Starting phenix.real_space_refine on Sun Aug 24 03:10:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8frz_29411/08_2025/8frz_29411.cif Found real_map, /net/cci-nas-00/data/ceres_data/8frz_29411/08_2025/8frz_29411.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8frz_29411/08_2025/8frz_29411.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8frz_29411/08_2025/8frz_29411.map" model { file = "/net/cci-nas-00/data/ceres_data/8frz_29411/08_2025/8frz_29411.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8frz_29411/08_2025/8frz_29411.cif" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 4 Type Number sf(0) Gaussians S 45 5.16 5 C 10855 2.51 5 N 2675 2.21 5 O 2905 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16480 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3241 Classifications: {'peptide': 391} Link IDs: {'PTRANS': 20, 'TRANS': 370} Chain breaks: 1 Chain: "A" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {'NAG': 3, 'SRO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Restraints were copied for chains: B, C, D, E Time building chain proxies: 3.19, per 1000 atoms: 0.19 Number of scatterers: 16480 At special positions: 0 Unit cell: (95.7, 95.7, 176, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 45 16.00 O 2905 8.00 N 2675 7.00 C 10855 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 149 " distance=2.03 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 149 " distance=2.03 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 Links applied NAG-ASN " NAG A 502 " - " ASN A 82 " " NAG A 503 " - " ASN A 148 " " NAG A 504 " - " ASN A 164 " " NAG B 502 " - " ASN B 82 " " NAG B 503 " - " ASN B 148 " " NAG B 504 " - " ASN B 164 " " NAG C 502 " - " ASN C 82 " " NAG C 503 " - " ASN C 148 " " NAG C 504 " - " ASN C 164 " " NAG D 502 " - " ASN D 82 " " NAG D 503 " - " ASN D 148 " " NAG D 504 " - " ASN D 164 " " NAG E 502 " - " ASN E 82 " " NAG E 503 " - " ASN E 148 " " NAG E 504 " - " ASN E 164 " Time building additional restraints: 1.38 Conformation dependent library (CDL) restraints added in 746.9 milliseconds Enol-peptide restraints added in 1.2 microseconds 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3800 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 10 sheets defined 45.8% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 12 through 21 removed outlier: 3.749A pdb=" N SER A 16 " --> pdb=" O LEU A 12 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N HIS A 18 " --> pdb=" O ARG A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 81 removed outlier: 4.095A pdb=" N ASP A 81 " --> pdb=" O GLU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 93 removed outlier: 3.786A pdb=" N ILE A 93 " --> pdb=" O THR A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 176 Processing helix chain 'A' and resid 220 through 243 Proline residue: A 230 - end of helix removed outlier: 4.003A pdb=" N CYS A 243 " --> pdb=" O ILE A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 269 removed outlier: 4.109A pdb=" N SER A 253 " --> pdb=" O GLY A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 308 removed outlier: 3.902A pdb=" N VAL A 285 " --> pdb=" O PRO A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 325 removed outlier: 3.577A pdb=" N LEU A 321 " --> pdb=" O VAL A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 331 removed outlier: 3.792A pdb=" N TRP A 331 " --> pdb=" O ARG A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 461 removed outlier: 3.510A pdb=" N LEU A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 21 removed outlier: 3.749A pdb=" N SER B 16 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N HIS B 18 " --> pdb=" O ARG B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 81 removed outlier: 4.096A pdb=" N ASP B 81 " --> pdb=" O GLU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 93 removed outlier: 3.787A pdb=" N ILE B 93 " --> pdb=" O THR B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 176 Processing helix chain 'B' and resid 220 through 243 Proline residue: B 230 - end of helix removed outlier: 4.002A pdb=" N CYS B 243 " --> pdb=" O ILE B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 269 removed outlier: 4.108A pdb=" N SER B 253 " --> pdb=" O GLY B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 308 removed outlier: 3.902A pdb=" N VAL B 285 " --> pdb=" O PRO B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 325 removed outlier: 3.578A pdb=" N LEU B 321 " --> pdb=" O VAL B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 331 removed outlier: 3.792A pdb=" N TRP B 331 " --> pdb=" O ARG B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 461 removed outlier: 3.510A pdb=" N LEU B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 21 removed outlier: 3.748A pdb=" N SER C 16 " --> pdb=" O LEU C 12 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N HIS C 18 " --> pdb=" O ARG C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 81 removed outlier: 4.095A pdb=" N ASP C 81 " --> pdb=" O GLU C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 93 removed outlier: 3.787A pdb=" N ILE C 93 " --> pdb=" O THR C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 176 Processing helix chain 'C' and resid 220 through 243 Proline residue: C 230 - end of helix removed outlier: 4.003A pdb=" N CYS C 243 " --> pdb=" O ILE C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 269 removed outlier: 4.109A pdb=" N SER C 253 " --> pdb=" O GLY C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 308 removed outlier: 3.903A pdb=" N VAL C 285 " --> pdb=" O PRO C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 325 removed outlier: 3.577A pdb=" N LEU C 321 " --> pdb=" O VAL C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 331 removed outlier: 3.791A pdb=" N TRP C 331 " --> pdb=" O ARG C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 461 removed outlier: 3.510A pdb=" N LEU C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 21 removed outlier: 3.749A pdb=" N SER D 16 " --> pdb=" O LEU D 12 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N HIS D 18 " --> pdb=" O ARG D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 81 removed outlier: 4.096A pdb=" N