Starting phenix.real_space_refine on Wed Mar 4 17:22:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7upk_26668/03_2026/7upk_26668.cif Found real_map, /net/cci-nas-00/data/ceres_data/7upk_26668/03_2026/7upk_26668.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7upk_26668/03_2026/7upk_26668.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7upk_26668/03_2026/7upk_26668.map" model { file = "/net/cci-nas-00/data/ceres_data/7upk_26668/03_2026/7upk_26668.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7upk_26668/03_2026/7upk_26668.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.037 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 84 5.16 5 C 9654 2.51 5 N 2514 2.21 5 O 3024 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15276 Number of models: 1 Model: "" Number of chains: 9 Chain: "D" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3367 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 16, 'TRANS': 421} Chain breaks: 1 Chain: "H" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 903 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "L" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "A" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3367 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 16, 'TRANS': 421} Chain breaks: 1 Chain: "C" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 903 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "F" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "B" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3367 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 16, 'TRANS': 421} Chain breaks: 1 Chain: "E" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 903 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "G" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Time building chain proxies: 3.43, per 1000 atoms: 0.22 Number of scatterers: 15276 At special positions: 0 Unit cell: (144.18, 132.84, 103.68, 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 84 16.00 O 3024 8.00 N 2514 7.00 C 9654 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS D 71 " - pdb=" SG CYS D 192 " distance=2.03 Simple disulfide: pdb=" SG CYS D 104 " - pdb=" SG CYS D 114 " distance=2.03 Simple disulfide: pdb=" SG CYS D 331 " - pdb=" SG CYS D 340 " distance=2.03 Simple disulfide: pdb=" SG CYS D 355 " - pdb=" SG CYS D 363 " distance=2.03 Simple disulfide: pdb=" SG CYS D 387 " - pdb=" SG CYS D 392 " distance=2.03 Simple disulfide: pdb=" SG CYS D 394 " - pdb=" SG CYS D 417 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 71 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 104 " - pdb=" SG CYS A 114 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 340 " distance=2.03 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 363 " distance=2.02 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 392 " distance=2.03 Simple disulfide: pdb=" SG CYS A 394 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 71 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 104 " - pdb=" SG CYS B 114 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 340 " distance=2.03 Simple disulfide: pdb=" SG CYS B 355 " - pdb=" SG CYS B 363 " distance=2.02 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 392 " distance=2.03 Simple disulfide: pdb=" SG CYS B 394 " - pdb=" SG CYS B 417 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " 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 Time building additional restraints: 1.46 Conformation dependent library (CDL) restraints added in 554.4 milliseconds 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3678 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 31 sheets defined 27.7% alpha, 37.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'D' and resid 29 through 37 Processing helix chain 'D' and resid 65 through 72 removed outlier: 3.565A pdb=" N SER D 69 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N GLN D 70 " --> pdb=" O ASN D 67 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N CYS D 71 " --> pdb=" O MET D 68 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR D 72 " --> pdb=" O SER D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 99 Proline residue: D 89 - end of helix removed outlier: 3.911A pdb=" N TYR D 97 " --> pdb=" O ALA D 93 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN D 99 " --> pdb=" O GLU D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 121 Processing helix chain 'D' and resid 125 through 146 removed outlier: 4.438A pdb=" N LYS D 139 " --> pdb=" O TYR D 135 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ASN D 140 " --> pdb=" O GLU D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 153 Processing helix chain 'D' and resid 175 through 183 Processing helix chain 'D' and resid 191 through 215 removed outlier: 3.812A pdb=" N THR D 195 " --> pdb=" O PRO D 191 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N PHE D 212 " --> pdb=" O SER D 208 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N VAL D 213 " --> pdb=" O ASP D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 232 Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 238 through 246 removed outlier: 3.568A pdb=" N LEU D 242 " --> pdb=" O ASN D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 259 