Starting phenix.real_space_refine on Mon Nov 18 13:51:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frz_29411/11_2024/8frz_29411.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frz_29411/11_2024/8frz_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frz_29411/11_2024/8frz_29411.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frz_29411/11_2024/8frz_29411.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frz_29411/11_2024/8frz_29411.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frz_29411/11_2024/8frz_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-5513/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: 7.33, per 1000 atoms: 0.44 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=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 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: 4.55 Conformation dependent library (CDL) restraints added in 2.1 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: 1.54 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: 4.86 Time building geometry restraints manager: 5.17 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: 844 33.93 - 50.89: 158 50.89 - 67.86: 26 67.86 - 84.82: 20 Dihedral angle restraints: 10138 sinusoidal: 4303 harmonic: 5835 Sorted by residual: dihedral pdb=" CB CYS A 135 " pdb=" SG CYS A 135 " pdb=" SG CYS A 149 " pdb=" CB CYS A 149 " ideal model delta sinusoidal sigma weight residual 93.00 61.66 31.34 1 1.00e+01 1.00e-02 1.40e+01 dihedral pdb=" CA LEU D 131 " pdb=" C LEU D 131 " pdb=" N VAL D 132 " pdb=" CA VAL D 132 " ideal model delta harmonic sigma weight residual 180.00 162.70 17.30 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA LEU B 131 " pdb=" C LEU B 131 " pdb=" N VAL B 132 " pdb=" CA VAL B 132 " ideal model delta harmonic sigma weight residual 180.00 162.72 17.28 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 10135 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: 2.03 - 2.61: 70 2.61 - 3.18: 13779 3.18 - 3.75: 25482 3.75 - 4.33: 32673 4.33 - 4.90: 55607 Nonbonded interactions: 127611 Sorted by model distance: nonbonded pdb=" SG CYS B 135 " pdb=" SG CYS B 149 " model vdw 2.033 3.760 nonbonded pdb=" SG CYS C 135 " pdb=" SG CYS C 149 " model vdw 2.033 3.760 nonbonded pdb=" SG CYS E 135 " pdb=" SG CYS E 149 " model vdw 2.033 3.760 nonbonded pdb=" SG CYS D 135 " pdb=" SG CYS D 149 " model vdw 2.034 3.760 nonbonded pdb=" O GLY E 185 " pdb=" NH1 ARG E 219 " model vdw 2.290 3.120 ... (remaining 127606 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 1.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.610 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 34.310 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.050 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:13.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.460 ------------------------------------------------------------------------------- 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 16935 Z= 0.220 Angle : 0.759 9.885 23135 Z= 0.394 Chirality : 0.046 0.262 2710 Planarity : 0.004 0.031 2815 Dihedral : 13.710 84.820 6335 Min Nonbonded Distance : 2.033 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 *********************** 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 : 1.951 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.8932 time to fit residues: 137.5968 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 : 1.942 ------------------------------------------------------------------------------- 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 111 ASN B 323 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 16935 Z= 0.312 Angle : 0.644 7.832 23135 Z= 0.324 Chirality : 0.045 0.233 2710 Planarity : 0.004 0.035 2815 Dihedral : 7.431 79.268 2485 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.08 % Allowed : 8.71 % 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: 2.69 (0.18), residues: 800 sheet: -0.56 (0.25), residues: 395 loop : -1.81 (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 D 118 PHE 0.015 0.001 PHE E 144 TYR 0.018 0.001 TYR A 67 ARG 0.004 0.000 ARG A 219 *********************** 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 126 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 88 time to evaluate : 2.008 Fit side-chains REVERT: B 235 MET cc_start: 0.8773 (mmp) cc_final: 0.8535 (mmp) REVERT: C 15 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8320 (tp) REVERT: E 15 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8250 (tp) outliers start: 38 outliers final: 16 residues processed: 113 average time/residue: 0.9924 time to fit residues: 130.5509 Evaluate side-chains 89 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 1.798 ------------------------------------------------------------------------------- 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 203 ILE Chi-restraints excluded: chain E residue 323 HIS 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 98 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 147 optimal weight: 4.9990 chunk 120 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 177 optimal weight: 6.9990 chunk 191 optimal weight: 0.7980 chunk 157 optimal weight: 1.9990 chunk 175 optimal weight: 0.4980 chunk 60 optimal weight: 0.9980 chunk 142 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 D 309 HIS D 323 HIS E 323 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16935 Z= 0.176 Angle : 0.545 6.415 23135 Z= 0.275 Chirality : 0.043 0.256 2710 Planarity : 0.003 0.029 2815 Dihedral : 5.907 64.582 2485 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.74 % Allowed : 10.25 % 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: 0.63 (0.20), residues: 1935 helix: 2.87 (0.18), residues: 800 sheet: -0.62 (0.25), residues: 395 loop : -1.85 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 320 HIS 0.009 0.001 HIS B 323 PHE 0.008 0.001 PHE D 254 TYR 0.011 0.001 TYR A 67 ARG 0.001 0.000 ARG D 315 *********************** 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 132 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 82 time to evaluate : 2.313 Fit side-chains REVERT: B 15 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8259 (tp) REVERT: C 15 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8340 (tp) REVERT: D 15 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8197 (tp) outliers start: 50 outliers final: 23 residues processed: 125 average time/residue: 0.9028 time to fit residues: 133.4619 Evaluate side-chains 98 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 72 time to evaluate : 1.