ASP D 81 " --> pdb=" O GLU D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 93 removed outlier: 3.787A pdb=" N ILE D 93 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 176 Processing helix chain 'D' and resid 220 through 243 Proline residue: D 230 - end of helix removed outlier: 4.003A pdb=" N CYS D 243 " --> pdb=" O ILE D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 269 removed outlier: 4.108A pdb=" N SER D 253 " --> pdb=" O GLY D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 308 removed outlier: 3.902A pdb=" N VAL D 285 " --> pdb=" O PRO D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 325 removed outlier: 3.578A pdb=" N LEU D 321 " --> pdb=" O VAL D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 331 removed outlier: 3.792A pdb=" N TRP D 331 " --> pdb=" O ARG D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 461 removed outlier: 3.510A pdb=" N LEU D 403 " --> pdb=" O VAL D 399 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 21 removed outlier: 3.749A pdb=" N SER E 16 " --> pdb=" O LEU E 12 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N HIS E 18 " --> pdb=" O ARG E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 81 removed outlier: 4.095A pdb=" N ASP E 81 " --> pdb=" O GLU E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 93 removed outlier: 3.786A pdb=" N ILE E 93 " --> pdb=" O THR E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 176 Processing helix chain 'E' and resid 220 through 243 Proline residue: E 230 - end of helix removed outlier: 4.004A pdb=" N CYS E 243 " --> pdb=" O ILE E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 269 removed outlier: 4.109A pdb=" N SER E 253 " --> pdb=" O GLY E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 308 removed outlier: 3.902A pdb=" N VAL E 285 " --> pdb=" O PRO E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 325 removed outlier: 3.578A pdb=" N LEU E 321 " --> pdb=" O VAL E 317 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 331 removed outlier: 3.791A pdb=" N TRP E 331 " --> pdb=" O ARG E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 461 removed outlier: 3.510A pdb=" N LEU E 403 " --> pdb=" O VAL E 399 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 88 removed outlier: 3.623A pdb=" N TYR A 116 " --> pdb=" O GLN A 124 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLU A 122 " --> pdb=" O HIS A 118 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N GLY A 121 " --> pdb=" O ASP A 70 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ASN A 50 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N TYR A 61 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N ILE A 48 " --> pdb=" O TYR A 61 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N TRP A 63 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N TYR A 46 " --> pdb=" O TRP A 63 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N ARG A 65 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ILE A 44 " --> pdb=" O ARG A 65 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N TYR A 67 " --> pdb=" O ASP A 42 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N ASP A 42 " --> pdb=" O TYR A 67 " (cutoff:3.500A) removed outlier: 8.759A pdb=" N THR A 69 " --> pdb=" O SER A 40 " (cutoff:3.500A) removed outlier: 9.570A pdb=" N SER A 40 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 9.794A pdb=" N GLU A 71 " --> pdb=" O THR A 38 " (cutoff:3.500A) removed outlier: 12.683A pdb=" N THR A 38 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 100 removed outlier: 4.249A pdb=" N SER A 155 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ALA A 208 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N TYR A 207 " --> pdb=" O GLU A 198 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLU A 198 " --> pdb=" O TYR A 207 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLU A 209 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N PHE A 196 " --> pdb=" O GLU A 209 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LYS A 211 " --> pdb=" O PRO A 194 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N TYR A 213 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N VAL A 192 " --> pdb=" O TYR A 213 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE A 215 " --> pdb=" O LEU A 190 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 85 through 88 removed outlier: 3.624A pdb=" N TYR B 116 " --> pdb=" O GLN B 124 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLU B 122 " --> pdb=" O HIS B 118 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N GLY B 121 " --> pdb=" O ASP B 70 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ASN B 50 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N TYR B 61 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ILE B 48 " --> pdb=" O TYR B 61 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N TRP B 63 " --> pdb=" O TYR B 46 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N TYR B 46 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N ARG B 65 " --> pdb=" O ILE B 44 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ILE B 44 " --> pdb=" O ARG B 65 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N TYR B 67 " --> pdb=" O ASP B 42 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N ASP B 42 " --> pdb=" O TYR B 67 " (cutoff:3.500A) removed outlier: 8.759A pdb=" N THR B 69 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 9.570A pdb=" N SER B 40 " --> pdb=" O THR B 69 " (cutoff:3.500A) removed outlier: 9.794A pdb=" N GLU B 71 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 12.683A pdb=" N THR B 38 " --> pdb=" O GLU B 71 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 98 through 100 removed outlier: 4.249A pdb=" N SER B 155 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ALA B 208 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N TYR B 207 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLU B 198 " --> pdb=" O TYR B 207 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N GLU B 209 " --> pdb=" O PHE B 196 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N PHE B 196 " --> pdb=" O GLU B 209 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LYS B 211 " --> pdb=" O PRO B 194 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N TYR B 213 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N VAL B 192 " --> pdb=" O TYR B 213 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE B 215 " --> pdb=" O LEU B 190 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 85 through 88 removed outlier: 3.622A pdb=" N TYR C 116 " --> pdb=" O GLN C 124 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLU C 122 " --> pdb=" O HIS C 118 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N GLY C 121 " --> pdb=" O ASP C 70 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ASN C 50 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N TYR C 61 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N ILE C 48 " --> pdb=" O TYR C 61 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N TRP C 63 " --> pdb=" O TYR C 46 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N TYR C 46 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N ARG C 65 " --> pdb=" O ILE C 44 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ILE C 44 " --> pdb=" O ARG C 65 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N TYR C 67 " --> pdb=" O ASP C 42 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N ASP C 42 " --> pdb=" O TYR C 67 " (cutoff:3.500A) removed outlier: 8.759A pdb=" N THR C 69 " --> pdb=" O SER C 40 " (cutoff:3.500A) removed outlier: 9.571A pdb=" N SER C 40 " --> pdb=" O THR C 69 " (cutoff:3.500A) removed outlier: 9.794A pdb=" N GLU C 71 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 12.683A pdb=" N THR C 38 " --> pdb=" O GLU C 71 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 98 through 100 removed outlier: 4.249A pdb=" N SER C 155 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ALA C 208 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N TYR C 207 " --> pdb=" O GLU C 198 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLU C 198 " --> pdb=" O TYR C 207 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N GLU C 209 " --> pdb=" O PHE C 196 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N PHE C 196 " --> pdb=" O GLU C 209 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LYS C 211 " --> pdb=" O PRO C 194 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N TYR C 213 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N VAL C 192 " --> pdb=" O TYR C 213 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE C 215 " --> pdb=" O LEU C 190 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 85 through 88 removed outlier: 3.623A pdb=" N TYR D 116 " --> pdb=" O GLN D 124 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLU D 122 " --> pdb=" O HIS D 118 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N GLY D 121 " --> pdb=" O ASP D 70 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ASN D 50 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N TYR D 61 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ILE D 48 " --> pdb=" O TYR D 61 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N TRP D 63 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N TYR D 46 " --> pdb=" O TRP D 63 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ARG D 65 " --> pdb=" O ILE D 44 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ILE D 44 " --> pdb=" O ARG D 65 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N TYR D 67 " --> pdb=" O ASP D 42 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N ASP D 42 " --> pdb=" O TYR D 67 " (cutoff:3.500A) removed outlier: 8.759A pdb=" N THR D 69 " --> pdb=" O SER D 40 " (cutoff:3.500A) removed outlier: 9.570A pdb=" N SER D 40 " --> pdb=" O THR D 69 " (cutoff:3.500A) removed outlier: 9.794A pdb=" N GLU D 71 " --> pdb=" O THR D 38 " (cutoff:3.500A) removed outlier: 12.684A pdb=" N THR D 38 " --> pdb=" O GLU D 71 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 98 through 100 removed outlier: 4.249A pdb=" N SER D 155 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ALA D 208 " --> pdb=" O SER D 155 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N TYR D 207 " --> pdb=" O GLU D 198 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLU D 198 " --> pdb=" O TYR D 207 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLU D 209 " --> pdb=" O PHE D 196 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N PHE D 196 " --> pdb=" O GLU D 209 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LYS D 211 " --> pdb=" O PRO D 194 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N TYR D 213 " --> pdb=" O VAL D 192 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N VAL D 192 " --> pdb=" O TYR D 213 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE D 215 " --> pdb=" O LEU D 190 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 85 through 88 removed outlier: 3.623A pdb=" N TYR E 116 " --> pdb=" O GLN E 124 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLU E 122 " --> pdb=" O HIS E 118 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N GLY E 121 " --> pdb=" O ASP E 70 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ASN E 50 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N TYR E 61 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N ILE E 48 " --> pdb=" O TYR E 61 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N TRP E 63 " --> pdb=" O TYR E 46 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N TYR E 46 " --> pdb=" O TRP E 63 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N ARG E 65 " --> pdb=" O ILE E 44 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ILE E 44 " --> pdb=" O ARG E 65 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N TYR E 67 " --> pdb=" O ASP E 42 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N ASP E 42 " --> pdb=" O TYR E 67 " (cutoff:3.500A) removed outlier: 8.759A pdb=" N THR E 69 " --> pdb=" O SER E 40 " (cutoff:3.500A) removed outlier: 9.570A pdb=" N SER E 40 " --> pdb=" O THR E 69 " (cutoff:3.500A) removed outlier: 9.794A pdb=" N GLU E 71 " --> pdb=" O THR E 38 " (cutoff:3.500A) removed outlier: 12.683A pdb=" N THR E 38 " --> pdb=" O GLU E 71 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 98 through 100 removed outlier: 4.249A pdb=" N SER E 155 " --> pdb=" O ALA E 208 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ALA E 208 " --> pdb=" O SER E 155 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N TYR E 207 " --> pdb=" O GLU E 198 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLU E 198 " --> pdb=" O TYR E 207 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N GLU E 209 " --> pdb=" O PHE E 196 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N PHE E 196 " --> pdb=" O GLU E 209 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LYS E 211 " --> pdb=" O PRO E 194 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N TYR E 213 " --> pdb=" O VAL E 192 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N VAL E 192 " --> pdb=" O TYR E 213 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE E 215 " --> pdb=" O LEU E 190 " (cutoff:3.500A) 840 hydrogen bonds defined for protein. 