695.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xvb_38695/07_2026/8xvb_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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: 3.99, per 1000 atoms: 0.24 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: 1.53 Conformation dependent library (CDL) restraints added in 649.2 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: 2.10 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: 2.83 Time building geometry restraints manager: 2.01 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: 22194 1.03 - 2.07: 759 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: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.370 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: 21.930 ------------------------------------------------------------------------------- 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 : 0.519 5.163 23312 Z= 0.354 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 0.51922 / 0.35 (23312) hydrogen bonds : bond 0.14697 / 14.79 ( 924) hydrogen bonds : angle 5.88866 / 5.74 ( 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 : 0.420 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: 0.1462 time to fit residues: 52.8915 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 : 0.605 ------------------------------------------------------------------------------- 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 = 0.055994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.042641 restraints weight = 79740.168| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 3.57 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 17070 Z= 0.236 Angle : 0.634 6.817 23312 Z= 0.338 Chirality : 0.040 0.182 2672 Planarity : 0.005 0.048 2824 Dihedral : 17.965 169.811 3026 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 11.43 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: -0.07 (0.42), residues: 216 loop : 0.60 (0.29), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 268 TYR 0.007 0.001 TYR H 206 PHE 0.014 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 0.00516 / 0.24 (17070) covalent geometry : angle 0.63426 / 0.34 (23312) hydrogen bonds : bond 0.03667 / 3.73 ( 924) hydrogen bonds : angle 4.90391 / 4.93 ( 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 : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 305 ASP cc_start: 0.8934 (t0) cc_final: 0.8698 (t70) REVERT: B 305 ASP cc_start: 0.8918 (t0) cc_final: 0.8661 (t0) REVERT: C 305 ASP cc_start: 0.9032 (t0) cc_final: 0.8768 (t0) REVERT: E 305 ASP cc_start: 0.9065 (t0) cc_final: 0.8821 (t0) REVERT: F 305 ASP cc_start: 0.8915 (t0) cc_final: 0.8698 (t0) REVERT: G 259 GLN cc_start: 0.9474 (mt0) cc_final: 0.9267 (mp10) outliers start: 6 outliers final: 3 residues processed: 137 average time/residue: 0.1240 time to fit residues: 27.0868 Evaluate side-chains 120 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 117 time to evaluate : 0.664 ------------------------------------------------------------------------------- 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: 8.9990 chunk 94 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 158 optimal weight: 10.0000 chunk 194 optimal weight: 50.0000 chunk 7 optimal weight: 9.9990 chunk 39 optimal weight: 0.6980 overall best weight: 2.9388 ------------------------------------------------------------------------------- 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 = 0.3418 r_free = 0.3418 target = 0.054898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.041028 restraints weight = 81181.335| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 3.79 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17070 Z= 0.154 Angle : 0.549 5.757 23312 Z= 0.295 Chirality : 0.038 0.191 2672 Planarity : 0.004 0.043 2824 Dihedral : 17.891 170.597 3026 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.48 % Allowed : 11.47 % Favored : 88.04 % 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: -0.22 (0.41), residues: 216 loop : 0.81 (0.30), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 311 TYR 0.008 0.001 TYR H 206 PHE 0.009 0.001 PHE D 297 TRP 0.009 0.001 TRP C 121 HIS 0.007 0.001 HIS G 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (17070) covalent