Starting phenix.real_space_refine on Sat Jun 14 21:14:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8frz_29411/06_2025/8frz_29411.cif Found real_map, /net/cci-nas-00/data/ceres_data/8frz_29411/06_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_29411/06_2025/8frz_29411.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8frz_29411/06_2025/8frz_29411.map" model { file = "/net/cci-nas-00/data/ceres_data/8frz_29411/06_2025/8frz_29411.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8frz_29411/06_2025/8frz_29411.cif" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: C, B, E, D Time building chain proxies: 7.37, per 1000 atoms: 0.45 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 C 135 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 149 " distance=2.03 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 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: 4.05 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.66 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: 4.82 Time building geometry restraints manager: 4.60 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: 0.13 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } 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: 0.000 Normalize map: mean=0, sd=1: 1.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.610 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 34.800 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.840 ------------------------------------------------------------------------------- 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 : 3.53 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.038 0.002 TRP C 331 HIS 0.017 0.002 HIS B 323 PHE 0.006 0.001 PHE A 254 TYR 0.012 0.001 TYR E 64 ARG 0.002 0.000 ARG E 219 Details of bonding type rmsd link_NAG-ASN : bond 0.01458 ( 15) link_NAG-ASN : angle 4.85218 ( 45) hydrogen bonds : bond 0.12522 ( 840) hydrogen bonds : angle 4.75545 ( 2415) SS BOND : bond 0.00223 ( 5) SS BOND : angle 1.69742 ( 10) covalent geometry : bond 0.00340 (16935) covalent geometry : angle 0.75892 (23135) *********************** 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 : 2.175 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.8747 time to fit residues: 135.6478 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 : 2.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 0.9990 chunk 147 optimal weight: 8.9990 chunk 82 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 152 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 177 optimal weight: 7.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 323 HIS E 323 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.094637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.063781 restraints weight = 33814.602| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 2.75 r_work: 0.2786 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 16955 Z= 0.200 Angle : 0.658 7.733 23190 Z= 0.328 Chirality : 0.045 0.267 2710 Planarity : 0.004 0.035 2815 Dihedral : 7.412 78.883 2485 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.19 % Allowed : 8.60 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.20), residues: 1935 helix: 2.68 (0.18), residues: 800 sheet: -0.55 (0.25), residues: 395 loop : -1.80 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 331 HIS 0.005 0.001 HIS A 118 PHE 0.015 0.001 PHE E 144 TYR 0.018 0.002 TYR A 67 ARG 0.004 0.000 ARG A 219 Details of bonding type rmsd link_NAG-ASN : bond 0.01165 ( 15) link_NAG-ASN : angle 3.18243 ( 45) hydrogen bonds : bond 0.05444 ( 840) hydrogen bonds : angle 4.08290 ( 2415) SS BOND : bond 0.00456 ( 5) SS BOND : angle 1.68920 ( 10) covalent geometry : bond 0.00479 (16935) covalent geometry : angle 0.64302 (23135) *********************** 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 133 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 93 time to evaluate : 1.939 Fit side-chains REVERT: C 15 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8263 (tp) REVERT: C 456 TRP cc_start: 0.6795 (t60) cc_final: 0.6484 (t60) REVERT: E 15 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8178 (tp) outliers start: 40 outliers final: 15 residues processed: 120 average time/residue: 1.0229 time to fit residues: 143.1979 Evaluate side-chains 91 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 2.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain B residue 123 VAL 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 323 HIS Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 323 HIS Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 453 VAL 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 89 optimal weight: 0.6980 chunk 86 optimal weight: 0.8980 chunk 176 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 173 optimal weight: 0.9990 chunk 179 optimal weight: 0.4980 chunk 23 optimal weight: 0.0020 chunk 180 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 112 optimal weight: 0.7980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 HIS B 309 HIS C 111 ASN C 309 HIS C 323 HIS D 309 HIS D 323 HIS E 323 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.097088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.066660 restraints weight = 33658.785| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 2.73 r_work: 0.2852 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1724 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= 0.116 Angle : 0.554 7.458 23190 Z= 0.275 Chirality : 0.042 0.261 2710 Planarity : 0.003 0.028 2815 Dihedral : 5.945 65.877 2485 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.68 % Allowed : 10.30 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.20), residues: 1935 helix: 2.87 (0.19), residues: 800 sheet: -0.59 (0.25), residues: 395 loop : -1.83 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 320 HIS 0.009 0.001 HIS B 323 PHE 0.008 0.001 PHE B 254 TYR 0.010 0.001 TYR D 64 ARG 0.002 0.000 ARG C 400 