Starting phenix.real_space_refine on Sat Jun 14 21:09:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xvb_38695/06_2025/8xvb_38695.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xvb_38695/06_2025/8xvb_38695.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xvb_38695/06_2025/8xvb_38695.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xvb_38695/06_2025/8xvb_38695.map" model { file = "/net/cci-nas-00/data/ceres_data/8xvb_38695/06_2025/8xvb_38695.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xvb_38695/06_2025/8xvb_38695.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.94, per 1000 atoms: 0.59 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: 3.88 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 5.57 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: 5.15 Time building geometry restraints manager: 4.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5174 1.34 - 1.45: 2236 1.45 - 1.57: 9406 1.57 - 1.69: 134 1.69 - 1.81: 120 Bond restraints: 17070 Sorted by residual: bond pdb=" C3' DT J 10 " pdb=" C2' DT J 10 " ideal model delta sigma weight residual 1.525 1.546 -0.021 2.00e-02 2.50e+03 1.06e+00 bond pdb=" C3' DT J 22 " pdb=" C2' DT J 22 " ideal model delta sigma weight residual 1.525 1.544 -0.019 2.00e-02 2.50e+03 9.25e-01 bond pdb=" CG ARG E 268 " pdb=" CD ARG E 268 " ideal model delta sigma weight residual 1.520 1.492 0.028 3.00e-02 1.11e+03 8.85e-01 bond pdb=" C3' DT J 7 " pdb=" O3' DT J 7 " ideal model delta sigma weight residual 1.422 1.450 -0.028 3.00e-02 1.11e+03 8.78e-01 bond pdb=" CG ARG B 161 " pdb=" CD ARG B 161 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 8.05e-01 ... (remaining 17065 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.03: 22356 1.03 - 2.07: 669 2.07 - 3.10: 226 3.10 - 4.13: 44 4.13 - 5.16: 17 Bond angle restraints: 23312 Sorted by residual: angle pdb=" N VAL B 216 " pdb=" CA VAL B 216 " pdb=" C VAL B 216 " ideal model delta sigma weight residual 112.96 108.77 4.19 1.00e+00 1.00e+00 1.75e+01 angle pdb=" C GLY B 265 " pdb=" N ALA B 266 " pdb=" CA ALA B 266 " ideal model delta sigma weight residual 120.79 124.31 -3.52 1.39e+00 5.18e-01 6.40e+00 angle pdb=" N ALA B 266 " pdb=" CA ALA B 266 " pdb=" C ALA B 266 " ideal model delta sigma weight residual 111.02 114.09 -3.07 1.22e+00 6.72e-01 6.32e+00 angle pdb=" N ILE G 306 " pdb=" CA ILE G 306 " pdb=" C ILE G 306 " ideal model delta sigma weight residual 113.00 109.94 3.06 1.30e+00 5.92e-01 5.54e+00 angle pdb=" N GLU D 299 " pdb=" CA GLU D 299 " pdb=" C GLU D 299 " ideal model delta sigma weight residual 110.19 107.28 2.91 1.24e+00 6.50e-01 5.51e+00 ... (remaining 23307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.98: 9971 34.98 - 69.96: 557 69.96 - 104.94: 33 104.94 - 139.92: 0 139.92 - 174.89: 1 Dihedral angle restraints: 10562 sinusoidal: 4898 harmonic: 5664 Sorted by residual: dihedral pdb=" C4' DT J 7 " pdb=" C3' DT J 7 " pdb=" O3' DT J 7 " pdb=" P DT J 8 " ideal model delta sinusoidal sigma weight residual -140.00 34.89 -174.89 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" CG ARG B 311 " pdb=" CD ARG B 311 " pdb=" NE ARG B 311 " pdb=" CZ ARG B 311 " ideal model delta sinusoidal sigma weight residual -180.00 -135.45 -44.55 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CG ARG C 204 " pdb=" CD ARG C 204 " pdb=" NE ARG C 204 " pdb=" CZ ARG C 204 " ideal model delta sinusoidal sigma weight residual 90.00 133.89 -43.89 2 1.50e+01 4.44e-03 1.03e+01 ... (remaining 10559 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1882 0.030 - 0.059: 524 0.059 - 0.089: 160 0.089 - 0.119: 97 0.119 - 0.149: 9 Chirality restraints: 2672 Sorted by residual: chirality pdb=" CA ILE A 171 " pdb=" N ILE A 171 " pdb=" C ILE A 171 " pdb=" CB ILE A 171 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.53e-01 chirality pdb=" CG LEU A 267 " pdb=" CB LEU A 267 " pdb=" CD1 LEU A 267 " pdb=" CD2 LEU A 267 " both_signs ideal model delta sigma weight residual False -2.59 -2.74 0.15 2.00e-01 2.50e+01 5.47e-01 chirality pdb=" CG LEU F 267 " pdb=" CB LEU F 267 " pdb=" CD1 LEU F 267 " pdb=" CD2 LEU F 267 " both_signs ideal model delta sigma weight residual False -2.59 -2.73 0.14 2.00e-01 2.50e+01 5.00e-01 ... (remaining 2669 not shown) Planarity restraints: 2824 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN G 101 " -0.042 5.00e-02 4.00e+02 6.26e-02 6.27e+00 pdb=" N PRO G 102 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO G 102 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO G 102 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 263 " -0.033 5.00e-02 4.00e+02 5.02e-02 4.03e+00 pdb=" N PRO D 264 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO D 264 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 264 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY H 153 " -0.025 5.00e-02 4.00e+02 3.82e-02 2.33e+00 pdb=" N PRO H 154 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO H 154 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO H 154 " -0.021 5.00e-02 4.00e+02 ... (remaining 2821 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3125 2.78 - 3.31: 16546 3.31 - 3.84: 29228 3.84 - 4.37: 33407 4.37 - 4.90: 57434 Nonbonded interactions: 139740 Sorted by model distance: nonbonded pdb=" OE1 GLU G 191 " pdb=" NH2 ARG G 224 " model vdw 2.248 3.120 nonbonded pdb=" O LEU H 189 " pdb=" OG1 THR H 193 " model vdw 2.251 3.040 nonbonded pdb=" ND2 ASN B 232 " pdb=" O ASN C 312 " model vdw 2.252 3.120 nonbonded pdb=" OE1 GLU A 191 " pdb=" NH2 ARG B 268 " model vdw 2.255 3.120 nonbonded pdb=" O ASN A 312 " pdb=" ND2 ASN F 232 " model vdw 2.256 3.120 ... (remaining 139735 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.640 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 40.770 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.080 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: 0.010 Load rotamer database and sin/cos tables:3.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6777 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17070 Z= 0.109 Angle : 0.489 5.163 23312 Z= 0.266 Chirality : 0.036 0.149 2672 Planarity : 0.004 0.063 2824 Dihedral : 18.531 174.895 6882 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (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 TRP 0.006 0.001 TRP B 121 HIS 0.010 0.001 HIS B 177 PHE 0.006 0.001 PHE C 218 TYR 0.011 0.001 TYR G 206 ARG 0.014 0.001 ARG D 224 Details of bonding type rmsd hydrogen bonds : bond 0.14697 ( 924) hydrogen bonds : angle 5.88866 ( 2674) covalent geometry : bond 0.00242 (17070) covalent geometry : angle 0.48892 (23312) *********************** 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 : 1.799 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: 0.3098 time to fit residues: 111.0608 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 : 1.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 9.9990 chunk 148 optimal weight: 7.9990 chunk 82 optimal weight: 10.0000 chunk 50 optimal weight: 30.0000 chunk 100 optimal weight: 0.9980 chunk 79 optimal weight: 10.0000 chunk 153 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 93 optimal weight: 9.9990 chunk 114 optimal weight: 8.9990 chunk 177 optimal weight: 9.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 GLN D 117 ASN G 262 GLN H 146 ASN H 262 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.055242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.042043 restraints weight = 79667.497| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 3.46 r_work: 0.2830 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.2047 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= 0.241 Angle : 0.625 7.437 23312 Z= 0.329 Chirality : 0.039 0.135 2672 Planarity : 0.005 0.047 2824 Dihedral : 17.727 173.534 3026 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.30 % Allowed : 9.66 % Favored : 90.