Starting phenix.real_space_refine on Tue Jan 21 08:29:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xvb_38695/01_2025/8xvb_38695.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xvb_38695/01_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_38695/01_2025/8xvb_38695.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xvb_38695/01_2025/8xvb_38695.map" model { file = "/net/cci-nas-00/data/ceres_data/8xvb_38695/01_2025/8xvb_38695.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xvb_38695/01_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 9.32, per 1000 atoms: 0.56 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: 4.43 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: 5.44 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: 5.28 Time building geometry restraints manager: 4.99 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: 14.730 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 40.380 Find NCS groups from input model: 0.740 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: 0.000 Load rotamer database and sin/cos tables:3.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.160 ------------------------------------------------------------------------------- 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= 0.157 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 *********************** 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 : 1.861 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: 0.3283 time to fit residues: 117.1182 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 : 1.843 ------------------------------------------------------------------------------- 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 = 33)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.042047 restraints weight = 79667.399| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 3.46 r_work: 0.2831 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.2831 ------------------------------------------------------------------------------- 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= 0.349 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 *********************** 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 : 1.740 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.9257 (ttt) cc_final: 0.8948 (ttp) REVERT: A 305 ASP cc_start: 0.8990 (t0) cc_final: 0.8769 (t0) REVERT: B 305 ASP cc_start: 0.9086 (t0) cc_final: 0.8835 (t0) REVERT: C 305 ASP cc_start: 0.9147 (t0) cc_final: 0.8833 (t0) REVERT: E 305 ASP cc_start: 0.9151 (t0) cc_final: 0.8893 (t0) REVERT: F 259 GLN cc_start: 0.9565 (mt0) cc_final: 0.9357 (mp10) REVERT: F 305 ASP cc_start: 0.9038 (t0) cc_final: 0.8806 (t0) outliers start: 5 outliers final: 4 residues processed: 133 average time/residue: 0.2823 time to fit residues: 59.1211 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 : 1.858 ------------------------------------------------------------------------------- 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: 0.9990 chunk 26 optimal weight: 30.0000 chunk 191 optimal weight: 6.9990 chunk 119 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 84 optimal weight: 0.9990 chunk 174 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 = 0.3832 r_free = 0.3832 target = 0.073026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.059783 restraints weight = 102524.109| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 3.37 r_work: 0.2870 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17070 Z= 0.208 Angle : 0.526 6.121 23312 Z= 0.281 Chirality : 0.037 0.130 2672 Planarity : 0.004 0.042 2824 Dihedral : 17.625 174.566 3026 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.48 % Allowed : 10.63 % Favored : 88.89 % 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: -0.39 (0.36), residues: 264 loop : 1.47 (0.32), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 121 HIS 0.008 0.001 HIS G 282 PHE 0.012 0.001 PHE D 297 TYR 0.008 0.001 TYR H 206 ARG 