Details of bonding type rmsd link_NAG-ASN : bond 0.01029 ( 15) link_NAG-ASN : angle 2.88805 ( 45) hydrogen bonds : bond 0.04699 ( 840) hydrogen bonds : angle 3.75102 ( 2415) SS BOND : bond 0.00341 ( 5) SS BOND : angle 1.27797 ( 10) covalent geometry : bond 0.00247 (16935) covalent geometry : angle 0.53911 (23135) *********************** 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 129 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 80 time to evaluate : 1.902 Fit side-chains REVERT: A 15 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8120 (tp) REVERT: A 151 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8791 (pp) REVERT: B 15 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8040 (tp) REVERT: B 30 VAL cc_start: 0.9430 (OUTLIER) cc_final: 0.9218 (m) REVERT: C 15 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8223 (tp) REVERT: C 151 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8830 (pp) REVERT: D 15 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8071 (tp) REVERT: D 151 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8771 (pp) REVERT: E 151 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8738 (pp) outliers start: 49 outliers final: 19 residues processed: 125 average time/residue: 0.8235 time to fit residues: 122.5703 Evaluate side-chains 103 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 75 time to evaluate : 1.952 ------------------------------------------------------------------------------- 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 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 A residue 323 HIS Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 30 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 C residue 15 LEU 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 317 VAL Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 317 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 12 optimal weight: 0.7980 chunk 156 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 86 optimal weight: 0.6980 chunk 177 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 49 optimal weight: 0.0970 chunk 162 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 152 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN ** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 HIS D 309 HIS E 323 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.095877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.065335 restraints weight = 33625.778| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 2.72 r_work: 0.2823 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16955 Z= 0.128 Angle : 0.551 6.381 23190 Z= 0.273 Chirality : 0.042 0.236 2710 Planarity : 0.003 0.027 2815 Dihedral : 5.416 52.140 2485 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.29 % Allowed : 11.62 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.20), residues: 1935 helix: 3.00 (0.18), residues: 795 sheet: -0.54 (0.25), residues: 395 loop : -1.86 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 320 HIS 0.009 0.001 HIS B 323 PHE 0.008 0.001 PHE B 254 TYR 0.012 0.001 TYR A 67 ARG 0.002 0.000 ARG A 315 Details of bonding type rmsd link_NAG-ASN : bond 0.00980 ( 15) link_NAG-ASN : angle 2.47166 ( 45) hydrogen bonds : bond 0.04738 ( 840) hydrogen bonds : angle 3.72374 ( 2415) SS BOND : bond 0.00388 ( 5) SS BOND : angle 1.32270 ( 10) covalent geometry : bond 0.00288 (16935) covalent geometry : angle 0.53967 (23135) *********************** 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 144 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 84 time to evaluate : 1.899 Fit side-chains REVERT: A 15 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8224 (tp) REVERT: A 151 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8720 (pp) REVERT: B 15 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8108 (tp) REVERT: C 15 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8291 (tp) REVERT: C 151 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8831 (pp) REVERT: C 315 ARG cc_start: 0.6693 (tmt170) cc_final: 0.6482 (tpt170) REVERT: D 15 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8211 (tp) REVERT: E 30 VAL cc_start: 0.9466 (OUTLIER) cc_final: 0.9246 (m) outliers start: 60 outliers final: 29 residues processed: 135 average time/residue: 0.8072 time to fit residues: 128.7858 Evaluate side-chains 111 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 75 time to evaluate : 1.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU 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 A residue 323 HIS 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 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 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 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 450 ILE Chi-restraints excluded: chain E residue 30 VAL 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 7 optimal weight: 1.9990 chunk 167 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 142 optimal weight: 0.7980 chunk 77 optimal weight: 5.9990 chunk 146 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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 B 111 ASN B 309 HIS C 309 HIS D 125 ASN D 309 HIS E 309 HIS E 323 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.091729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.060866 restraints weight = 34057.771| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 2.74 r_work: 0.2723 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2598 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 16955 Z= 0.239 Angle : 0.659 7.025 23190 Z= 0.333 Chirality : 0.045 0.202 2710 Planarity : 0.004 0.030 2815 Dihedral : 5.371 31.082 2485 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.68 % Favored : 94.16 % Rotamer: Outliers : 4.60 % Allowed : 12.49 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.20), residues: 1935 helix: 2.79 (0.18), residues: 800 sheet: -0.72 (0.24), residues: 