Processing helix chain 'D' and resid 328 through 331 Processing helix chain 'D' and resid 349 through 358 Processing helix chain 'D' and resid 359 through 363 Processing helix chain 'D' and resid 452 through 471 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.733A pdb=" N VAL L 83 " --> pdb=" O THR L 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 37 Processing helix chain 'A' and resid 65 through 72 removed outlier: 5.773A pdb=" N GLN A 70 " --> pdb=" O ASN A 67 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR A 72 " --> pdb=" O SER A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 99 Proline residue: A 89 - end of helix removed outlier: 3.878A pdb=" N TYR A 97 " --> pdb=" O ALA A 93 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN A 99 " --> pdb=" O GLU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 121 Processing helix chain 'A' and resid 125 through 146 removed outlier: 4.441A pdb=" N LYS A 139 " --> pdb=" O TYR A 135 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ASN A 140 " --> pdb=" O GLU A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 153 Processing helix chain 'A' and resid 175 through 182 Processing helix chain 'A' and resid 192 through 215 removed outlier: 4.128A pdb=" N PHE A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N VAL A 213 " --> pdb=" O ASP A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 232 Processing helix chain 'A' and resid 233 through 236 Processing helix chain 'A' and resid 238 through 246 removed outlier: 3.612A pdb=" N LEU A 242 " --> pdb=" O ASN A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 349 through 358 Processing helix chain 'A' and resid 359 through 363 Processing helix chain 'A' and resid 452 through 471 Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.749A pdb=" N VAL F 83 " --> pdb=" O THR F 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 37 Processing helix chain 'B' and resid 65 through 72 removed outlier: 3.540A pdb=" N SER B 69 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N GLN B 70 " --> pdb=" O ASN B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 99 Proline residue: B 89 - end of helix removed outlier: 3.916A pdb=" N TYR B 97 " --> pdb=" O ALA B 93 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN B 99 " --> pdb=" O GLU B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 121 Processing helix chain 'B' and resid 125 through 146 removed outlier: 4.442A pdb=" N LYS B 139 " --> pdb=" O TYR B 135 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ASN B 140 " --> pdb=" O GLU B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 153 Processing helix chain 'B' and resid 175 through 182 Processing helix chain 'B' and resid 191 through 215 removed outlier: 4.093A pdb=" N PHE B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N VAL B 213 " --> pdb=" O ASP B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 232 Processing helix chain 'B' and resid 233 through 236 Processing helix chain 'B' and resid 238 through 247 removed outlier: 3.571A pdb=" N LEU B 242 " --> pdb=" O ASN B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 259 Processing helix chain 'B' and resid 349 through 358 Processing helix chain 'B' and resid 359 through 363 Processing helix chain 'B' and resid 452 through 471 Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'G' and resid 79 through 83 removed outlier: 3.710A pdb=" N VAL G 83 " --> pdb=" O THR G 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 158 through 162 removed outlier: 18.193A pdb=" N THR D 168 " --> pdb=" O PRO D 52 " (cutoff:3.500A) removed outlier: 12.467A pdb=" N THR D 54 " --> pdb=" O THR D 168 " (cutoff:3.500A) removed outlier: 10.940A pdb=" N TYR D 170 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N ASP D 56 " --> pdb=" O TYR D 170 " (cutoff:3.500A) removed outlier: 8.876A pdb=" N PHE D 172 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL D 58 " --> pdb=" O PHE D 172 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N LEU D 38 " --> pdb=" O LEU D 296 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU D 296 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N LYS D 40 " --> pdb=" O GLN D 294 " (cutoff:3.500A) removed outlier: 9.863A pdb=" N GLN D 294 " --> pdb=" O LYS D 40 " (cutoff:3.500A) removed outlier: 11.020A pdb=" N VAL D 42 " --> pdb=" O TYR D 292 " (cutoff:3.500A) removed outlier: 9.789A pdb=" N TYR D 292 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 11.264A pdb=" N ARG D 44 " --> pdb=" O GLN D 290 " (cutoff:3.500A) removed outlier: 9.571A pdb=" N GLN D 290 " --> pdb=" O ARG D 44 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N TYR D 46 " --> pdb=" O ILE D 288 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N PHE D 282 " --> pdb=" O PRO D 52 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N THR D 54 " --> pdb=" O VAL D 280 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL D 280 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ASP D 56 " --> pdb=" O VAL D 278 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL D 278 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL D 58 " --> pdb=" O ILE D 276 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE D 276 " --> pdb=" O VAL D 58 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 