geometry : angle 0.54934 / 0.29 (23312) hydrogen bonds : bond 0.03112 / 3.15 ( 924) hydrogen bonds : angle 4.60103 / 4.65 ( 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 130 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 122 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 305 ASP cc_start: 0.8979 (t0) cc_final: 0.8675 (t70) REVERT: B 305 ASP cc_start: 0.8981 (t0) cc_final: 0.8636 (t0) REVERT: C 122 MET cc_start: 0.8920 (ttt) cc_final: 0.8694 (ttp) REVERT: C 259 GLN cc_start: 0.9336 (mt0) cc_final: 0.9077 (mp10) REVERT: C 305 ASP cc_start: 0.9076 (t0) cc_final: 0.8736 (t0) REVERT: E 305 ASP cc_start: 0.9100 (t0) cc_final: 0.8698 (t0) REVERT: F 305 ASP cc_start: 0.8986 (t0) cc_final: 0.8711 (t0) REVERT: G 259 GLN cc_start: 0.9431 (mt0) cc_final: 0.9205 (mp10) outliers start: 8 outliers final: 2 residues processed: 126 average time/residue: 0.1135 time to fit residues: 23.3611 Evaluate side-chains 119 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 117 time to evaluate : 0.781 ------------------------------------------------------------------------------- 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: 9.9990 chunk 191 optimal weight: 20.0000 chunk 38 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 chunk 141 optimal weight: 10.0000 chunk 162 optimal weight: 20.0000 chunk 7 optimal weight: 9.9990 chunk 65 optimal weight: 9.9990 chunk 80 optimal weight: 6.9990 chunk 76 optimal weight: 10.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN D 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 = 0.3773 r_free = 0.3773 target = 0.070244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.056891 restraints weight = 104203.047| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 3.40 r_work: 0.2929 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 17070 Z= 0.296 Angle : 0.654 9.007 23312 Z= 0.337 Chirality : 0.040 0.183 2672 Planarity : 0.004 0.051 2824 Dihedral : 17.945 168.741 3026 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.72 % Allowed : 13.10 % Favored : 86.17 % 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: 1.87 (0.20), residues: 1952 helix: 1.74 (0.15), residues: 1200 sheet: -0.35 (0.37), residues: 264 loop : 1.22 (0.32), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 268 TYR 0.011 0.001 TYR H 206 PHE 0.013 0.001 PHE D 297 TRP 0.013 0.001 TRP D 121 HIS 0.005 0.001 HIS B 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00641 / 0.30 (17070) covalent geometry : angle 0.65364 / 0.34 (23312) hydrogen bonds : bond 0.03316 / 3.34 ( 924) hydrogen bonds : angle 4.62930 / 4.64 ( 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 121 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.9260 (ttt) cc_final: 0.9039 (ttp) REVERT: A 305 ASP cc_start: 0.9027 (t0) cc_final: 0.8688 (t70) REVERT: B 305 ASP cc_start: 0.9069 (t0) cc_final: 0.8729 (t0) REVERT: C 259 GLN cc_start: 0.9368 (mt0) cc_final: 0.9132 (mp10) REVERT: C 305 ASP cc_start: 0.9128 (t0) cc_final: 0.8775 (t0) REVERT: D 305 ASP cc_start: 0.9367 (t0) cc_final: 0.9053 (t0) REVERT: D 308 THR cc_start: 0.9234 (OUTLIER) cc_final: 0.8722 (t) REVERT: E 181 GLU cc_start: 0.7363 (tp30) cc_final: 0.7124 (tp30) REVERT: E 305 ASP cc_start: 0.9207 (t0) cc_final: 0.8811 (t0) REVERT: F 259 GLN cc_start: 0.9474 (mt0) cc_final: 0.9249 (mp10) REVERT: F 305 ASP cc_start: 0.9020 (t0) cc_final: 0.8741 (t0) REVERT: G 259 GLN cc_start: 0.9420 (mt0) cc_final: 0.9191 (mp10) REVERT: H 200 MET cc_start: 0.9072 (tpp) cc_final: 0.8486 (ttt) outliers start: 12 outliers final: 5 residues processed: 117 average time/residue: 0.1080 time to fit residues: 20.6746 Evaluate side-chains 113 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 107 time to evaluate : 0.659 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 125 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 113 optimal weight: 6.9990 chunk 174 optimal weight: 9.9990 chunk 58 optimal weight: 9.9990 chunk 149 optimal weight: 7.9990 chunk 133 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 186 optimal weight: 20.0000 chunk 2 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 ** 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 = 0.3385 r_free = 0.3385 target = 