405 loop : -1.96 (0.21), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 320 HIS 0.009 0.001 HIS B 323 PHE 0.016 0.002 PHE B 144 TYR 0.020 0.002 TYR A 67 ARG 0.005 0.000 ARG C 219 Details of bonding type rmsd link_NAG-ASN : bond 0.01049 ( 15) link_NAG-ASN : angle 1.95055 ( 45) hydrogen bonds : bond 0.05997 ( 840) hydrogen bonds : angle 4.11755 ( 2415) SS BOND : bond 0.00608 ( 5) SS BOND : angle 1.63046 ( 10) covalent geometry : bond 0.00585 (16935) covalent geometry : angle 0.65347 (23135) *********************** 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 170 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 86 time to evaluate : 1.982 Fit side-chains revert: symmetry clash REVERT: A 151 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8927 (pp) REVERT: A 456 TRP cc_start: 0.6750 (t60) cc_final: 0.6513 (t60) REVERT: B 58 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8730 (pp) REVERT: B 456 TRP cc_start: 0.6898 (t60) cc_final: 0.6510 (t60) REVERT: C 151 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.9007 (pp) REVERT: C 456 TRP cc_start: 0.6703 (t60) cc_final: 0.6388 (t60) REVERT: D 456 TRP cc_start: 0.6634 (t60) cc_final: 0.6387 (t60) outliers start: 84 outliers final: 45 residues processed: 161 average time/residue: 0.7186 time to fit residues: 140.4304 Evaluate side-chains 129 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 81 time to evaluate : 2.027 ------------------------------------------------------------------------------- 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 A residue 454 THR Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 58 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 152 THR Chi-restraints excluded: chain B residue 157 LEU 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 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 268 ILE Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 454 THR Chi-restraints excluded: chain C residue 458 ILE 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 D residue 445 VAL Chi-restraints excluded: chain D residue 450 ILE Chi-restraints excluded: chain D residue 454 THR 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 458 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 151 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 69 optimal weight: 5.9990 chunk 115 optimal weight: 0.7980 chunk 188 optimal weight: 5.9990 chunk 96 optimal weight: 0.7980 chunk 149 optimal weight: 0.0470 chunk 103 optimal weight: 5.9990 chunk 15 optimal weight: 0.5980 chunk 12 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- 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 B 309 HIS C 309 HIS D 125 ASN D 309 HIS E 309 HIS E 323 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.095033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.064604 restraints weight = 33980.739| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 2.75 r_work: 0.2809 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16955 Z= 0.120 Angle : 0.557 8.895 23190 Z= 0.274 Chirality : 0.042 0.207 2710 Planarity : 0.003 0.029 2815 Dihedral : 4.823 36.892 2485 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.34 % Allowed : 14.03 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.20), residues: 1935 helix: 2.94 (0.18), residues: 800 sheet: -0.66 (0.24), residues: 395 loop : -1.99 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 320 HIS 0.009 0.001 HIS B 323 PHE 0.013 0.001 PHE A 233 TYR 0.010 0.001 TYR D 64 ARG 0.003 0.000 ARG B 400 Details of bonding type rmsd link_NAG-ASN : bond 0.00764 ( 15) link_NAG-ASN : angle 1.90141 ( 45) hydrogen bonds : bond 0.04963 ( 840) hydrogen bonds : angle 3.75466 ( 2415) SS BOND : bond 0.00338 ( 5) SS BOND : angle 1.22606 ( 10) covalent geometry : bond 0.00255 (16935) covalent geometry : angle 0.55067 (23135) *********************** 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 144 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 83 time to evaluate : 1.875 Fit side-chains REVERT: A 15 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8203 (tp) REVERT: A 151 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8810 (pp) REVERT: B 15 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8182 (tp) REVERT: C 15 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8269 (tp) REVERT: D 15 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8274 (tp) outliers start: 61 outliers final: 34 residues processed: 137 average time/residue: 0.7886 time to fit residues: 129.8020 Evaluate side-chains 118 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 79 time to evaluate : 1.961 ------------------------------------------------------------------------------- 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 309 HIS Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 104 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 C residue 15 LEU Chi-restraints excluded: chain C residue 116 TYR 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 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 458 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 165 optimal weight: 0.9990 chunk 79 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 47 optimal weight: 0.0370 chunk 44 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 181 optimal weight: 0.9980 chunk 99 optimal weight: 0.8980 chunk 101 optimal weight: 0.0370 chunk 180 optimal weight: 0.6980 overall best weight: 0.4536 ------------------------------------------------------------------------------- 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 ** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 HIS C 309 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 = 0.3576 r_free = 0.3576 target = 0.096527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.066263 restraints weight = 34050.672| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 2.75 r_work: 0.2846 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2415 