275 through 298 current: chain 'D' and resid 332 through 333 Processing sheet with id=AA2, first strand: chain 'D' and resid 226 through 227 removed outlier: 3.885A pdb=" N MET D 226 " --> pdb=" O GLY D 264 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE D 277 " --> pdb=" O ILE D 267 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N VAL D 269 " --> pdb=" O TYR D 275 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N TYR D 275 " --> pdb=" O VAL D 269 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE D 276 " --> pdb=" O VAL D 58 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL D 58 " --> pdb=" O ILE D 276 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL D 278 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ASP D 56 " --> pdb=" O VAL D 278 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL D 280 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N THR D 54 " --> pdb=" O VAL D 280 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N PHE D 282 " --> pdb=" O PRO D 52 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N TYR D 46 " --> pdb=" O ILE D 288 " (cutoff:3.500A) removed outlier: 9.571A pdb=" N GLN D 290 " --> pdb=" O ARG D 44 " (cutoff:3.500A) removed outlier: 11.264A pdb=" N ARG D 44 " --> pdb=" O GLN D 290 " (cutoff:3.500A) removed outlier: 9.789A pdb=" N TYR D 292 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 11.020A pdb=" N VAL D 42 " --> pdb=" O TYR D 292 " (cutoff:3.500A) removed outlier: 9.863A pdb=" N GLN D 294 " --> pdb=" O LYS D 40 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N LYS D 40 " --> pdb=" O GLN D 294 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU D 296 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N LEU D 38 " --> pdb=" O LEU D 296 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 38 through 60 current: chain 'D' and resid 322 through 326 Processing sheet with id=AA3, first strand: chain 'D' and resid 101 through 102 Processing sheet with id=AA4, first strand: chain 'D' and resid 123 through 124 Processing sheet with id=AA5, first strand: chain 'D' and resid 301 through 302 removed outlier: 5.915A pdb=" N ARG D 365 " --> pdb=" O VAL D 449 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 410 through 412 Processing sheet with id=AA7, first strand: chain 'D' and resid 393 through 394 Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA9, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.392A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TRP H 33 " --> pdb=" O ARG H 95 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU H 34 " --> pdb=" O ASP H 50 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ASP H 50 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.392A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N THR H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.101A pdb=" N PHE L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU L 33 " --> pdb=" O SER L 49 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N SER L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 158 through 162 removed outlier: 18.099A pdb=" N THR A 168 " --> pdb=" O PRO A 52 " (cutoff:3.500A) removed outlier: 12.393A pdb=" N THR A 54 " --> pdb=" O THR A 168 " (cutoff:3.500A) removed outlier: 10.937A pdb=" N TYR A 170 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ASP A 56 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 8.840A pdb=" N PHE A 172 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL A 58 " --> pdb=" O PHE A 172 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N LEU A 38 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU A 296 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N LYS A 40 " --> pdb=" O GLN A 294 " (cutoff:3.500A) removed outlier: 9.852A pdb=" N GLN A 294 " --> pdb=" O LYS A 40 " (cutoff:3.500A) removed outlier: 10.990A pdb=" N VAL A 42 " --> pdb=" O TYR A 292 " (cutoff:3.500A) removed outlier: 9.774A pdb=" N TYR A 292 " --> pdb=" O VAL A 42 " (cutoff:3.500A) removed outlier: 11.224A pdb=" N ARG A 44 " --> pdb=" O GLN A 290 " (cutoff:3.500A) removed outlier: 9.503A pdb=" N GLN A 290 " --> pdb=" O ARG A 44 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N TYR A 46 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N PHE A 282 " --> pdb=" O PRO A 52 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR A 54 " --> pdb=" O VAL A 280 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL A 280 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ASP A 56 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL A 278 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N VAL A 58 " --> pdb=" O ILE A 276 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE A 276 " --> pdb=" O VAL A 58 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 275 through 298 current: chain 'A' and resid 332 through 333 Processing sheet with id=AB5, first strand: chain 'A' and resid 263 through 270 removed outlier: 6.227A pdb=" N ILE A 277 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N VAL A 269 " --> pdb=" O TYR A 275 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N TYR A 275 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE A 276 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N VAL A 58 " --> pdb=" O ILE A 276 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL A 278 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ASP A 56 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL A 280 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR A 54 " --> pdb=" O VAL A 280 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N PHE A 282 " --> pdb=" O PRO A 52 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N TYR A 46 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 9.503A pdb=" N GLN A 290 " --> pdb=" O ARG A 44 " (cutoff:3.500A) removed outlier: 11.224A pdb=" N ARG A 44 " --> pdb=" O GLN A 290 " (cutoff:3.500A) removed outlier: 9.774A pdb=" N TYR A 292 " --> pdb=" O VAL A 42 " (cutoff:3.500A) removed outlier: 10.990A pdb=" N VAL A 42 " --> pdb=" O TYR A 292 " (cutoff:3.500A) removed outlier: 9.852A pdb=" N GLN A 294 " --> pdb=" O LYS A 40 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N LYS A 40 " --> pdb=" O GLN A 294 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU A 296 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N LEU A 38 " --> pdb=" O LEU A 296 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 38 through 60 current: chain 'A' and resid 322 through 326 Processing sheet with id=AB6, first strand: chain 'A' and resid 101 through 102 removed outlier: 6.825A pdb=" N MET A 115 " --> pdb=" O SER B 428 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL B 425 " --> pdb=" O LEU B 422 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 123 through 124 Processing sheet with id=AB8, first strand: chain 'A' and resid 301 through 303 removed outlier: 5.885A pdb=" N ARG A 365 " --> pdb=" O VAL A 449 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AC1, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.437A pdb=" N GLU C 10 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TRP C 33 " --> pdb=" O ARG C 95 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N LEU C 34 " --> pdb=" O ASP C 50 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ASP C 50 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N TRP C 36 " --> pdb=" O ILE C 48 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.437A pdb=" N GLU C 10 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N CYS C 92 " --> pdb=" O TRP C 103 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N TRP C 103 " --> pdb=" O CYS C 92 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N THR C 94 " --> pdb=" O ASP C 101 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 4 through 6 Processing sheet with id=AC4, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.090A pdb=" N PHE F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LEU F 33 " --> pdb=" O SER F 49 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N SER F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 158 through 162 removed outlier: 18.067A pdb=" N THR B 168 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 12.367A pdb=" N THR B 54 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 10.961A pdb=" N TYR B 170 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ASP B 56 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 8.860A pdb=" N PHE B 172 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL B 58 " --> pdb=" O PHE B 172 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N LEU B 38 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU B 296 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N LYS B 40 " --> pdb=" O GLN B 294 " (cutoff:3.500A) removed outlier: 9.864A pdb=" N GLN B 294 " --> pdb=" O LYS B 40 " (cutoff:3.500A) removed outlier: 10.994A pdb=" N VAL B 42 " --> pdb=" O TYR B 292 " (cutoff:3.500A) removed outlier: 9.768A pdb=" N TYR B 292 " --> pdb=" O VAL B 42 " (cutoff:3.500A) removed outlier: 11.314A pdb=" N ARG B 44 " --> pdb=" O GLN B 290 " (cutoff:3.500A) removed outlier: 9.617A pdb=" N GLN B 290 " --> pdb=" O ARG B 44 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N TYR B 46 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N PHE B 282 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N THR B 54 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL B 280 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ASP B 56 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL B 278 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N VAL B 58 " --> pdb=" O ILE B 276 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE B 276 " --> pdb=" O VAL B 58 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 275 through 298 current: chain 'B' and resid 332 through 333 Processing sheet with id=AC6, first strand: chain 'B' and resid 263 through 270 removed outlier: 6.233A pdb=" N ILE B 277 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N VAL B 269 " --> pdb=" O TYR B 275 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N TYR B 275 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE B 276 " --> pdb=" O VAL B 58 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N VAL B 58 " --> pdb=" O ILE B 276 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL B 278 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ASP B 56 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL B 280 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N THR B 54 