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.20), residues: 1952 helix: 1.67 (0.15), residues: 1184 sheet: -0.20 (0.38), residues: 240 loop : 0.91 (0.31), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 121 HIS 0.011 0.001 HIS G 282 PHE 0.012 0.001 PHE D 297 TYR 0.010 0.001 TYR D 292 ARG 0.009 0.001 ARG D 224 Details of bonding type rmsd hydrogen bonds : bond 0.03483 ( 924) hydrogen bonds : angle 4.75196 ( 2674) covalent geometry : bond 0.00531 (17070) covalent geometry : angle 0.62466 (23312) *********************** 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 135 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 130 time to evaluate : 1.968 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.9258 (ttt) cc_final: 0.8949 (ttp) REVERT: A 305 ASP cc_start: 0.8992 (t0) cc_final: 0.8770 (t0) REVERT: B 305 ASP cc_start: 0.9086 (t0) cc_final: 0.8836 (t0) REVERT: C 305 ASP cc_start: 0.9149 (t0) cc_final: 0.8835 (t0) REVERT: E 305 ASP cc_start: 0.9150 (t0) cc_final: 0.8893 (t0) REVERT: F 259 GLN cc_start: 0.9565 (mt0) cc_final: 0.9356 (mp10) REVERT: F 305 ASP cc_start: 0.9037 (t0) cc_final: 0.8805 (t0) outliers start: 5 outliers final: 4 residues processed: 133 average time/residue: 0.2704 time to fit residues: 56.7416 Evaluate side-chains 112 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 108 time to evaluate : 1.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain E residue 122 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 79 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 chunk 191 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 16 optimal weight: 8.9990 chunk 84 optimal weight: 0.6980 chunk 174 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN C 259 GLN D 259 GLN E 259 GLN G 117 ASN G 259 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.073091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.059873 restraints weight = 102509.789| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 3.37 r_work: 0.2887 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17070 Z= 0.142 Angle : 0.526 6.001 23312 Z= 0.281 Chirality : 0.037 0.130 2672 Planarity : 0.004 0.041 2824 Dihedral : 17.624 174.658 3026 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.54 % Allowed : 10.39 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.20), residues: 1952 helix: 1.74 (0.15), residues: 1200 sheet: -0.40 (0.36), residues: 264 loop : 1.48 (0.33), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 121 HIS 0.008 0.001 HIS G 282 PHE 0.013 0.001 PHE D 297 TYR 0.008 0.001 TYR H 206 ARG 0.005 0.000 ARG D 224 Details of bonding type rmsd hydrogen bonds : bond 0.02878 ( 924) hydrogen bonds : angle 4.45360 ( 2674) covalent geometry : bond 0.00316 (17070) covalent geometry : angle 0.52627 (23312) *********************** 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 135 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 126 time to evaluate : 1.930 Fit side-chains revert: symmetry clash REVERT: A 305 ASP cc_start: 0.9023 (t0) cc_final: 0.8710 (t70) REVERT: B 305 ASP cc_start: 0.9068 (t0) cc_final: 0.8730 (t0) REVERT: C 305 ASP cc_start: 0.9158 (t0) cc_final: 0.8803 (t0) REVERT: D 122 MET cc_start: 0.9191 (ttt) cc_final: 0.8816 (ttp) REVERT: E 305 ASP cc_start: 0.9079 (t0) cc_final: 0.8670 (t0) REVERT: F 259 GLN cc_start: 0.9553 (mt0) cc_final: 0.9331 (mp10) REVERT: F 305 ASP cc_start: 0.9038 (t0) cc_final: 0.8747 (t0) REVERT: G 122 MET cc_start: 0.9287 (ttt) cc_final: 0.9017 (ttp) outliers start: 9 outliers final: 3 residues processed: 131 average time/residue: 0.2761 time to fit residues: 57.0974 Evaluate side-chains 116 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 113 time to evaluate : 1.881 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 92 optimal weight: 8.9990 chunk 35 optimal weight: 7.9990 chunk 161 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 chunk 18 optimal weight: 20.0000 chunk 170 optimal weight: 20.0000 chunk 110 optimal weight: 10.0000 chunk 99 optimal weight: 4.9990 chunk 66 optimal weight: 20.0000 chunk 6 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN C 259 GLN D 259 GLN E 259 GLN G 259 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.052427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.039107 restraints weight = 80863.802| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 3.64 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 17070 Z= 0.244 Angle : 0.597 8.435 23312 Z= 0.311 Chirality : 0.038 0.134 2672 Planarity : 0.004 0.050 2824 Dihedral : 17.646 172.378 3026 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.15 % Allowed : 12.62 