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain B residue 15 LEU 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 203 ILE Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 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 123 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain E residue 458 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 175 optimal weight: 0.0980 chunk 133 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 19 optimal weight: 0.0670 chunk 84 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 178 optimal weight: 0.7980 chunk 188 optimal weight: 7.9990 chunk 93 optimal weight: 0.9990 chunk 168 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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 ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 HIS E 309 HIS E 323 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16935 Z= 0.156 Angle : 0.529 8.406 23135 Z= 0.262 Chirality : 0.042 0.240 2710 Planarity : 0.003 0.027 2815 Dihedral : 5.439 54.402 2485 Min Nonbonded Distance : 2.648 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.34 % Allowed : 11.62 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.20), residues: 1935 helix: 3.03 (0.18), residues: 795 sheet: -0.59 (0.25), residues: 395 loop : -1.83 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 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 315 *********************** 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 141 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 80 time to evaluate : 1.838 Fit side-chains REVERT: B 30 VAL cc_start: 0.9412 (OUTLIER) cc_final: 0.9211 (m) REVERT: B 58 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8727 (pt) REVERT: D 15 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8251 (tp) REVERT: E 30 VAL cc_start: 0.9406 (OUTLIER) cc_final: 0.9190 (m) outliers start: 61 outliers final: 28 residues processed: 135 average time/residue: 0.8551 time to fit residues: 136.6833 Evaluate side-chains 104 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 72 time to evaluate : 1.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain B residue 30 VAL 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 157 LEU Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 309 HIS Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 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 30 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain E residue 458 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 156 optimal weight: 0.8980 chunk 106 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 140 optimal weight: 0.9990 chunk 77 optimal weight: 8.9990 chunk 160 optimal weight: 4.9990 chunk 130 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 96 optimal weight: 0.7980 chunk 169 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 C 309 HIS ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 HIS E 309 HIS E 323 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16935 Z= 0.181 Angle : 0.540 8.449 23135 Z= 0.269 Chirality : 0.042 0.228 2710 Planarity : 0.003 0.026 2815 Dihedral : 5.300 51.205 2485 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.40 % Allowed : 12.60 % Favored : 84.00 % 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: 0.76 (0.20), residues: 1935 helix: 3.03 (0.18), residues: 795 sheet: -0.56 (0.24), residues: 395 loop : -1.82 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 320 HIS 0.009 0.001 HIS B 323 PHE 0.013 0.001 PHE A 233 TYR 0.012 0.001 TYR A 67 ARG 0.003 0.000 ARG A 400 *********************** 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 136 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 74 time to evaluate : 1.844 Fit side-chains REVERT: B 58 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8733 (pt) REVERT: D 15 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8287 (tp) REVERT: E 30 VAL cc_start: 0.9425 (OUTLIER) cc_final: 0.9216 (m) outliers start: 62 outliers final: 36 residues processed: 129 average time/residue: 0.7829 time to fit residues: 121.3555 Evaluate side-chains 114 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 75 time to evaluate : 2.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 323 HIS 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 152 THR Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 309 HIS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 458 ILE Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 323 HIS Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 317 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 63 optimal weight: 5.9990 chunk 169 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 110 optimal weight: 9.9990 chunk 46 optimal weight: 1.9990 chunk 188 optimal weight: 0.9990 chunk 156 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 62 optimal weight: 0.0770 chunk 99 optimal weight: 4.