2415 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.63 Time building geometry restraints manager: 1.83 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: 5015 1.34 - 1.46: 3938 1.46 - 1.58: 7912 1.58 - 1.70: 0 1.70 - 1.82: 70 Bond restraints: 16935 Sorted by residual: bond pdb=" C ARG D 315 " pdb=" N PRO D 316 " ideal model delta sigma weight residual 1.332 1.365 -0.033 1.32e-02 5.74e+03 6.36e+00 bond pdb=" C ARG E 315 " pdb=" N PRO E 316 " ideal model delta sigma weight residual 1.332 1.365 -0.033 1.32e-02 5.74e+03 6.28e+00 bond pdb=" C ARG C 315 " pdb=" N PRO C 316 " ideal model delta sigma weight residual 1.332 1.365 -0.033 1.32e-02 5.74e+03 6.26e+00 bond pdb=" C ARG A 315 " pdb=" N PRO A 316 " ideal model delta sigma weight residual 1.332 1.364 -0.033 1.32e-02 5.74e+03 6.15e+00 bond pdb=" C ARG B 315 " pdb=" N PRO B 316 " ideal model delta sigma weight residual 1.332 1.364 -0.033 1.32e-02 5.74e+03 6.13e+00 ... (remaining 16930 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 22476 1.98 - 3.95: 534 3.95 - 5.93: 85 5.93 - 7.91: 25 7.91 - 9.89: 15 Bond angle restraints: 23135 Sorted by residual: angle pdb=" C ARG C 315 " pdb=" N PRO C 316 " pdb=" CA PRO C 316 " ideal model delta sigma weight residual 119.76 114.60 5.16 1.00e+00 1.00e+00 2.66e+01 angle pdb=" C ARG E 315 " pdb=" N PRO E 316 " pdb=" CA PRO E 316 " ideal model delta sigma weight residual 119.76 114.62 5.14 1.00e+00 1.00e+00 2.64e+01 angle pdb=" C ARG D 315 " pdb=" N PRO D 316 " pdb=" CA PRO D 316 " ideal model delta sigma weight residual 119.76 114.62 5.14 1.00e+00 1.00e+00 2.64e+01 angle pdb=" C ARG A 315 " pdb=" N PRO A 316 " pdb=" CA PRO A 316 " ideal model delta sigma weight residual 119.76 114.66 5.10 1.00e+00 1.00e+00 2.60e+01 angle pdb=" C ARG B 315 " pdb=" N PRO B 316 " pdb=" CA PRO B 316 " ideal model delta sigma weight residual 119.76 114.68 5.08 1.00e+00 1.00e+00 2.58e+01 ... (remaining 23130 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.96: 9090 16.96 - 33.93: 848 33.93 - 50.89: 166 50.89 - 67.86: 26 67.86 - 84.82: 20 Dihedral angle restraints: 10150 sinusoidal: 4315 harmonic: 5835 Sorted by residual: dihedral pdb=" CB CYS B 135 " pdb=" SG CYS B 135 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 61.64 31.36 1 1.00e+01 1.00e-02 1.40e+01 dihedral pdb=" CB CYS E 135 " pdb=" SG CYS E 135 " pdb=" SG CYS E 149 " pdb=" CB CYS E 149 " ideal model delta sinusoidal sigma weight residual 93.00 61.64 31.36 1 1.00e+01 1.00e-02 1.40e+01 dihedral pdb=" CB CYS D 135 " pdb=" SG CYS D 135 " pdb=" SG CYS D 149 " pdb=" CB CYS D 149 " ideal model delta sinusoidal sigma weight residual 93.00 61.65 31.35 1 1.00e+01 1.00e-02 1.40e+01 ... (remaining 10147 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2091 0.052 - 0.105: 518 0.105 - 0.157: 96 0.157 - 0.210: 0 0.210 - 0.262: 5 Chirality restraints: 2710 Sorted by residual: chirality pdb=" C1 NAG D 502 " pdb=" ND2 ASN D 82 " pdb=" C2 NAG D 502 " pdb=" O5 NAG D 502 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" C1 NAG B 502 " pdb=" ND2 ASN B 82 " pdb=" C2 NAG B 502 " pdb=" O5 NAG B 502 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" C1 NAG E 502 " pdb=" ND2 ASN E 82 " pdb=" C2 NAG E 502 " pdb=" O5 NAG E 502 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 2707 not shown) Planarity restraints: 2830 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 331 " -0.013 2.00e-02 2.50e+03 1.43e-02 5.11e+00 pdb=" CG TRP C 331 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP C 331 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP C 331 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 331 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 331 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 331 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 331 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 331 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 331 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 331 " -0.013 2.00e-02 2.50e+03 1.43e-02 5.09e+00 pdb=" CG TRP E 331 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP E 331 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP E 331 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 331 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP E 331 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 331 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 331 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 331 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP E 331 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 331 " -0.013 2.00e-02 2.50e+03 1.42e-02 5.07e+00 pdb=" CG TRP D 331 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP D 331 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP D 331 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 331 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP D 331 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 331 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 331 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 331 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 331 " -0.000 2.00e-02 2.50e+03 ... (remaining 2827 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 4169 2.81 - 3.33: 15631 3.33 - 3.86: 26911 3.86 - 4.38: 29229 4.38 - 4.90: 51659 Nonbonded interactions: 127599 Sorted by model distance: nonbonded pdb=" O GLY E 185 " pdb=" NH1 ARG E 219 " model vdw 2.290 3.120 nonbonded pdb=" O GLY B 185 " pdb=" NH1 ARG B 219 " model vdw 2.291 3.120 nonbonded pdb=" O GLY A 185 " pdb=" NH1 ARG A 219 " model vdw 2.291 3.120 nonbonded pdb=" O GLY D 185 " pdb=" NH1 ARG D 219 " model vdw 2.291 3.120 nonbonded pdb=" O GLY C 185 " pdb=" NH1 ARG C 219 " model vdw 2.291 3.120 ... (remaining 127594 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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=1.00 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: 0.010 Normalize map: mean=0, sd=1: 1.