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.20), residues: 1952 helix: 1.84 (0.15), residues: 1200 sheet: -0.66 (0.34), residues: 280 loop : 1.52 (0.33), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 121 HIS 0.004 0.001 HIS B 177 PHE 0.010 0.001 PHE B 297 TYR 0.010 0.001 TYR H 206 ARG 0.007 0.000 ARG E 275 Details of bonding type rmsd hydrogen bonds : bond 0.03070 ( 924) hydrogen bonds : angle 4.43358 ( 2674) covalent geometry : bond 0.00537 (17070) covalent geometry : angle 0.59686 (23312) *********************** 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 134 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 1.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.8984 (ttt) cc_final: 0.8716 (ttp) REVERT: A 305 ASP cc_start: 0.9021 (t0) cc_final: 0.8649 (t70) REVERT: B 305 ASP cc_start: 0.9056 (t0) cc_final: 0.8686 (t0) REVERT: C 305 ASP cc_start: 0.9134 (t0) cc_final: 0.8755 (t0) REVERT: D 122 MET cc_start: 0.8974 (ttt) cc_final: 0.8750 (ttp) REVERT: E 305 ASP cc_start: 0.9124 (t0) cc_final: 0.8696 (t0) REVERT: F 200 MET cc_start: 0.8842 (mmm) cc_final: 0.8531 (mmm) REVERT: F 259 GLN cc_start: 0.9436 (mt0) cc_final: 0.9230 (mp10) REVERT: F 305 ASP cc_start: 0.9045 (t0) cc_final: 0.8745 (t0) REVERT: G 122 MET cc_start: 0.9073 (ttt) cc_final: 0.8807 (ttp) REVERT: H 200 MET cc_start: 0.8801 (tpp) cc_final: 0.8340 (ttt) outliers start: 19 outliers final: 8 residues processed: 128 average time/residue: 0.2742 time to fit residues: 55.3313 Evaluate side-chains 118 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 1.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain H residue 259 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 34 optimal weight: 4.9990 chunk 178 optimal weight: 9.9990 chunk 114 optimal weight: 20.0000 chunk 51 optimal weight: 1.9990 chunk 154 optimal weight: 9.9990 chunk 182 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 192 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 GLN D 259 GLN E 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.052492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.039234 restraints weight = 81074.815| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 3.67 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17070 Z= 0.185 Angle : 0.552 10.521 23312 Z= 0.291 Chirality : 0.037 0.145 2672 Planarity : 0.004 0.046 2824 Dihedral : 17.634 172.941 3026 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.79 % Allowed : 13.95 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.20), residues: 1952 helix: 1.90 (0.15), residues: 1200 sheet: -0.43 (0.35), residues: 264 loop : 1.61 (0.33), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 121 HIS 0.002 0.001 HIS B 177 PHE 0.015 0.001 PHE D 297 TYR 0.010 0.001 TYR A 206 ARG 0.008 0.000 ARG D 311 Details of bonding type rmsd hydrogen bonds : bond 0.02815 ( 924) hydrogen bonds : angle 4.33544 ( 2674) covalent geometry : bond 0.00412 (17070) covalent geometry : angle 0.55224 (23312) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 1.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.9076 (ttt) cc_final: 0.8785 (ttp) REVERT: A 305 ASP cc_start: 0.9047 (t0) cc_final: 0.8645 (t70) REVERT: B 305 ASP cc_start: 0.9049 (t0) cc_final: 0.8656 (t0) REVERT: C 305 ASP cc_start: 0.9106 (t0) cc_final: 0.8702 (t0) REVERT: D 311 ARG cc_start: 0.7284 (mtm110) cc_final: 0.6980 (mtm110) REVERT: E 305 ASP cc_start: 0.9117 (t0) cc_final: 0.8684 (t0) REVERT: F 259 GLN cc_start: 0.9434 (mt0) cc_final: 0.9218 (mp10) REVERT: F 305 ASP cc_start: 0.9073 (t0) cc_final: 0.8727 (t0) REVERT: G 122 MET cc_start: 0.9147 (ttt) cc_final: 0.8832 (ttp) REVERT: G 259 GLN cc_start: 0.9443 (mt0) cc_final: 0.9235 (mp10) REVERT: H 167 GLN cc_start: 0.8292 (mm-40) cc_final: 0.7772 (mm-40) REVERT: H 200 MET cc_start: 0.8673 (tpp) cc_final: 0.8389 (ttt) outliers start: 13 outliers final: 8 residues processed: 120 average time/residue: 0.2539 time to fit residues: 49.5830 Evaluate side-chains 118 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 1.947 ------------------------------------------------------------------------------- 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 