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- 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 C 309 HIS ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 HIS E 309 HIS E 323 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16935 Z= 0.159 Angle : 0.524 7.813 23135 Z= 0.260 Chirality : 0.042 0.214 2710 Planarity : 0.003 0.026 2815 Dihedral : 5.198 51.774 2485 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.56 % Allowed : 12.55 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.20), residues: 1935 helix: 3.03 (0.18), residues: 800 sheet: -0.55 (0.24), residues: 395 loop : -1.78 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 320 HIS 0.009 0.001 HIS B 323 PHE 0.014 0.001 PHE A 233 TYR 0.010 0.001 TYR A 67 ARG 0.003 0.000 ARG E 315 *********************** 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 146 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 81 time to evaluate : 1.899 Fit side-chains REVERT: B 58 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8737 (pt) REVERT: E 30 VAL cc_start: 0.9411 (OUTLIER) cc_final: 0.9198 (m) outliers start: 65 outliers final: 37 residues processed: 138 average time/residue: 0.8565 time to fit residues: 139.3827 Evaluate side-chains 114 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 75 time to evaluate : 1.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 58 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 309 HIS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 58 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 234 LEU 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 30 VAL 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 30 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 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 181 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 137 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 158 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 187 optimal weight: 6.9990 chunk 117 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 86 optimal weight: 0.3980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 ** B 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 HIS ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 HIS E 309 HIS E 323 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16935 Z= 0.200 Angle : 0.556 7.965 23135 Z= 0.277 Chirality : 0.042 0.198 2710 Planarity : 0.003 0.026 2815 Dihedral : 5.131 45.947 2485 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.40 % Allowed : 13.59 % Favored : 83.01 % 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: 0.77 (0.20), residues: 1935 helix: 3.01 (0.18), residues: 800 sheet: -0.57 (0.24), residues: 395 loop : -1.82 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 320 HIS 0.009 0.001 HIS B 323 PHE 0.018 0.001 PHE A 233 TYR 0.014 0.001 TYR A 67 ARG 0.006 0.000 ARG C 400 *********************** 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 139 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 77 time to evaluate : 1.720 Fit side-chains REVERT: B 58 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8760 (pt) REVERT: B 157 LEU cc_start: 0.9453 (OUTLIER) cc_final: 0.9200 (tm) REVERT: E 30 VAL cc_start: 0.9429 (OUTLIER) cc_final: 0.9218 (m) outliers start: 62 outliers final: 34 residues processed: 130 average time/residue: 0.8223 time to fit residues: 127.3282 Evaluate side-chains 112 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 75 time to evaluate : 1.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 58 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 30 VAL Chi-restraints excluded: chain C residue 58 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 317 VAL Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 458 ILE Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 323 HIS Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 317 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 116 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 56 optimal weight: 0.0970 chunk 36 optimal weight: 0.8980 chunk 119 optimal weight: 0.0670 chunk 128 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 147 optimal weight: 0.0270 chunk 170 optimal weight: 1.9990 overall best weight: 0.3974 ------------------------------------------------------------------------------- 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 ** B 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 HIS ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 HIS E 309 HIS E 323 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16935 Z= 0.141 Angle : 0.523 7.866 23135 Z= 0.258 Chirality : 0.041 0.202 2710 Planarity : 0.003 0.030 2815 Dihedral : 5.203 54.135 2485 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.01 % Allowed : 14.14 % Favored : 82.85 % 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: 0.78 (0.20), residues: 1935 helix: 3.10 (0.18), residues: 795 sheet: -0.56 (0.24), residues: 395 loop : -1.88 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 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 0.004 0.000 ARG D 315 *********************** 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 134 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 79 time to evaluate : 1.749 Fit side-chains REVERT: B 58 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8758 (pt) REVERT: E 30 VAL cc_start: 0.9359 (OUTLIER) cc_final: 0.9135 (m) outliers start: 55 outliers final: 32 residues processed: 127 average time/residue: 0.8031 time to fit residues: 121.6436 Evaluate side-chains 109 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 75 time to evaluate : 1.