0.005 0.000 ARG D 224 *********************** 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 : 1.851 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 305 ASP cc_start: 0.9023 (t0) cc_final: 0.8715 (t70) REVERT: B 305 ASP cc_start: 0.9072 (t0) cc_final: 0.8738 (t0) REVERT: C 305 ASP cc_start: 0.9149 (t0) cc_final: 0.8817 (t0) REVERT: D 122 MET cc_start: 0.9176 (ttt) cc_final: 0.8808 (ttp) REVERT: E 305 ASP cc_start: 0.9082 (t0) cc_final: 0.8682 (t0) REVERT: F 259 GLN cc_start: 0.9554 (mt0) cc_final: 0.9334 (mp10) REVERT: F 305 ASP cc_start: 0.9044 (t0) cc_final: 0.8757 (t0) REVERT: G 122 MET cc_start: 0.9283 (ttt) cc_final: 0.9014 (ttp) outliers start: 8 outliers final: 4 residues processed: 126 average time/residue: 0.2753 time to fit residues: 54.9810 Evaluate side-chains 115 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 111 time to evaluate : 1.858 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain H residue 259 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 92 optimal weight: 1.9990 chunk 35 optimal weight: 0.0870 chunk 161 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 18 optimal weight: 20.0000 chunk 170 optimal weight: 20.0000 chunk 110 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 66 optimal weight: 20.0000 chunk 6 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 259 GLN D 259 GLN E 259 GLN G 259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.054223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.040565 restraints weight = 80783.832| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 3.77 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17070 Z= 0.200 Angle : 0.521 9.488 23312 Z= 0.278 Chirality : 0.037 0.129 2672 Planarity : 0.004 0.043 2824 Dihedral : 17.544 173.713 3026 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.85 % Allowed : 11.65 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.20), residues: 1952 helix: 1.83 (0.15), residues: 1200 sheet: -0.41 (0.35), residues: 264 loop : 1.55 (0.33), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 121 HIS 0.003 0.001 HIS B 177 PHE 0.006 0.001 PHE B 297 TYR 0.008 0.001 TYR H 206 ARG 0.007 0.000 ARG E 311 *********************** 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 137 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 1.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 ASP cc_start: 0.9032 (t0) cc_final: 0.8665 (t70) REVERT: B 305 ASP cc_start: 0.9032 (t0) cc_final: 0.8651 (t0) REVERT: C 305 ASP cc_start: 0.9113 (t0) cc_final: 0.8724 (t0) REVERT: E 305 ASP cc_start: 0.9075 (t0) cc_final: 0.8635 (t0) REVERT: E 311 ARG cc_start: 0.8357 (ttp-110) cc_final: 0.8151 (ttp-110) REVERT: F 259 GLN cc_start: 0.9482 (mt0) cc_final: 0.9252 (mp10) REVERT: F 305 ASP cc_start: 0.9024 (t0) cc_final: 0.8680 (t0) REVERT: H 200 MET cc_start: 0.8761 (tpp) cc_final: 0.8313 (ttt) outliers start: 14 outliers final: 7 residues processed: 132 average time/residue: 0.2838 time to fit residues: 59.3087 Evaluate side-chains 126 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 119 time to evaluate : 1.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain E residue 122 MET 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: 10.0000 chunk 178 optimal weight: 10.0000 chunk 114 optimal weight: 0.3980 chunk 51 optimal weight: 9.9990 chunk 154 optimal weight: 9.9990 chunk 182 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 192 optimal weight: 7.9990 chunk 104 optimal weight: 9.9990 chunk 45 optimal weight: 8.9990 chunk 103 optimal weight: 4.9990 overall best weight: 4.