209 MET Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain H residue 259 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 138 optimal weight: 20.0000 chunk 56 optimal weight: 0.9990 chunk 120 optimal weight: 9.9990 chunk 192 optimal weight: 8.9990 chunk 167 optimal weight: 7.9990 chunk 193 optimal weight: 7.9990 chunk 95 optimal weight: 8.9990 chunk 66 optimal weight: 20.0000 chunk 160 optimal weight: 6.9990 chunk 185 optimal weight: 5.9990 chunk 92 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.053452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.040252 restraints weight = 82058.602| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 3.57 r_work: 0.2774 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.3029 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= 0.240 Angle : 0.597 12.353 23312 Z= 0.310 Chirality : 0.038 0.185 2672 Planarity : 0.004 0.047 2824 Dihedral : 17.717 171.428 3026 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.51 % Allowed : 13.95 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.20), residues: 1952 helix: 1.98 (0.15), residues: 1192 sheet: -0.63 (0.34), residues: 280 loop : 1.53 (0.34), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 121 HIS 0.003 0.001 HIS B 177 PHE 0.010 0.001 PHE B 297 TYR 0.025 0.002 TYR G 206 ARG 0.004 0.000 ARG D 311 Details of bonding type rmsd hydrogen bonds : bond 0.03033 ( 924) hydrogen bonds : angle 4.39104 ( 2674) covalent geometry : bond 0.00530 (17070) covalent geometry : angle 0.59674 (23312) *********************** 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 134 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 1.748 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 305 ASP cc_start: 0.9117 (t0) cc_final: 0.8724 (t0) REVERT: B 305 ASP cc_start: 0.9145 (t0) cc_final: 0.8764 (t0) REVERT: C 305 ASP cc_start: 0.9141 (t0) cc_final: 0.8731 (t0) REVERT: D 122 MET cc_start: 0.9250 (ttt) cc_final: 0.9016 (ttp) REVERT: D 311 ARG cc_start: 0.7575 (mtm110) cc_final: 0.7282 (mtm110) REVERT: E 181 GLU cc_start: 0.6798 (tp30) cc_final: 0.6502 (tp30) REVERT: E 200 MET cc_start: 0.9139 (ttm) cc_final: 0.8838 (mtp) REVERT: E 305 ASP cc_start: 0.9223 (t0) cc_final: 0.8843 (t0) REVERT: F 92 THR cc_start: 0.9651 (OUTLIER) cc_final: 0.9409 (t) REVERT: F 305 ASP cc_start: 0.9132 (t0) cc_final: 0.8755 (t0) REVERT: G 259 GLN cc_start: 0.9456 (mt0) cc_final: 0.9255 (mp10) REVERT: H 167 GLN cc_start: 0.8607 (mm-40) cc_final: 0.8097 (mm-40) outliers start: 25 outliers final: 12 residues processed: 127 average time/residue: 0.2343 time to fit residues: 49.0560 Evaluate side-chains 119 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain E residue 291 ASP Chi-restraints excluded: chain E residue 306 ILE Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 301 ASP Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain H residue 259 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 121 optimal weight: 7.9990 chunk 109 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 168 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 189 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 chunk 85 optimal weight: 5.9990 chunk 179 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.052213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.039082 restraints weight = 81238.830| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 3.55 r_work: 0.2755 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17070 Z= 0.198 Angle : 0.565 11.964 23312 Z= 0.296 Chirality : 0.038 0.162 2672 Planarity : 0.004 0.046 2824 Dihedral : 17.737 171.736 3026 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.21 % Allowed : 15.04 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.20), residues: 1952 helix: 1.98 (0.15), residues: 1200 sheet: -0.49 (0.34), residues: 256 loop : 1.39 (0.33), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 121 HIS 0.002 0.000 HIS B 177 PHE 0.011 0.001 PHE D 297 TYR 0.027 0.001 TYR G 206 ARG 0.004 0.000 ARG D 311 Details of bonding type rmsd hydrogen bonds : bond 0.02872 ( 924) hydrogen bonds : angle 4.31946 ( 2674) covalent geometry : bond 0.00441 (17070) covalent geometry : angle 0.56459 (23312) *********************** 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: 20 poor density : 111 time to evaluate : 1.