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.140 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 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:6.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16955 Z= 0.185 Angle : 0.788 11.473 23190 Z= 0.400 Chirality : 0.046 0.262 2710 Planarity : 0.004 0.031 2815 Dihedral : 13.710 84.820 6335 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.19), residues: 1935 helix: 2.23 (0.18), residues: 785 sheet: -0.21 (0.25), residues: 410 loop : -1.87 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 219 TYR 0.012 0.001 TYR E 64 PHE 0.006 0.001 PHE A 254 TRP 0.038 0.002 TRP C 331 HIS 0.017 0.002 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00340 (16935) covalent geometry : angle 0.75892 (23135) SS BOND : bond 0.00223 ( 5) SS BOND : angle 1.69742 ( 10) hydrogen bonds : bond 0.12522 ( 840) hydrogen bonds : angle 4.75545 ( 2415) link_NAG-ASN : bond 0.01458 ( 15) link_NAG-ASN : angle 4.85218 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.693 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.4518 time to fit residues: 68.9507 Evaluate side-chains 69 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.0870 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.0000 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.3966 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 323 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.096280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.065586 restraints weight = 33612.214| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.74 r_work: 0.2826 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 16955 Z= 0.170 Angle : 0.622 7.775 23190 Z= 0.309 Chirality : 0.044 0.232 2710 Planarity : 0.004 0.033 2815 Dihedral : 7.682 86.381 2485 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.03 % Allowed : 7.95 % Favored : 90.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.20), residues: 1935 helix: 2.73 (0.18), residues: 800 sheet: -0.58 (0.25), residues: 395 loop : -1.78 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 219 TYR 0.016 0.001 TYR A 67 PHE 0.012 0.001 PHE B 144 TRP 0.020 0.002 TRP C 331 HIS 0.004 0.001 HIS D 118 Details of bonding type rmsd covalent geometry : bond 0.00404 (16935) covalent geometry : angle 0.60534 (23135) SS BOND : bond 0.00430 ( 5) SS BOND : angle 1.60246 ( 10) hydrogen bonds : bond 0.05002 ( 840) hydrogen bonds : angle 4.00562 ( 2415) link_NAG-ASN : bond 0.01421 ( 15) link_NAG-ASN : angle 3.27085 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 90 time to evaluate : 0.656 Fit side-chains outliers start: 37 outliers final: 18 residues processed: 110 average time/residue: 0.4862 time to fit residues: 61.3665 Evaluate side-chains 91 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 323 HIS Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain E residue 323 HIS Chi-restraints excluded: chain E residue 458 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 142 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 56 optimal weight: 0.0670 chunk 187 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 189 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 overall best weight: 1.1320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 HIS B 309 HIS C 309 HIS D 309 HIS D 323 HIS E 323 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.095530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.064895 restraints weight = 34098.670| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 2.76 r_work: 0.2811 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16955 Z= 0.146 Angle : 0.577 6.522 23190 Z= 0.288 Chirality : 0.043 0.235 2710 Planarity : 0.003 0.029 2815 Dihedral : 6.040 65.753 2485 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.90 % Allowed : 10.19 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.20), residues: 1935 helix: 2.90 (0.18), residues: 795 sheet: -0.58 (0.25), residues: 395 loop : -1.91 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 315 TYR 0.013 0.001 TYR A 67 PHE 0.009 0.001 PHE E 144 TRP 0.015 0.001 TRP C 331 HIS 0.009 0.001 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00339 (16935) covalent geometry : angle 0.56469 (23135) SS BOND : bond 0.00437 ( 5) SS BOND : angle 1.48674 ( 10) hydrogen bonds : bond 0.05007 ( 840) hydrogen bonds : angle 3.85109 ( 2415) link_NAG-ASN : bond 0.01114 ( 15) link_NAG-ASN : angle 2.69377 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 84 time to evaluate : 0.688 Fit side-chains revert: symmetry clash REVERT: A 151 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8759 (pp) REVERT: B 15 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8111 (tp) REVERT: C 15 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8295 (tp) REVERT: C 151 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8860 (pp) REVERT: E 15 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8276 (tp) outliers start: 53 outliers final: 26 residues processed: 131 average time/residue: 0.3965 time to fit residues: 61.2645 Evaluate side-chains 104 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 73 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 309 HIS Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain E residue 450 ILE Chi-restraints excluded: chain E residue 458 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 25 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 71 optimal weight: 8.9990 chunk 152 optimal weight: 4.9990 chunk 171 optimal weight: 0.6980 chunk 8 optimal weight: 5.9990 chunk 186 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 HIS A 323 HIS C 111 