0.053221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.039978 restraints weight = 80503.136| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 3.63 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17070 Z= 0.165 Angle : 0.547 8.385 23312 Z= 0.292 Chirality : 0.038 0.192 2672 Planarity : 0.004 0.047 2824 Dihedral : 17.927 169.591 3026 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.85 % Allowed : 14.31 % Favored : 84.84 % 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: 1.86 (0.15), residues: 1200 sheet: -0.50 (0.36), residues: 264 loop : 1.41 (0.33), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 311 TYR 0.009 0.001 TYR H 206 PHE 0.010 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/Z covalent geometry : bond 0.00358 / 0.16 (17070) covalent geometry : angle 0.54662 / 0.29 (23312) hydrogen bonds : bond 0.02863 / 2.88 ( 924) hydrogen bonds : angle 4.42514 / 4.42 ( 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 123 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.8906 (ttt) cc_final: 0.8673 (ttp) REVERT: A 305 ASP cc_start: 0.9023 (t0) cc_final: 0.8631 (t0) REVERT: B 305 ASP cc_start: 0.9044 (t0) cc_final: 0.8667 (t0) REVERT: C 122 MET cc_start: 0.9066 (ttt) cc_final: 0.8841 (ttp) REVERT: C 259 GLN cc_start: 0.9276 (mt0) cc_final: 0.9033 (mp10) REVERT: C 305 ASP cc_start: 0.9120 (t0) cc_final: 0.8729 (t0) REVERT: D 305 ASP cc_start: 0.9348 (t0) cc_final: 0.8996 (t0) REVERT: E 305 ASP cc_start: 0.9146 (t0) cc_final: 0.8734 (t0) REVERT: E 311 ARG cc_start: 0.8325 (ttp-110) cc_final: 0.8090 (ptp90) REVERT: F 200 MET cc_start: 0.8649 (ttm) cc_final: 0.8359 (mtp) REVERT: F 259 GLN cc_start: 0.9429 (mt0) cc_final: 0.9209 (mp10) REVERT: F 305 ASP cc_start: 0.9014 (t0) cc_final: 0.8702 (t0) REVERT: G 122 MET cc_start: 0.9009 (ttt) cc_final: 0.8753 (ttp) REVERT: G 259 GLN cc_start: 0.9392 (mt0) cc_final: 0.9173 (mp10) REVERT: H 200 MET cc_start: 0.8736 (tpp) cc_final: 0.8267 (ttt) outliers start: 14 outliers final: 5 residues processed: 120 average time/residue: 0.1186 time to fit residues: 22.7336 Evaluate side-chains 112 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 107 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain B residue 186 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 190 optimal weight: 10.0000 chunk 71 optimal weight: 7.9990 chunk 133 optimal weight: 2.9990 chunk 96 optimal weight: 7.9990 chunk 192 optimal weight: 5.9990 chunk 154 optimal weight: 4.9990 chunk 164 optimal weight: 6.9990 chunk 151 optimal weight: 5.9990 chunk 0 optimal weight: 50.0000 chunk 111 optimal weight: 2.9990 chunk 64 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 = 0.3381 r_free = 0.3381 target = 0.052990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.039346 restraints weight = 82222.002| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 3.79 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17070 Z= 0.196 Angle : 0.575 8.761 23312 Z= 0.303 Chirality : 0.039 0.190 2672 Planarity : 0.004 0.050 2824 Dihedral : 17.914 168.342 3026 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.79 % Allowed : 14.79 % Favored : 84.42 % 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: 2.06 (0.20), residues: 1952 helix: 1.89 (0.15), residues: 1200 sheet: -0.52 (0.35), residues: 264 loop : 1.45 (0.33), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 311 TYR 0.010 0.001 TYR H 206 PHE 0.011 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 0.00429 / 0.20 (17070) covalent geometry : angle 0.57454 / 0.30 (23312) hydrogen bonds : bond 0.02879 / 2.88 ( 924) hydrogen bonds : angle 4.39649 / 4.40 ( 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 121 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.9037 (ttt) cc_final: 0.8767 (ttp) REVERT: A 305 ASP cc_start: 0.9050 (t0) cc_final: 0.8651 (t0) REVERT: B 305 ASP cc_start: 0.9045 (t0) cc_final: 0.8664 (t0) REVERT: C 259 GLN cc_start: 0.9294 (mt0) cc_final: 0.9040 (mp10) REVERT: C 305 ASP cc_start: 0.9122 (t0) cc_final: 0.8726 (t0) REVERT: D 122 MET cc_start: 0.9059 (ttt) cc_final: 0.8743 (ttp) REVERT: E 305 ASP cc_start: 0.9133 (t0) cc_final: 0.8691 (t0) REVERT: E 311 ARG cc_start: 0.8304 (ttp-110) cc_final: 0.8079 (ptp90) REVERT: F 200 MET cc_start: 0.8738 (ttm) cc_final: 0.8334 (mtp) REVERT: F 259 GLN cc_start: 0.9424 (mt0) cc_final: 0.9212 (mp10) REVERT: F 305 ASP cc_start: 0.9030 (t0) cc_final: 0.8668 (t0) REVERT: G 86 MET cc_start: 0.9204 (mmm) cc_final: 0.8923 (mmm) REVERT: G 122 MET cc_start: 0.9112 (ttt) cc_final: 0.8832 (ttp) REVERT: G 259 GLN cc_start: 0.9373 (mt0) cc_final: 0.9147 (mp10) REVERT: H 167 GLN cc_start: 0.8281 (mm-40) cc_final: 0.7784 (mm-40) outliers start: 13 outliers final: 8 residues processed: 117 average time/residue: 0.1089 time to fit residues: 20.8881 Evaluate side-chains 115 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 107 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 291 ASP 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 H residue 92 THR Chi-restraints excluded: chain H residue 145 MET 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: 4.9990 chunk 158 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 190 optimal weight: 9.9990 chunk 113 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.052611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.039318 restraints weight = 80812.784| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 3.65 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.2754 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= 0.180 Angle : 0.567 11.567 23312 Z= 0.299 Chirality : 0.038 0.192 2672 Planarity : 0.004 0.045 2824 Dihedral : 17.932 167.900 3026 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.97 % Allowed : 15.46 % 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: 2.04 (0.20), residues: 1952 helix: 1.91 (0.15), residues: 1200 sheet: -0.75 (0.34), residues: 280 loop : 1.57 (0.34), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 224 TYR 0.023 0.001 TYR G 206 PHE 0.008 0.001 PHE D 297 TRP 0.009 0.001 TRP A 121 HIS 0.002 0.001 HIS H 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 (17070) covalent geometry : angle 0.56671 / 0.30 (23312) hydrogen bonds : bond 0.02811 / 2.81 ( 924) hydrogen bonds : angle 4.37744 / 4.36 ( 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 127 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 THR cc_start: 0.9550 (OUTLIER) cc_final: 0.9306 (t) REVERT: A 122 MET cc_start: 0.9061 (ttt) cc_final: 0.8811 (ttp) REVERT: A 305 ASP cc_start: 0.9063 (t0) cc_final: 0.8670 (t0) REVERT: B 305 ASP cc_start: 0.9062 (t0) cc_final: 0.8668 (t0) REVERT: C 259 GLN cc_start: 0.9305 (mt0) cc_final: 0.9040 (mp10) REVERT: C 305 ASP cc_start: 0.9110 (t0) cc_final: 0.8699 (t0) REVERT: E 305 ASP cc_start: 0.9131 (t0) cc_final: 0.8690 (t0) REVERT: F 200 MET cc_start: 0.8727 (ttm) cc_final: 0.8357 (mtp) REVERT: F 305 ASP cc_start: 0.9046 (t0) cc_final: 0.8670 (t0) REVERT: G 92 THR cc_start: 0.9599 (OUTLIER) cc_final: 0.9313 (p) REVERT: G 122 MET cc_start: 0.9112 (ttt) cc_final: 0.8828 (ttp) REVERT: H 167 GLN cc_start: 0.8331 (mm-40) cc_final: 0.7819 (mm-40) outliers start: 16 outliers final: 7 residues processed: 123 average time/residue: 0.1096 time to fit residues: 21.9117 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 : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain B residue 186 LEU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 1.9990 chunk 192 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 chunk 80 optimal weight: 0.6980 chunk 88 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 174 optimal weight: 10.0000 chunk 185 optimal weight: 0.6980 chunk 126 optimal weight: 4.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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 = 0.3391 r_free = 0.3391 target = 0.053199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.040034 restraints weight = 80836.974| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 3.66 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17070 Z= 0.132 Angle : 0.561 12.576 23312 Z= 0.297 Chirality : 0.038 0.195 2672 Planarity : 0.004 0.043 2824 Dihedral : 17.902 167.782 3026 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.91 % Allowed : 15.88 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.12 (0.20), residues: 1952 helix: 1.88 (0.15), residues: 1200 sheet: -0.52 (0.35), residues: 264 loop : 1.63 (0.34), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D 311 