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 THR cc_start: 0.9618 (OUTLIER) cc_final: 0.9412 (t) REVERT: A 200 MET cc_start: 0.8956 (tpp) cc_final: 0.8722 (mtp) REVERT: A 305 ASP cc_start: 0.9128 (t0) cc_final: 0.8740 (t70) REVERT: B 305 ASP cc_start: 0.9138 (t0) cc_final: 0.8771 (t0) REVERT: C 305 ASP cc_start: 0.9134 (t0) cc_final: 0.8731 (t0) REVERT: D 122 MET cc_start: 0.9333 (ttt) cc_final: 0.9050 (ttp) REVERT: D 305 ASP cc_start: 0.9390 (t0) cc_final: 0.9054 (t0) REVERT: D 311 ARG cc_start: 0.7632 (mtm110) cc_final: 0.7088 (ptt-90) REVERT: E 184 GLU cc_start: 0.7175 (tt0) cc_final: 0.6696 (mm-30) REVERT: E 200 MET cc_start: 0.9134 (ttm) cc_final: 0.8811 (mtp) REVERT: E 305 ASP cc_start: 0.9172 (t0) cc_final: 0.8771 (t0) REVERT: F 92 THR cc_start: 0.9647 (OUTLIER) cc_final: 0.9403 (t) REVERT: F 305 ASP cc_start: 0.9125 (t0) cc_final: 0.8743 (t0) REVERT: G 86 MET cc_start: 0.9440 (mmm) cc_final: 0.8920 (mtm) REVERT: G 92 THR cc_start: 0.9642 (OUTLIER) cc_final: 0.9371 (p) REVERT: G 259 GLN cc_start: 0.9453 (mt0) cc_final: 0.9235 (mp10) REVERT: H 167 GLN cc_start: 0.8726 (mm-40) cc_final: 0.8188 (mm-40) REVERT: H 305 ASP cc_start: 0.9124 (t70) cc_final: 0.8785 (t0) outliers start: 20 outliers final: 13 residues processed: 125 average time/residue: 0.2458 time to fit residues: 50.7211 Evaluate side-chains 123 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 1.954 ------------------------------------------------------------------------------- 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 A residue 259 GLN Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain C residue 291 ASP Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 259 GLN Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain E residue 291 ASP Chi-restraints excluded: chain E residue 306 ILE Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain H residue 259 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 108 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 178 optimal weight: 7.9990 chunk 138 optimal weight: 5.9990 chunk 102 optimal weight: 8.9990 chunk 159 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 47 optimal weight: 20.0000 chunk 54 optimal weight: 5.9990 chunk 1 optimal weight: 20.0000 chunk 188 optimal weight: 20.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 259 GLN E 259 GLN F 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.052700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.039533 restraints weight = 81699.804| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 3.58 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17070 Z= 0.160 Angle : 0.550 10.108 23312 Z= 0.293 Chirality : 0.037 0.137 2672 Planarity : 0.004 0.043 2824 Dihedral : 17.731 171.715 3026 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.21 % Allowed : 15.46 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.20), residues: 1952 helix: 2.00 (0.15), residues: 1200 sheet: -0.58 (0.33), residues: 280 loop : 1.78 (0.34), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 121 HIS 0.001 0.000 HIS A 203 PHE 0.012 0.001 PHE D 297 TYR 0.027 0.001 TYR G 206 ARG 0.004 0.000 ARG D 311 Details of bonding type rmsd hydrogen bonds : bond 0.02738 ( 924) hydrogen bonds : angle 4.24929 ( 2674) covalent geometry : bond 0.00360 (17070) covalent geometry : angle 0.55010 (23312) *********************** 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 133 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 1.