ASN ** C 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 HIS D 309 HIS E 309 HIS E 323 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.094997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.064373 restraints weight = 33944.194| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 2.75 r_work: 0.2802 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16955 Z= 0.142 Angle : 0.572 7.438 23190 Z= 0.284 Chirality : 0.043 0.230 2710 Planarity : 0.003 0.028 2815 Dihedral : 5.512 51.817 2485 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.95 % Allowed : 11.56 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.20), residues: 1935 helix: 2.91 (0.18), residues: 800 sheet: -0.60 (0.24), residues: 395 loop : -1.89 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 219 TYR 0.014 0.001 TYR A 67 PHE 0.009 0.001 PHE E 144 TRP 0.016 0.001 TRP A 320 HIS 0.009 0.001 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00328 (16935) covalent geometry : angle 0.56213 (23135) SS BOND : bond 0.00436 ( 5) SS BOND : angle 1.40059 ( 10) hydrogen bonds : bond 0.05015 ( 840) hydrogen bonds : angle 3.80744 ( 2415) link_NAG-ASN : bond 0.00971 ( 15) link_NAG-ASN : angle 2.34721 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 79 time to evaluate : 0.705 Fit side-chains REVERT: A 15 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8290 (tp) REVERT: A 151 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8772 (pp) REVERT: B 15 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8127 (tp) REVERT: C 15 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8322 (tp) REVERT: C 151 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8863 (pp) REVERT: C 309 HIS cc_start: 0.7293 (OUTLIER) cc_final: 0.7064 (t70) REVERT: C 315 ARG cc_start: 0.6876 (tmt170) cc_final: 0.6669 (tpt170) REVERT: D 15 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8206 (tp) REVERT: E 15 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8292 (tp) outliers start: 72 outliers final: 37 residues processed: 143 average time/residue: 0.3877 time to fit residues: 65.8701 Evaluate side-chains 118 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 73 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 309 HIS Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 458 ILE Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 323 HIS Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 450 ILE Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain E residue 458 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 46 optimal weight: 1.9990 chunk 139 optimal weight: 0.0170 chunk 49 optimal weight: 0.0050 chunk 187 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 140 optimal weight: 1.9990 chunk 171 optimal weight: 0.5980 chunk 134 optimal weight: 2.9990 chunk 169 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 159 optimal weight: 1.9990 overall best weight: 0.4032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 HIS A 323 HIS B 309 HIS ** C 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 HIS E 309 HIS E 323 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.097663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.067296 restraints weight = 33967.938| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 2.76 r_work: 0.2868 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16955 Z= 0.107 Angle : 0.526 7.382 23190 Z= 0.259 Chirality : 0.042 0.225 2710 Planarity : 0.003 0.027 2815 Dihedral : 5.407 55.877 2485 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.29 % Allowed : 12.66 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.20), residues: 1935 helix: 2.97 (0.18), residues: 800 sheet: -0.55 (0.25), residues: 395 loop : -1.86 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 400 TYR 0.010 0.001 TYR D 64 PHE 0.010 0.001 PHE A 233 TRP 0.021 0.001 TRP D 320 HIS 0.009 0.001 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00222 (16935) covalent geometry : angle 0.51714 (23135) SS BOND : bond 0.00285 ( 5) SS BOND : angle 1.12958 ( 10) hydrogen bonds : bond 0.04391 ( 840) hydrogen bonds : angle 3.58711 ( 2415) link_NAG-ASN : bond 0.00803 ( 15) link_NAG-ASN : angle 2.18286 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 81 time to evaluate : 0.641 Fit side-chains REVERT: A 15 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8174 (tp) REVERT: C 15 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8252 (tp) REVERT: C 315 ARG cc_start: 0.6762 (tmt170) cc_final: 0.6554 (tpt170) REVERT: D 15 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8182 (tp) REVERT: D 151 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8711 (pp) outliers start: 60 outliers final: 26 residues processed: 136 average time/residue: 0.3806 time to fit residues: 61.1139 Evaluate side-chains 106 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 76 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 458 ILE Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 323 HIS Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 317 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 149 optimal weight: 9.9990 chunk 166 optimal weight: 0.9990 chunk 108 optimal weight: 0.0050 chunk 45 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 176 optimal weight: 3.9990 chunk 26 optimal weight: 0.4980 chunk 184 optimal weight: 2.9990 chunk 183 optimal weight: 0.8980 chunk 131 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN ** A 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 HIS E 309 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.096810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.066364 restraints weight = 33980.081| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 2.76 r_work: 0.2846 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16955 Z= 0.113 Angle : 0.534 8.260 23190 Z= 0.263 Chirality : 0.042 0.210 2710 Planarity : 0.003 0.026 2815 Dihedral : 5.206 51.995 2485 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.40 % Allowed : 12.99 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.20), residues: 1935 helix: 2.99 (0.18), residues: 800 sheet: -0.53 (0.25), residues: 395 loop : -1.85 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 315 TYR 0.010 