TYR 0.024 0.001 TYR G 206 PHE 0.006 0.001 PHE F 218 TRP 0.008 0.001 TRP A 121 HIS 0.001 0.000 HIS A 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (17070) covalent geometry : angle 0.56130 / 0.30 (23312) hydrogen bonds : bond 0.02672 / 2.65 ( 924) hydrogen bonds : angle 4.33067 / 4.29 ( 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 127 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 THR cc_start: 0.9546 (OUTLIER) cc_final: 0.9324 (t) REVERT: A 122 MET cc_start: 0.8992 (ttt) cc_final: 0.8773 (ttp) REVERT: A 200 MET cc_start: 0.8630 (tpp) cc_final: 0.8205 (mtp) REVERT: A 305 ASP cc_start: 0.9067 (t0) cc_final: 0.8663 (t0) REVERT: B 305 ASP cc_start: 0.9044 (t0) cc_final: 0.8637 (t0) REVERT: C 122 MET cc_start: 0.9126 (ttt) cc_final: 0.8865 (ttp) REVERT: C 259 GLN cc_start: 0.9309 (mt0) cc_final: 0.9031 (mp10) REVERT: C 305 ASP cc_start: 0.9103 (t0) cc_final: 0.8677 (t0) REVERT: E 305 ASP cc_start: 0.9151 (t0) cc_final: 0.8725 (t0) REVERT: F 92 THR cc_start: 0.9593 (OUTLIER) cc_final: 0.9344 (t) REVERT: F 200 MET cc_start: 0.8629 (ttm) cc_final: 0.8314 (mtp) REVERT: F 305 ASP cc_start: 0.9046 (t0) cc_final: 0.8655 (t0) REVERT: G 86 MET cc_start: 0.9234 (mmm) cc_final: 0.8673 (mtm) REVERT: G 92 THR cc_start: 0.9599 (OUTLIER) cc_final: 0.9334 (p) REVERT: H 167 GLN cc_start: 0.8336 (mm-40) cc_final: 0.7848 (mm-40) outliers start: 15 outliers final: 7 residues processed: 122 average time/residue: 0.1097 time to fit residues: 21.7629 Evaluate side-chains 118 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain D residue 259 GLN 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 H residue 92 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 154 optimal weight: 0.9980 chunk 87 optimal weight: 7.9990 chunk 65 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 190 optimal weight: 10.0000 chunk 172 optimal weight: 5.9990 chunk 1 optimal weight: 50.0000 chunk 152 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 173 optimal weight: 9.9990 chunk 121 optimal weight: 9.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 = 0.3393 r_free = 0.3393 target = 0.053302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.039787 restraints weight = 81687.172| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 3.77 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17070 Z= 0.123 Angle : 0.563 12.415 23312 Z= 0.300 Chirality : 0.038 0.196 2672 Planarity : 0.004 0.044 2824 Dihedral : 17.878 167.490 3026 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.79 % Allowed : 16.67 % 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 are not related in a simple way. whole: 2.13 (0.20), residues: 1952 helix: 1.88 (0.15), residues: 1200 sheet: -0.49 (0.35), residues: 264 loop : 1.66 (0.33), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 311 TYR 0.025 0.001 TYR G 206 PHE 0.015 0.001 PHE D 297 TRP 0.008 0.001 TRP A 121 HIS 0.001 0.000 HIS D 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (17070) covalent geometry : angle 0.56317 / 0.30 (23312) hydrogen bonds : bond 0.02599 / 2.59 ( 924) hydrogen bonds : angle 4.29974 / 4.29 ( 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 125 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 THR cc_start: 0.9542 (OUTLIER) cc_final: 0.9330 (t) REVERT: A 122 MET cc_start: 0.8995 (ttt) cc_final: 0.8764 (ttp) REVERT: A 200 MET cc_start: 0.8607 (tpp) cc_final: 0.8108 (mtm) REVERT: A 305 ASP cc_start: 0.9060 (t0) cc_final: 0.8659 (t0) REVERT: B 305 ASP cc_start: 0.9050 (t0) cc_final: 0.8640 (t0) REVERT: C 122 MET cc_start: 0.9124 (ttt) cc_final: 0.8891 (ttp) REVERT: C 305 ASP cc_start: 0.9101 (t0) cc_final: 0.8675 (t0) REVERT: E 305 ASP cc_start: 0.9128 (t0) cc_final: 0.8692 (t0) REVERT: F 92 THR cc_start: 0.9594 (OUTLIER) cc_final: 0.9353 (p) REVERT: F 200 MET cc_start: 0.8608 (ttm) cc_final: 0.8232 (mtp) REVERT: F 305 ASP cc_start: 0.9038 (t0) cc_final: 0.8651 (t0) REVERT: G 86 MET cc_start: 0.9273 (mmm) cc_final: 0.8707 (mtm) REVERT: G 92 THR cc_start: 0.9597 (OUTLIER) cc_final: 0.9333 (p) REVERT: G 122 MET cc_start: 0.9026 (ttt) cc_final: 0.8776 (ttp) REVERT: H 167 GLN cc_start: 0.8398 (mm-40) cc_final: 0.7905 (mm-40) outliers start: 13 outliers final: 7 residues processed: 119 average time/residue: 0.0888 time to fit residues: 17.7409 Evaluate side-chains 120 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain D residue 259 GLN 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 133 optimal weight: 2.9990 chunk 143 optimal weight: 5.9990 chunk 165 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 161 optimal weight: 9.9990 chunk 183 optimal weight: 0.7980 chunk 178 optimal weight: 0.6980 chunk 177 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 194 optimal weight: 50.0000 chunk 67 optimal weight: 8.