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.8844 (ttt) cc_final: 0.8626 (ttp) REVERT: A 305 ASP cc_start: 0.9108 (t0) cc_final: 0.8699 (t70) REVERT: B 200 MET cc_start: 0.8502 (ttm) cc_final: 0.8293 (mtp) REVERT: B 305 ASP cc_start: 0.9090 (t0) cc_final: 0.8706 (t0) REVERT: C 305 ASP cc_start: 0.9122 (t0) cc_final: 0.8685 (t0) REVERT: D 122 MET cc_start: 0.8928 (ttt) cc_final: 0.8636 (ttp) REVERT: D 305 ASP cc_start: 0.9395 (t0) cc_final: 0.9029 (t0) REVERT: D 311 ARG cc_start: 0.7469 (mtm110) cc_final: 0.7022 (ptt-90) REVERT: E 305 ASP cc_start: 0.9131 (t0) cc_final: 0.8715 (t0) REVERT: F 92 THR cc_start: 0.9594 (OUTLIER) cc_final: 0.9357 (t) REVERT: F 305 ASP cc_start: 0.9083 (t0) cc_final: 0.8685 (t0) REVERT: G 86 MET cc_start: 0.9188 (mmm) cc_final: 0.8640 (mtm) REVERT: G 92 THR cc_start: 0.9609 (OUTLIER) cc_final: 0.9355 (p) REVERT: G 259 GLN cc_start: 0.9414 (mt0) cc_final: 0.9213 (mp10) REVERT: H 167 GLN cc_start: 0.8448 (mm-40) cc_final: 0.7930 (mm-40) REVERT: H 305 ASP cc_start: 0.9147 (t70) cc_final: 0.8816 (t0) outliers start: 20 outliers final: 15 residues processed: 126 average time/residue: 0.2902 time to fit residues: 60.2189 Evaluate side-chains 126 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 2.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain C residue 291 ASP Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 259 GLN Chi-restraints excluded: chain E residue 279 MET Chi-restraints excluded: chain E residue 306 ILE Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 259 GLN Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain H residue 259 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 114 optimal weight: 20.0000 chunk 123 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 184 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 158 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 170 optimal weight: 7.9990 chunk 135 optimal weight: 0.9990 chunk 156 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 259 GLN E 259 GLN F 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.052880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.039777 restraints weight = 81393.564| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 3.58 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17070 Z= 0.166 Angle : 0.569 12.830 23312 Z= 0.301 Chirality : 0.038 0.185 2672 Planarity : 0.004 0.043 2824 Dihedral : 17.732 171.348 3026 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.27 % Allowed : 15.58 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.20), residues: 1952 helix: 1.99 (0.15), residues: 1200 sheet: -0.40 (0.34), residues: 256 loop : 1.51 (0.33), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 121 HIS 0.001 0.000 HIS D 177 PHE 0.007 0.001 PHE D 297 TYR 0.028 0.001 TYR G 206 ARG 0.004 0.000 ARG E 187 Details of bonding type rmsd hydrogen bonds : bond 0.02721 ( 924) hydrogen bonds : angle 4.25692 ( 2674) covalent geometry : bond 0.00373 (17070) covalent geometry : angle 0.56948 (23312) *********************** 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: 21 poor density : 113 time to evaluate : 2.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 ASP cc_start: 0.9108 (t0) cc_final: 0.8694 (t70) REVERT: B 200 MET cc_start: 0.8523 (ttm) cc_final: 0.8322 (mtp) REVERT: B 305 ASP cc_start: 0.9087 (t0) cc_final: 0.8703 (t0) REVERT: C 305 ASP cc_start: 0.9121 (t0) cc_final: 0.8681 (t0) REVERT: D 122 MET cc_start: 0.9006 (ttt) cc_final: 0.8692 (ttp) REVERT: E 305 ASP cc_start: 0.9128 (t0) cc_final: 0.8709 (t0) REVERT: F 92 THR cc_start: 0.9597 (OUTLIER) cc_final: 0.9363 (t) REVERT: F 305 ASP cc_start: 0.9087 (t0) cc_final: 0.8687 (t0) REVERT: G 86 MET cc_start: 0.9243 (mmm) cc_final: 0.8682 (mtm) REVERT: G 92 THR cc_start: 0.9603 (OUTLIER) cc_final: 0.9345 (p) REVERT: G 259 GLN cc_start: 0.9412 (mt0) cc_final: 0.9208 (mp10) REVERT: H 305 ASP cc_start: 0.9146 (t70) cc_final: 0.8765 (t0) outliers start: 21 outliers final: 14 residues processed: 127 average time/residue: 0.2927 time to fit residues: 62.0130 Evaluate side-chains 125 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 4.