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 259 GLN D 259 GLN E 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.056056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.042663 restraints weight = 81545.594| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 3.55 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 17070 Z= 0.298 Angle : 0.554 10.851 23312 Z= 0.292 Chirality : 0.037 0.148 2672 Planarity : 0.004 0.043 2824 Dihedral : 17.567 172.812 3026 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.79 % Allowed : 13.29 % Favored : 85.93 % 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: 2.20 (0.20), residues: 1952 helix: 1.94 (0.15), residues: 1200 sheet: -0.37 (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 0.009 0.001 PHE D 297 TYR 0.010 0.001 TYR A 206 ARG 0.005 0.000 ARG H 275 *********************** 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 130 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 1.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 ASP cc_start: 0.9056 (t0) cc_final: 0.8653 (t70) REVERT: B 305 ASP cc_start: 0.9068 (t0) cc_final: 0.8675 (t0) REVERT: C 305 ASP cc_start: 0.9125 (t0) cc_final: 0.8719 (t0) REVERT: D 311 ARG cc_start: 0.7162 (mtm110) cc_final: 0.6935 (mtm110) REVERT: E 305 ASP cc_start: 0.9091 (t0) cc_final: 0.8609 (t0) REVERT: F 259 GLN cc_start: 0.9425 (mt0) cc_final: 0.9215 (mp10) REVERT: F 305 ASP cc_start: 0.9076 (t0) cc_final: 0.8701 (t0) REVERT: G 122 MET cc_start: 0.9061 (ttt) cc_final: 0.8785 (ttp) REVERT: G 259 GLN cc_start: 0.9414 (mt0) cc_final: 0.9211 (mp10) REVERT: H 167 GLN cc_start: 0.8206 (mm-40) cc_final: 0.7725 (mm-40) REVERT: H 200 MET cc_start: 0.8676 (tpp) cc_final: 0.8349 (ttt) outliers start: 13 outliers final: 9 residues processed: 125 average time/residue: 0.2588 time to fit residues: 52.2098 Evaluate side-chains 125 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 116 time to evaluate : 1.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain H residue 259 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 138 optimal weight: 8.9990 chunk 56 optimal weight: 0.7980 chunk 120 optimal weight: 10.0000 chunk 192 optimal weight: 7.9990 chunk 167 optimal weight: 10.0000 chunk 193 optimal weight: 6.9990 chunk 95 optimal weight: 0.0970 chunk 66 optimal weight: 2.9990 chunk 160 optimal weight: 8.9990 chunk 185 optimal weight: 9.9990 chunk 92 optimal weight: 6.9990 overall best weight: 3.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.071026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.057667 restraints weight = 104511.349| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 3.44 r_work: 0.2799 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.2844 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= 0.238 Angle : 0.533 12.677 23312 Z= 0.282 Chirality : 0.037 0.173 2672 Planarity : 0.004 0.041 2824 Dihedral : 17.567 172.844 3026 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.85 % Allowed : 13.89 % 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: 2.28 (0.20), residues: 1952 helix: 1.99 (0.15), residues: 1200 sheet: -0.39 (0.35), residues: 264 loop : 1.70 (0.33), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 121 HIS 0.002 0.000 HIS B 177 PHE 0.006 0.001 PHE B 297 TYR 0.009 0.001 TYR A 206 ARG 0.007 0.000 ARG E 311 *********************** 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 131 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 1.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 ASP cc_start: 0.9092 (t0) cc_final: 0.8683 (t70) REVERT: B 305 ASP cc_start: 0.9104 (t0) cc_final: 0.8721 (t0) REVERT: C 305 ASP cc_start: 0.9128 (t0) cc_final: 0.8709 (t0) REVERT: D 122 MET cc_start: 0.9238 (ttt) cc_final: 0.8977 (ttt) REVERT: D 311 ARG cc_start: 0.7457 (mtm110) cc_final: 0.7217 (mtm110) REVERT: E 181 GLU cc_start: 0.6707 (tp30) cc_final: 0.6450 (tp30) REVERT: E 200 MET cc_start: 0.9081 (ttm) cc_final: 0.8712 (mtp) REVERT: E 305 ASP cc_start: 0.9162 (t0) cc_final: 0.8714 (t0) REVERT: F 200 MET cc_start: 0.9176 (tpp) cc_final: 0.8472 (ttt) REVERT: F 259 GLN cc_start: 0.9501 (mt0) cc_final: 0.9269 (mp10) REVERT: F 305 ASP cc_start: 0.9089 (t0) cc_final: 0.8706 (t0) REVERT: G 86 MET cc_start: 0.9321 (mmm) cc_final: 0.9029 (mmm) REVERT: G 122 MET cc_start: 0.9322 (ttt) cc_final: 0.9085 (ttp) REVERT: G 259 GLN cc_start: 0.9475 (mt0) cc_final: 0.9269 (mp10) REVERT: H 167 GLN cc_start: 0.8600 (mm-40) cc_final: 0.8113 (mm-40) outliers start: 14 outliers final: 9 residues processed: 126 average time/residue: 0.2547 time to fit residues: 51.8513 Evaluate side-chains 123 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 1.