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= 0.111 Angle : 0.543 7.929 23190 Z= 0.267 Chirality : 0.042 0.202 2710 Planarity : 0.003 0.032 2815 Dihedral : 4.910 49.037 2485 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.90 % Allowed : 14.58 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.20), residues: 1935 helix: 2.98 (0.18), residues: 800 sheet: -0.61 (0.24), residues: 395 loop : -1.97 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 320 HIS 0.009 0.001 HIS B 323 PHE 0.015 0.001 PHE A 233 TYR 0.010 0.001 TYR D 64 ARG 0.005 0.000 ARG D 400 Details of bonding type rmsd link_NAG-ASN : bond 0.00699 ( 15) link_NAG-ASN : angle 1.71508 ( 45) hydrogen bonds : bond 0.04514 ( 840) hydrogen bonds : angle 3.61017 ( 2415) SS BOND : bond 0.00275 ( 5) SS BOND : angle 1.18575 ( 10) covalent geometry : bond 0.00235 (16935) covalent geometry : angle 0.53800 (23135) *********************** 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 134 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 81 time to evaluate : 2.351 Fit side-chains REVERT: A 15 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8190 (tp) REVERT: B 15 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8186 (tp) REVERT: B 157 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.8983 (tm) REVERT: B 315 ARG cc_start: 0.6709 (tpt170) cc_final: 0.6449 (tpm170) REVERT: C 15 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8214 (tp) REVERT: D 15 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8270 (tp) outliers start: 53 outliers final: 27 residues processed: 128 average time/residue: 0.9624 time to fit residues: 144.8506 Evaluate side-chains 110 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 78 time to evaluate : 2.372 ------------------------------------------------------------------------------- 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 132 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain B residue 15 LEU 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 157 LEU 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 188 optimal weight: 2.9990 chunk 51 optimal weight: 0.0670 chunk 26 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 120 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 70 optimal weight: 0.0270 chunk 109 optimal weight: 6.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN ** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 HIS C 309 HIS 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 = 0.3563 r_free = 0.3563 target = 0.095667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.065302 restraints weight = 33884.273| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.73 r_work: 0.2824 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16955 Z= 0.120 Angle : 0.557 8.444 23190 Z= 0.273 Chirality : 0.042 0.190 2710 Planarity : 0.003 0.033 2815 Dihedral : 4.905 46.526 2485 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.85 % Allowed : 15.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.20), residues: 1935 helix: 2.99 (0.18), residues: 800 sheet: -0.58 (0.24), residues: 395 loop : -2.00 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 320 HIS 0.009 0.001 HIS B 323 PHE 0.019 0.001 PHE A 233 TYR 0.011 0.001 TYR A 67 ARG 0.003 0.000 ARG D 315 Details of bonding type rmsd link_NAG-ASN : bond 0.00696 ( 15) link_NAG-ASN : angle 1.49263 ( 45) hydrogen bonds : bond 0.04574 ( 840) hydrogen bonds : angle 3.63378 ( 2415) SS BOND : bond 0.00335 ( 5) SS BOND : angle 1.22518 ( 10) covalent geometry : bond 0.00270 (16935) covalent geometry : angle 0.55336 (23135) *********************** 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 132 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 80 time to evaluate : 2.273 Fit side-chains REVERT: A 15 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8247 (tp) REVERT: B 15 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8167 (tp) REVERT: B 157 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.9059 (tm) REVERT: C 15 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8253 (tp) REVERT: D 15 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8302 (tp) outliers start: 52 outliers final: 34 residues processed: 127 average time/residue: 1.0821 time to fit residues: 165.0727 Evaluate side-chains 116 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 77 time to evaluate : 2.540 ------------------------------------------------------------------------------- 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 311 GLN Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain B residue 15 LEU 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 157 LEU 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 116 TYR 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 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 203 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 67 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 154 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 183 optimal weight: 6.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 ** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 HIS C 309 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 = 0.3543 r_free = 0.3543 target = 0.094457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.063907 restraints weight = 34081.232| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 2.78 r_work: 0.2793 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16955 Z= 0.144 Angle : 0.591 14.205 23190 Z= 0.291 Chirality : 0.043 0.178 2710 Planarity : 0.003 0.033 2815 Dihedral : 4.978 42.090 2485 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.96 % Allowed : 15.29 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.20), residues: 1935 helix: 2.97 (0.18), residues: 795 sheet: -0.58 (0.24), residues: 395 loop : -2.03 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 320 HIS 0.009 0.001 HIS B 323 PHE 0.021 0.001 PHE