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 259 GLN F 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 = 0.3810 r_free = 0.3810 target = 0.071435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.058170 restraints weight = 103669.699| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 3.43 r_work: 0.2790 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17070 Z= 0.131 Angle : 0.579 12.188 23312 Z= 0.310 Chirality : 0.038 0.196 2672 Planarity : 0.004 0.041 2824 Dihedral : 17.861 167.089 3026 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.79 % Allowed : 17.03 % 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 are not related in a simple way. whole: 2.15 (0.20), residues: 1952 helix: 1.89 (0.15), residues: 1200 sheet: -0.44 (0.35), residues: 264 loop : 1.66 (0.33), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 311 TYR 0.026 0.001 TYR G 206 PHE 0.006 0.001 PHE F 218 TRP 0.008 0.001 TRP A 121 HIS 0.001 0.000 HIS D 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (17070) covalent geometry : angle 0.57932 / 0.31 (23312) hydrogen bonds : bond 0.02601 / 2.59 ( 924) hydrogen bonds : angle 4.30931 / 4.29 ( 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 124 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 MET cc_start: 0.8918 (tpp) cc_final: 0.8478 (mtm) REVERT: A 305 ASP cc_start: 0.9070 (t0) cc_final: 0.8664 (t0) REVERT: B 305 ASP cc_start: 0.9079 (t0) cc_final: 0.8674 (t0) REVERT: C 305 ASP cc_start: 0.9109 (t0) cc_final: 0.8686 (t0) REVERT: E 181 GLU cc_start: 0.6566 (tp30) cc_final: 0.6343 (tp30) REVERT: E 305 ASP cc_start: 0.9152 (t0) cc_final: 0.8710 (t0) REVERT: F 92 THR cc_start: 0.9621 (OUTLIER) cc_final: 0.9413 (p) REVERT: F 305 ASP cc_start: 0.9069 (t0) cc_final: 0.8677 (t0) REVERT: G 86 MET cc_start: 0.9372 (mmm) cc_final: 0.8934 (mmm) REVERT: G 92 THR cc_start: 0.9626 (OUTLIER) cc_final: 0.9389 (p) REVERT: G 122 MET cc_start: 0.9301 (ttt) cc_final: 0.9082 (ttp) REVERT: H 167 GLN cc_start: 0.8604 (mm-40) cc_final: 0.8113 (mm-40) outliers start: 13 outliers final: 6 residues processed: 119 average time/residue: 0.0881 time to fit residues: 17.8285 Evaluate side-chains 115 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 107 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain B residue 186 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: 9.9990 chunk 162 optimal weight: 7.9990 chunk 190 optimal weight: 9.9990 chunk 176 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 69 optimal weight: 9.9990 chunk 49 optimal weight: 20.0000 chunk 42 optimal weight: 20.0000 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.069913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.056743 restraints weight = 103305.678| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 3.44 r_work: 0.2755 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 17070 Z= 0.191 Angle : 0.616 12.055 23312 Z= 0.327 Chirality : 0.039 0.192 2672 Planarity : 0.004 0.045 2824 Dihedral : 17.879 166.171 3026 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.79 % Allowed : 17.09 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.94 (0.15), residues: 1200 sheet: -0.64 (0.34), residues: 280 loop : 1.65 (0.34), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 311 TYR 0.028 0.001 TYR G 206 PHE 0.016 0.001 PHE D 297 TRP 0.010 0.001 TRP A 121 HIS 0.002 0.001 HIS B 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.19 (17070) covalent geometry : angle 0.61593 / 0.33 (23312) hydrogen bonds : bond 0.02830 / 2.79 ( 924) hydrogen bonds : angle 4.41053 / 4.38 ( 2674) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2580.31 seconds wall clock time: 45 minutes 31.94 seconds (2731.94 seconds total)