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain H residue 259 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 121 optimal weight: 10.0000 chunk 109 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 168 optimal weight: 20.0000 chunk 23 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 189 optimal weight: 8.9990 chunk 16 optimal weight: 9.9990 chunk 85 optimal weight: 5.9990 chunk 179 optimal weight: 0.8980 overall best weight: 2.9786 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.070969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.057692 restraints weight = 103852.254| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 3.44 r_work: 0.2798 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17070 Z= 0.218 Angle : 0.529 12.807 23312 Z= 0.280 Chirality : 0.037 0.186 2672 Planarity : 0.004 0.045 2824 Dihedral : 17.568 172.307 3026 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.03 % Allowed : 14.37 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.36 (0.20), residues: 1952 helix: 2.05 (0.15), residues: 1200 sheet: -0.33 (0.35), residues: 264 loop : 1.75 (0.34), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 121 HIS 0.002 0.000 HIS B 177 PHE 0.006 0.001 PHE F 218 TYR 0.009 0.001 TYR A 206 ARG 0.005 0.000 ARG E 311 *********************** 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 133 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 1.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 ASP cc_start: 0.9095 (t0) cc_final: 0.8688 (t70) REVERT: B 200 MET cc_start: 0.9146 (mtm) cc_final: 0.8846 (mtp) REVERT: B 305 ASP cc_start: 0.9102 (t0) cc_final: 0.8710 (t0) REVERT: C 305 ASP cc_start: 0.9130 (t0) cc_final: 0.8699 (t0) REVERT: D 122 MET cc_start: 0.9178 (ttt) cc_final: 0.8931 (ttt) REVERT: E 184 GLU cc_start: 0.7197 (tt0) cc_final: 0.6818 (mm-30) REVERT: E 200 MET cc_start: 0.9104 (ttm) cc_final: 0.8774 (mtp) REVERT: E 305 ASP cc_start: 0.9164 (t0) cc_final: 0.8763 (t0) REVERT: F 92 THR cc_start: 0.9612 (OUTLIER) cc_final: 0.9404 (p) REVERT: F 305 ASP cc_start: 0.9100 (t0) cc_final: 0.8719 (t0) REVERT: G 86 MET cc_start: 0.9329 (mmm) cc_final: 0.8892 (mmm) REVERT: G 122 MET cc_start: 0.9294 (ttt) cc_final: 0.9082 (ttp) REVERT: G 259 GLN cc_start: 0.9470 (mt0) cc_final: 0.9257 (mp10) REVERT: H 167 GLN cc_start: 0.8596 (mm-40) cc_final: 0.8093 (mm-40) outliers start: 17 outliers final: 12 residues processed: 126 average time/residue: 0.2357 time to fit residues: 48.4286 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 : 1.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain D residue 259 GLN Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain E residue 259 GLN Chi-restraints excluded: chain E residue 306 ILE Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 145 MET 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: 10.0000 chunk 9 optimal weight: 0.9990 chunk 178 optimal weight: 10.0000 chunk 138 optimal weight: 6.9990 chunk 102 optimal weight: 7.9990 chunk 159 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 1 optimal weight: 20.0000 chunk 188 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 167 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 = 0.3777 r_free = 0.3777 target = 0.069704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.056610 restraints weight = 104750.010| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 3.46 r_work: 0.2765 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.3050 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= 0.283 Angle : 0.560 11.947 23312 Z= 0.295 Chirality : 0.038 0.185 2672 Planarity : 0.004 0.045 2824 Dihedral : 17.594 171.743 3026 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.97 % Allowed : 15.10 % Favored : 83.94 % 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: 2.34 (0.20), residues: 1952 helix: 2.11 (0.15), residues: 1192 sheet: -0.54 (0.34), residues: 280 loop : 1.74 (0.34), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 121 HIS 0.002 0.000 HIS B 177 PHE 0.013 0.001 PHE D 297 TYR 0.010 0.001 TYR A 206 ARG 0.004 0.000 ARG E 311 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 1.