A 233 TYR 0.014 0.001 TYR A 67 ARG 0.005 0.000 ARG D 315 Details of bonding type rmsd link_NAG-ASN : bond 0.00724 ( 15) link_NAG-ASN : angle 1.36447 ( 45) hydrogen bonds : bond 0.04859 ( 840) hydrogen bonds : angle 3.72691 ( 2415) SS BOND : bond 0.00410 ( 5) SS BOND : angle 1.32776 ( 10) covalent geometry : bond 0.00336 (16935) covalent geometry : angle 0.58783 (23135) *********************** 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 133 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 79 time to evaluate : 1.797 Fit side-chains REVERT: A 15 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8298 (tp) REVERT: B 15 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8216 (tp) REVERT: B 157 LEU cc_start: 0.9404 (OUTLIER) cc_final: 0.9116 (tm) REVERT: C 15 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8332 (tp) REVERT: D 15 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8341 (tp) outliers start: 54 outliers final: 32 residues processed: 127 average time/residue: 0.8380 time to fit residues: 130.0896 Evaluate side-chains 113 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 76 time to evaluate : 1.868 ------------------------------------------------------------------------------- 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 62 ILE 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 15 LEU 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 157 LEU 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 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 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 203 ILE Chi-restraints excluded: chain E residue 317 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 28 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 187 optimal weight: 7.9990 chunk 107 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 177 optimal weight: 0.9990 chunk 149 optimal weight: 8.9990 chunk 188 optimal weight: 9.9990 chunk 128 optimal weight: 1.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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 ** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 HIS C 309 HIS ** E 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 323 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.094499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.064079 restraints weight = 34086.999| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 2.76 r_work: 0.2798 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16955 Z= 0.136 Angle : 0.581 8.284 23190 Z= 0.288 Chirality : 0.043 0.174 2710 Planarity : 0.003 0.033 2815 Dihedral : 5.117 46.427 2485 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.36 % Allowed : 16.05 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.20), residues: 1935 helix: 3.01 (0.18), residues: 795 sheet: -0.57 (0.24), residues: 395 loop : -2.06 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 320 HIS 0.009 0.001 HIS B 323 PHE 0.021 0.001 PHE C 233 TYR 0.012 0.001 TYR A 67 ARG 0.002 0.000 ARG C 219 Details of bonding type rmsd link_NAG-ASN : bond 0.00674 ( 15) link_NAG-ASN : angle 1.34089 ( 45) hydrogen bonds : bond 0.04850 ( 840) hydrogen bonds : angle 3.72432 ( 2415) SS BOND : bond 0.00389 ( 5) SS BOND : angle 1.30561 ( 10) covalent geometry : bond 0.00313 (16935) covalent geometry : angle 0.57794 (23135) ********************** 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 123 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 80 time to evaluate : 1.834 Fit side-chains REVERT: A 15 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8298 (tp) REVERT: B 15 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8246 (tp) REVERT: B 157 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.9100 (tm) REVERT: C 15 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8284 (tp) REVERT: D 15 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8344 (tp) outliers start: 43 outliers final: 32 residues processed: 118 average time/residue: 0.8513 time to fit residues: 119.1980 Evaluate side-chains 114 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 77 time to evaluate : 2.182 ------------------------------------------------------------------------------- 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 15 LEU 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 157 LEU 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 168 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 70 optimal weight: 7.9990 chunk 61 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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** ** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 HIS ** E 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 323 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.094831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.064450 restraints weight = 34166.274| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 2.76 r_work: 0.2806 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16955 Z= 0.128 Angle : 0.571 8.159 23190 Z= 0.283 Chirality : 0.042 0.170 2710 Planarity : 0.003 0.034 2815 Dihedral : 5.086 46.493 2485 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.68 % Allowed : 15.84 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.20), residues: 1935 helix: 2.96 (0.19), residues: 800 sheet: -0.44 (0.24), residues: 390 loop : -2.05 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 320 HIS 0.009 0.001 HIS B 323 PHE 0.019 0.001 PHE C 233 TYR 0.012 0.001 TYR A 67 ARG 0.002 0.000 ARG C 315 Details of bonding type rmsd link_NAG-ASN : bond 0.00642 ( 15) link_NAG-ASN : angle 1.30228 ( 45) hydrogen bonds : bond 0.04755 ( 840) hydrogen bonds : angle 3.69571 ( 2415) SS BOND : bond 0.00363 ( 5) SS BOND : angle 1.27519 ( 10) covalent geometry : bond 0.00290 (16935) covalent geometry : angle 0.56841 (23135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8347.83 seconds wall clock time: 145 minutes 21.28 seconds (8721.28 seconds total)