0.001 TYR A 67 PHE 0.015 0.001 PHE A 233 TRP 0.021 0.001 TRP D 320 HIS 0.009 0.001 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00247 (16935) covalent geometry : angle 0.52800 (23135) SS BOND : bond 0.00330 ( 5) SS BOND : angle 1.24122 ( 10) hydrogen bonds : bond 0.04386 ( 840) hydrogen bonds : angle 3.57671 ( 2415) link_NAG-ASN : bond 0.00775 ( 15) link_NAG-ASN : angle 1.82891 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 79 time to evaluate : 0.672 Fit side-chains REVERT: A 15 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8240 (tp) REVERT: C 15 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8294 (tp) REVERT: D 15 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8106 (tp) REVERT: D 151 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8775 (pp) REVERT: D 315 ARG cc_start: 0.6658 (tpm170) cc_final: 0.6402 (tpm170) outliers start: 62 outliers final: 31 residues processed: 133 average time/residue: 0.4094 time to fit residues: 64.1541 Evaluate side-chains 109 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 74 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 323 HIS Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain E residue 323 HIS Chi-restraints excluded: chain E residue 458 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 185 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 48 optimal weight: 0.0670 chunk 71 optimal weight: 10.0000 chunk 61 optimal weight: 0.1980 chunk 20 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 94 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 overall best weight: 0.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN ** A 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 HIS E 309 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.096275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.065747 restraints weight = 33863.092| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.74 r_work: 0.2834 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16955 Z= 0.121 Angle : 0.551 7.955 23190 Z= 0.270 Chirality : 0.042 0.199 2710 Planarity : 0.003 0.029 2815 Dihedral : 5.163 49.709 2485 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.23 % Allowed : 13.53 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.20), residues: 1935 helix: 2.98 (0.18), residues: 800 sheet: -0.53 (0.24), residues: 395 loop : -1.90 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 400 TYR 0.011 0.001 TYR A 67 PHE 0.018 0.001 PHE A 233 TRP 0.023 0.001 TRP D 320 HIS 0.009 0.001 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00274 (16935) covalent geometry : angle 0.54658 (23135) SS BOND : bond 0.00344 ( 5) SS BOND : angle 1.22269 ( 10) hydrogen bonds : bond 0.04469 ( 840) hydrogen bonds : angle 3.60334 ( 2415) link_NAG-ASN : bond 0.00744 ( 15) link_NAG-ASN : angle 1.62109 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 77 time to evaluate : 0.573 Fit side-chains REVERT: A 15 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8225 (tp) REVERT: C 15 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8291 (tp) REVERT: D 15 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8157 (tp) REVERT: D 151 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8783 (pp) outliers start: 59 outliers final: 36 residues processed: 128 average time/residue: 0.4323 time to fit residues: 65.0942 Evaluate side-chains 115 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 75 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 323 HIS Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain E residue 323 HIS Chi-restraints excluded: chain E residue 458 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 59 optimal weight: 0.9990 chunk 100 optimal weight: 0.0770 chunk 2 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 139 optimal weight: 0.0000 chunk 32 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 160 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 overall best weight: 1.8148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN A 125 ASN ** A 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 HIS ** C 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN D 309 HIS E 309 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.092610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.061905 restraints weight = 34099.263| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 2.74 r_work: 0.2746 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 16955 Z= 0.200 Angle : 0.639 7.887 23190 Z= 0.319 Chirality : 0.044 0.171 2710 Planarity : 0.003 0.031 2815 Dihedral : 5.170 33.577 2485 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 3.73 % Allowed : 14.19 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.20), residues: 1935 helix: 2.88 (0.18), residues: 800 sheet: -0.66 (0.24), residues: 405 loop : -2.00 (0.21), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 315 TYR 0.018 0.001 TYR A 67 PHE 0.021 0.002 PHE A 233 TRP 0.024 0.002 TRP E 320 HIS 0.009 0.001 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00486 (16935) covalent geometry : angle 0.63571 (23135) SS BOND : bond 0.00520 ( 5) SS BOND : angle 1.48443 ( 10) hydrogen bonds : bond 0.05540 ( 840) hydrogen bonds : angle 3.94344 ( 2415) link_NAG-ASN : bond 0.00825 ( 15) link_NAG-ASN : angle 1.50418 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 78 time to evaluate : 0.807 Fit side-chains REVERT: A 15 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8456 (tp) REVERT: B 235 MET cc_start: 0.8832 (tpp) cc_final: 0.8630 (tpp) REVERT: C 456 TRP cc_start: 0.6649 (t60) cc_final: 0.6338 (t60) outliers start: 68 outliers final: 40 residues processed: 133 average time/residue: 0.3890 time to fit residues: 60.9125 Evaluate side-chains 116 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 75 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 323 HIS Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 268 ILE Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain E residue 458 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 79 optimal weight: 0.4980 chunk 148 optimal weight: 8.9990 chunk 48 optimal weight: 0.8980 chunk 157 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 76 optimal weight: 0.8980 chunk 178 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 127 optimal weight: 0.9980 chunk 97 optimal weight: 0.0570 chunk 31 optimal weight: 9.