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 ASP cc_start: 0.9124 (t0) cc_final: 0.8719 (t70) REVERT: B 200 MET cc_start: 0.9159 (mtm) cc_final: 0.8874 (mtp) REVERT: B 305 ASP cc_start: 0.9101 (t0) cc_final: 0.8705 (t0) REVERT: C 305 ASP cc_start: 0.9156 (t0) cc_final: 0.8731 (t0) REVERT: D 122 MET cc_start: 0.9209 (ttt) cc_final: 0.8973 (ttt) REVERT: E 184 GLU cc_start: 0.7230 (tt0) cc_final: 0.6827 (mm-30) REVERT: E 200 MET cc_start: 0.9151 (ttm) cc_final: 0.8839 (mtp) REVERT: E 305 ASP cc_start: 0.9172 (t0) cc_final: 0.8764 (t0) REVERT: F 92 THR cc_start: 0.9619 (OUTLIER) cc_final: 0.9411 (p) REVERT: F 305 ASP cc_start: 0.9111 (t0) cc_final: 0.8726 (t0) REVERT: G 86 MET cc_start: 0.9353 (mmm) cc_final: 0.8866 (mtm) REVERT: G 259 GLN cc_start: 0.9443 (mt0) cc_final: 0.9226 (mp10) REVERT: H 167 GLN cc_start: 0.8625 (mm-40) cc_final: 0.8122 (mm-40) REVERT: H 305 ASP cc_start: 0.9152 (t70) cc_final: 0.8807 (t0) outliers start: 16 outliers final: 10 residues processed: 121 average time/residue: 0.2456 time to fit residues: 49.1823 Evaluate side-chains 120 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 1.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain C 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 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: 0.9990 chunk 11 optimal weight: 2.9990 chunk 184 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 158 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 170 optimal weight: 0.5980 chunk 135 optimal weight: 5.9990 chunk 156 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.054232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.041051 restraints weight = 81069.506| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 3.64 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17070 Z= 0.193 Angle : 0.554 12.514 23312 Z= 0.296 Chirality : 0.037 0.175 2672 Planarity : 0.004 0.041 2824 Dihedral : 17.587 172.293 3026 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.72 % Allowed : 15.64 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.40 (0.20), residues: 1952 helix: 2.07 (0.15), residues: 1192 sheet: -0.28 (0.35), residues: 264 loop : 1.79 (0.33), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 121 HIS 0.001 0.000 HIS H 282 PHE 0.006 0.001 PHE F 218 TYR 0.008 0.001 TYR A 206 ARG 0.004 0.000 ARG C 268 *********************** 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 127 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 2.052 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: 0.9085 (t0) cc_final: 0.8672 (t70) REVERT: B 200 MET cc_start: 0.8597 (mtm) cc_final: 0.8278 (mtp) REVERT: B 305 ASP cc_start: 0.9069 (t0) cc_final: 0.8670 (t0) REVERT: C 305 ASP cc_start: 0.9104 (t0) cc_final: 0.8659 (t0) REVERT: E 305 ASP cc_start: 0.9087 (t0) cc_final: 0.8666 (t0) REVERT: F 122 MET cc_start: 0.8960 (ttt) cc_final: 0.8733 (ttp) REVERT: F 200 MET cc_start: 0.8859 (tpp) cc_final: 0.8130 (mtp) REVERT: F 305 ASP cc_start: 0.9076 (t0) cc_final: 0.8679 (t0) REVERT: G 86 MET cc_start: 0.9222 (mmm) cc_final: 0.8651 (mtm) REVERT: G 259 GLN cc_start: 0.9414 (mt0) cc_final: 0.9199 (mp10) REVERT: H 305 ASP cc_start: 0.9137 (t70) cc_final: 0.8803 (t0) outliers start: 12 outliers final: 9 residues processed: 122 average time/residue: 0.2745 time to fit residues: 54.0838 Evaluate side-chains 118 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 109 time to evaluate : 1.