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain B residue 58 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 317 VAL Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 58 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 D residue 30 VAL Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain E residue 458 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 180 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 175 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 137 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 158 optimal weight: 0.4980 chunk 165 optimal weight: 0.7980 chunk 174 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 ** B 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 HIS ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 HIS E 309 HIS E 323 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16935 Z= 0.179 Angle : 0.553 8.146 23135 Z= 0.275 Chirality : 0.042 0.185 2710 Planarity : 0.003 0.030 2815 Dihedral : 5.035 47.890 2485 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.74 % Allowed : 14.85 % Favored : 82.41 % 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: 0.77 (0.20), residues: 1935 helix: 3.08 (0.18), residues: 795 sheet: -0.54 (0.24), residues: 395 loop : -1.88 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 320 HIS 0.009 0.001 HIS B 323 PHE 0.019 0.001 PHE B 233 TYR 0.012 0.001 TYR A 67 ARG 0.003 0.000 ARG E 315 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 76 time to evaluate : 2.082 Fit side-chains REVERT: B 58 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8729 (pt) REVERT: B 157 LEU cc_start: 0.9448 (OUTLIER) cc_final: 0.9126 (tm) REVERT: C 62 ILE cc_start: 0.9171 (OUTLIER) cc_final: 0.8802 (pt) REVERT: E 30 VAL cc_start: 0.9405 (OUTLIER) cc_final: 0.9183 (m) outliers start: 50 outliers final: 33 residues processed: 123 average time/residue: 0.8143 time to fit residues: 119.8955 Evaluate side-chains 110 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 73 time to evaluate : 2.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 317 VAL Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain B residue 58 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 30 VAL Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 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 30 VAL 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 E residue 30 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 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 185 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 87 optimal weight: 0.5980 chunk 128 optimal weight: 2.9990 chunk 194 optimal weight: 0.9980 chunk 178 optimal weight: 0.4980 chunk 154 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 119 optimal weight: 0.0470 chunk 94 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 overall best weight: 0.5878 ------------------------------------------------------------------------------- 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 ** B 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 HIS ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 HIS E 323 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16935 Z= 0.158 Angle : 0.547 8.241 23135 Z= 0.272 Chirality : 0.042 0.184 2710 Planarity : 0.003 0.030 2815 Dihedral : 5.081 49.967 2485 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.52 % Allowed : 15.12 % Favored : 82.36 % 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: 0.77 (0.20), residues: 1935 helix: 3.11 (0.18), residues: 795 sheet: -0.53 (0.24), residues: 395 loop : -1.91 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP D 320 HIS 0.009 0.001 HIS B 323 PHE 0.019 0.001 PHE C 233 TYR 0.010 0.001 TYR C 64 ARG 0.001 0.000 ARG E 219 ********************** 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 126 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 80 time to evaluate : 1.943 Fit side-chains REVERT: A 55 ASN cc_start: 0.9196 (m-40) cc_final: 0.8962 (m-40) REVERT: B 58 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8750 (pt) REVERT: B 157 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.9083 (tm) REVERT: C 62 ILE cc_start: 0.9142 (OUTLIER) cc_final: 0.8776 (pt) REVERT: E 30 VAL cc_start: 0.9371 (OUTLIER) cc_final: 0.9149 (m) outliers start: 46 outliers final: 34 residues processed: 121 average time/residue: 0.8412 time to fit residues: 121.0129 Evaluate side-chains 113 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 75 time to evaluate : 1.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain B residue 58 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 30 VAL Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 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 30 VAL Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 142 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 42 optimal weight: 0.4980 chunk 154 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 136 optimal weight: 0.0770 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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 ** B 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 HIS ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 HIS E 309 HIS E 323 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.096441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.065959 restraints weight = 34046.178| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 2.75 r_work: 0.2837 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16935 Z= 0.161 Angle : 0.560 10.650 23135 Z= 0.278 Chirality : 0.042 0.179 2710 Planarity : 0.003 0.047 2815 Dihedral : 5.068 49.517 2485 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.63 % Allowed : 15.40 % Favored : 81.97 % 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: 0.78 (0.20), residues: 1935 helix: 3.10 (0.19), residues: 795 sheet: -0.43 (0.24), residues: 390 loop : -1.94 (0.21), residues: 750 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 0.020 0.001 PHE C 233 TYR 0.010 0.001 TYR D 64 ARG 0.005 0.000 ARG C 315 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3428.73 seconds wall clock time: 63 minutes 26.06 seconds (3806.06 seconds total)