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN A 125 ASN ** A 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN D 309 HIS E 309 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.095470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.065155 restraints weight = 33994.106| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.75 r_work: 0.2822 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16955 Z= 0.117 Angle : 0.561 7.916 23190 Z= 0.277 Chirality : 0.042 0.179 2710 Planarity : 0.003 0.032 2815 Dihedral : 4.995 42.508 2485 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.68 % Allowed : 15.29 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.20), residues: 1935 helix: 3.02 (0.18), residues: 795 sheet: -0.61 (0.24), residues: 395 loop : -2.08 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 400 TYR 0.010 0.001 TYR C 64 PHE 0.019 0.001 PHE B 233 TRP 0.033 0.001 TRP E 320 HIS 0.009 0.001 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00252 (16935) covalent geometry : angle 0.55769 (23135) SS BOND : bond 0.00306 ( 5) SS BOND : angle 1.22073 ( 10) hydrogen bonds : bond 0.04734 ( 840) hydrogen bonds : angle 3.68577 ( 2415) link_NAG-ASN : bond 0.00655 ( 15) link_NAG-ASN : angle 1.49507 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 77 time to evaluate : 0.433 Fit side-chains REVERT: A 15 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8222 (tp) REVERT: C 15 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8303 (tp) REVERT: C 62 ILE cc_start: 0.9052 (OUTLIER) cc_final: 0.8676 (pt) REVERT: D 15 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8210 (tp) outliers start: 49 outliers final: 32 residues processed: 119 average time/residue: 0.3391 time to fit residues: 47.8245 Evaluate side-chains 110 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 74 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 323 HIS Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain E residue 323 HIS Chi-restraints excluded: chain E residue 458 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 154 optimal weight: 0.9980 chunk 109 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 19 optimal weight: 0.3980 chunk 170 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 22 optimal weight: 0.4980 chunk 40 optimal weight: 0.0270 chunk 97 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN ** A 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 HIS ** C 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 HIS E 309 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.096252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.066006 restraints weight = 33990.336| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.75 r_work: 0.2840 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16955 Z= 0.114 Angle : 0.560 9.229 23190 Z= 0.277 Chirality : 0.042 0.180 2710 Planarity : 0.003 0.033 2815 Dihedral : 5.119 48.084 2485 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.30 % Allowed : 15.78 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.20), residues: 1935 helix: 3.08 (0.18), residues: 795 sheet: -0.48 (0.24), residues: 390 loop : -2.06 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 219 TYR 0.010 0.001 TYR D 64 PHE 0.018 0.001 PHE C 233 TRP 0.041 0.002 TRP A 320 HIS 0.009 0.001 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00246 (16935) covalent geometry : angle 0.55708 (23135) SS BOND : bond 0.00284 ( 5) SS BOND : angle 1.20001 ( 10) hydrogen bonds : bond 0.04469 ( 840) hydrogen bonds : angle 3.61406 ( 2415) link_NAG-ASN : bond 0.00622 ( 15) link_NAG-ASN : angle 1.38291 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 80 time to evaluate : 0.704 Fit side-chains REVERT: A 15 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8234 (tp) REVERT: C 15 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8328 (tp) REVERT: D 15 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8227 (tp) REVERT: D 315 ARG cc_start: 0.6738 (tpm170) cc_final: 0.6500 (tpm170) outliers start: 42 outliers final: 31 residues processed: 114 average time/residue: 0.3866 time to fit residues: 51.3324 Evaluate side-chains 109 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 75 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 323 HIS Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain E residue 323 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 135 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 113 optimal weight: 6.9990 chunk 101 optimal weight: 0.0670 chunk 44 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 97 optimal weight: 0.8980 chunk 171 optimal weight: 0.8980 chunk 151 optimal weight: 3.9990 chunk 100 optimal weight: 0.5980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN ** A 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 HIS ** C 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.096266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.066004 restraints weight = 33990.486| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.74 r_work: 0.2839 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16955 Z= 0.115 Angle : 0.559 8.363 23190 Z= 0.276 Chirality : 0.042 0.172 2710 Planarity : 0.003 0.032 2815 Dihedral : 5.093 47.716 2485 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.25 % Allowed : 16.05 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.20), residues: 1935 helix: 3.08 (0.19), residues: 795 sheet: -0.45 (0.24), residues: 390 loop : -2.07 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 315 TYR 0.010 0.001 TYR D 64 PHE 0.018 0.001 PHE B 233 TRP 0.046 0.002 TRP A 320 HIS 0.009 0.001 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00253 (16935) covalent geometry : angle 0.55640 (23135) SS BOND : bond 0.00308 ( 5) SS BOND : angle 1.21952 ( 10) hydrogen bonds : bond 0.04402 ( 840) hydrogen bonds : angle 3.58762 ( 2415) link_NAG-ASN : bond 0.00617 ( 15) link_NAG-ASN : angle 1.29604 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3931.00 seconds wall clock time: 68 minutes 4.79 seconds (4084.79 seconds total)