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain E residue 306 ILE 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: 0.6980 chunk 76 optimal weight: 4.9990 chunk 67 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 149 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 16 optimal weight: 10.0000 chunk 12 optimal weight: 0.0870 chunk 147 optimal weight: 1.9990 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.054487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.041519 restraints weight = 81010.578| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 3.57 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.3234 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= 0.167 Angle : 0.556 11.573 23312 Z= 0.298 Chirality : 0.037 0.195 2672 Planarity : 0.004 0.051 2824 Dihedral : 17.527 172.147 3026 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.79 % Allowed : 15.82 % Favored : 83.39 % 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: 2.35 (0.20), residues: 1952 helix: 2.04 (0.15), residues: 1192 sheet: -0.08 (0.36), residues: 240 loop : 1.52 (0.32), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 121 HIS 0.002 0.000 HIS A 203 PHE 0.018 0.001 PHE D 297 TYR 0.006 0.001 TYR A 206 ARG 0.003 0.000 ARG E 311 ********************** 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 139 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 1.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 ASP cc_start: 0.9052 (t0) cc_final: 0.8616 (t70) REVERT: B 200 MET cc_start: 0.8476 (mtm) cc_final: 0.8187 (mtp) REVERT: B 305 ASP cc_start: 0.9058 (t0) cc_final: 0.8664 (t0) REVERT: C 222 PHE cc_start: 0.9051 (t80) cc_final: 0.8849 (t80) REVERT: C 305 ASP cc_start: 0.9084 (t0) cc_final: 0.8630 (t0) REVERT: E 305 ASP cc_start: 0.9054 (t0) cc_final: 0.8621 (t0) REVERT: F 122 MET cc_start: 0.8852 (ttt) cc_final: 0.8648 (ttp) REVERT: F 305 ASP cc_start: 0.9062 (t0) cc_final: 0.8649 (t0) REVERT: G 86 MET cc_start: 0.9185 (mmm) cc_final: 0.8723 (mmm) REVERT: G 92 THR cc_start: 0.9589 (OUTLIER) cc_final: 0.9374 (p) REVERT: G 259 GLN cc_start: 0.9429 (mt0) cc_final: 0.9211 (mp10) REVERT: H 92 THR cc_start: 0.9593 (OUTLIER) cc_final: 0.9325 (t) REVERT: H 305 ASP cc_start: 0.9146 (t70) cc_final: 0.8819 (t0) outliers start: 13 outliers final: 7 residues processed: 133 average time/residue: 0.2505 time to fit residues: 55.1950 Evaluate side-chains 126 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 2.086 ------------------------------------------------------------------------------- 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 306 ILE Chi-restraints excluded: chain F residue 259 GLN Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain H residue 259 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 92 optimal weight: 0.5980 chunk 8 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 167 optimal weight: 7.9990 chunk 86 optimal weight: 7.9990 chunk 129 optimal weight: 4.9990 chunk 181 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 167 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 = 0.3459 r_free = 0.3459 target = 0.054428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.041427 restraints weight = 80477.767| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 3.56 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.203 17070 Z= 0.263 Angle : 0.768 59.186 23312 Z= 0.438 Chirality : 0.038 0.404 2672 Planarity : 0.004 0.044 2824 Dihedral : 17.527 172.144 3026 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.60 % Allowed : 16.30 % Favored : 83.09 % 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: 2.34 (0.20), residues: 1952 helix: 2.02 (0.15), residues: 1192 sheet: -0.07 (0.36), residues: 240 loop : 1.50 (0.32), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 121 HIS 0.002 0.000 HIS A 203 PHE 0.013 0.001 PHE D 297 TYR 0.008 0.001 TYR G 206 ARG 0.004 0.000 ARG B 311 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5806.63 seconds wall clock time: 105 minutes 51.64 seconds (6351.64 seconds total)