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain C residue 259 GLN Chi-restraints excluded: chain C residue 291 ASP Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain E residue 279 MET Chi-restraints excluded: chain E residue 291 ASP Chi-restraints excluded: chain E residue 306 ILE Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain H residue 259 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 119 optimal weight: 8.9990 chunk 76 optimal weight: 6.9990 chunk 67 optimal weight: 8.9990 chunk 48 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 12 optimal weight: 8.9990 chunk 147 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.052418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.039319 restraints weight = 82049.900| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 3.52 r_work: 0.2784 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17070 Z= 0.176 Angle : 0.584 11.522 23312 Z= 0.309 Chirality : 0.038 0.190 2672 Planarity : 0.004 0.044 2824 Dihedral : 17.748 171.127 3026 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.03 % Allowed : 16.06 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.20), residues: 1952 helix: 2.01 (0.15), residues: 1200 sheet: -0.39 (0.34), residues: 256 loop : 1.53 (0.33), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 121 HIS 0.002 0.000 HIS A 203 PHE 0.009 0.001 PHE D 297 TYR 0.029 0.001 TYR G 206 ARG 0.004 0.000 ARG D 311 Details of bonding type rmsd hydrogen bonds : bond 0.02715 ( 924) hydrogen bonds : angle 4.23747 ( 2674) covalent geometry : bond 0.00397 (17070) covalent geometry : angle 0.58370 (23312) ********************** 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 128 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 2.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 ASP cc_start: 0.9121 (t0) cc_final: 0.8709 (t70) REVERT: B 305 ASP cc_start: 0.9126 (t0) cc_final: 0.8746 (t0) REVERT: C 305 ASP cc_start: 0.9131 (t0) cc_final: 0.8666 (t0) REVERT: D 122 MET cc_start: 0.9314 (ttt) cc_final: 0.9034 (ttp) REVERT: D 200 MET cc_start: 0.9031 (ttm) cc_final: 0.8767 (mtm) REVERT: E 181 GLU cc_start: 0.6767 (tp30) cc_final: 0.6567 (tp30) REVERT: E 200 MET cc_start: 0.9127 (ttm) cc_final: 0.8858 (mtp) REVERT: E 305 ASP cc_start: 0.9152 (t0) cc_final: 0.8720 (t0) REVERT: F 92 THR cc_start: 0.9645 (OUTLIER) cc_final: 0.9418 (t) REVERT: F 305 ASP cc_start: 0.9115 (t0) cc_final: 0.8718 (t0) REVERT: G 86 MET cc_start: 0.9407 (mmm) cc_final: 0.8907 (mtm) REVERT: G 92 THR cc_start: 0.9633 (OUTLIER) cc_final: 0.9391 (p) REVERT: G 259 GLN cc_start: 0.9444 (mt0) cc_final: 0.9239 (mp10) REVERT: H 305 ASP cc_start: 0.9170 (t70) cc_final: 0.8784 (t0) outliers start: 17 outliers final: 15 residues processed: 123 average time/residue: 0.2480 time to fit residues: 51.0959 Evaluate side-chains 126 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 1.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain C residue 259 GLN Chi-restraints excluded: chain C residue 291 ASP Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain E residue 279 MET Chi-restraints excluded: chain E residue 291 ASP Chi-restraints excluded: chain E residue 306 ILE Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain H residue 259 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 92 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 125 optimal weight: 6.9990 chunk 40 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 167 optimal weight: 7.9990 chunk 86 optimal weight: 9.9990 chunk 129 optimal weight: 1.9990 chunk 181 optimal weight: 7.9990 chunk 36 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.052575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.039530 restraints weight = 81463.056| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 3.48 r_work: 0.2785 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17070 Z= 0.171 Angle : 0.581 11.639 23312 Z= 0.309 Chirality : 0.038 0.193 2672 Planarity : 0.004 0.044 2824 Dihedral : 17.752 171.144 3026 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.03 % Allowed : 16.30 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.20), residues: 1952 helix: 2.02 (0.15), residues: 1200 sheet: -0.50 (0.34), residues: 280 loop : 1.86 (0.34), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 121 HIS 0.001 0.000 HIS A 203 PHE 0.006 0.001 PHE C 218 TYR 0.029 0.001 TYR G 206 ARG 0.006 0.000 ARG D 311 Details of bonding type rmsd hydrogen bonds : bond 0.02683 ( 924) hydrogen bonds : angle 4.23014 ( 2674) covalent geometry : bond 0.00384 (17070) covalent geometry : angle 0.58103 (23312) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6826.64 seconds wall clock time: 120 minutes 26.90 seconds (7226.90 seconds total)