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N PHE B 282 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N TYR B 46 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 9.617A pdb=" N GLN B 290 " --> pdb=" O ARG B 44 " (cutoff:3.500A) removed outlier: 11.314A pdb=" N ARG B 44 " --> pdb=" O GLN B 290 " (cutoff:3.500A) removed outlier: 9.768A pdb=" N TYR B 292 " --> pdb=" O VAL B 42 " (cutoff:3.500A) removed outlier: 10.994A pdb=" N VAL B 42 " --> pdb=" O TYR B 292 " (cutoff:3.500A) removed outlier: 9.864A pdb=" N GLN B 294 " --> pdb=" O LYS B 40 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N LYS B 40 " --> pdb=" O GLN B 294 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU B 296 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N LEU B 38 " --> pdb=" O LEU B 296 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 38 through 60 current: chain 'B' and resid 322 through 326 Processing sheet with id=AC7, first strand: chain 'B' and resid 301 through 303 removed outlier: 5.979A pdb=" N ARG B 365 " --> pdb=" O VAL B 449 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AC9, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.434A pdb=" N GLU E 10 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TRP E 33 " --> pdb=" O ARG E 95 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LEU E 34 " --> pdb=" O ASP E 50 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ASP E 50 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.434A pdb=" N GLU E 10 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N CYS E 92 " --> pdb=" O TRP E 103 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N TRP E 103 " --> pdb=" O CYS E 92 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N THR E 94 " --> pdb=" O ASP E 101 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 4 through 6 Processing sheet with id=AD3, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.153A pdb=" N PHE G 11 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU G 33 " --> pdb=" O SER G 49 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N SER G 49 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.153A pdb=" N PHE G 11 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR G 97 " --> pdb=" O GLN G 90 " (cutoff:3.500A) 644 hydrogen bonds defined for protein. 1668 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: 3.04 Time building geometry restraints manager: 1.87 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: 4912 1.34 - 1.46: 3581 1.46 - 1.58: 6933 1.58 - 1.70: 0 1.70 - 1.82: 120 Bond restraints: 15546 Sorted by residual: bond pdb=" CB THR B 250 " pdb=" CG2 THR B 250 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.10e+00 bond pdb=" N GLU D 95 " pdb=" CA GLU D 95 " ideal model delta sigma weight residual 1.458 1.471 -0.014 1.42e-02 4.96e+03 9.06e-01 bond pdb=" CD GLU D 95 " pdb=" OE1 GLU D 95 " ideal model delta sigma weight residual 1.249 1.232 0.017 1.90e-02 2.77e+03 7.83e-01 bond pdb=" CB VAL B 449 " pdb=" CG1 VAL B 449 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.78e-01 bond pdb=" CB THR A 245 " pdb=" CG2 THR A 245 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.71e-01 ... (remaining 15541 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 20480 1.39 - 2.79: 496 2.79 - 4.18: 103 4.18 - 5.58: 23 5.58 - 6.97: 3 Bond angle restraints: 21105 Sorted by residual: angle pdb=" N GLU D 95 " pdb=" CA GLU D 95 " pdb=" CB GLU D 95 " ideal model delta sigma weight residual 110.42 115.36 -4.94 1.76e+00 3.23e-01 7.87e+00 angle pdb=" CA TRP F 96 " pdb=" CB TRP F 96 " pdb=" CG TRP F 96 " ideal model delta sigma weight residual 113.60 109.60 4.00 1.90e+00 2.77e-01 4.44e+00 angle pdb=" C VAL D 39 " pdb=" N LYS D 40 " pdb=" CA LYS D 40 " ideal model delta sigma weight residual 120.87 117.95 2.92 1.42e+00 4.96e-01 4.22e+00 angle pdb=" CA TRP L 96 " pdb=" CB TRP L 96 " pdb=" CG TRP L 96 " ideal model delta sigma weight residual 113.60 109.71 3.89 1.90e+00 2.77e-01 4.19e+00 angle pdb=" CA CYS A 192 " pdb=" CB CYS A 192 " pdb=" SG CYS A 192 " ideal model delta sigma weight residual 114.40 119.07 -4.67 2.30e+00 1.89e-01 4.12e+00 ... (remaining 21100 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 8767 17.95 - 35.90: 478 35.90 - 53.85: 96 53.85 - 71.80: 28 71.80 - 89.75: 18 Dihedral angle restraints: 9387 sinusoidal: 3642 harmonic: 5745 Sorted by residual: dihedral pdb=" CB CYS D 71 " pdb=" SG CYS D 71 " pdb=" SG CYS D 192 " pdb=" CB CYS D 192 " ideal model delta sinusoidal sigma weight residual -86.00 -142.13 56.13 1 1.00e+01 1.00e-02 4.25e+01 dihedral pdb=" CB CYS A 71 " pdb=" SG CYS A 71 " pdb=" SG CYS A 192 " pdb=" CB CYS A 192 " ideal model delta sinusoidal sigma weight residual -86.00 -134.66 48.66 1 1.00e+01 1.00e-02 3.26e+01 dihedral pdb=" CA CYS A 192 " pdb=" C CYS A 192 " pdb=" N LYS A 193 " pdb=" CA LYS A 193 " ideal model delta harmonic sigma weight residual 180.00 155.06 24.94 0 5.00e+00 4.00e-02 2.49e+01 ... (remaining 9384 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1896 0.047 - 0.095: 418 0.095 - 0.142: 155 0.142 - 0.190: 5 0.190 - 0.237: 1 Chirality restraints: 2475 Sorted by residual: chirality pdb=" CA GLU D 95 " pdb=" N GLU D 95 " pdb=" C GLU D 95 " pdb=" CB GLU D 95 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA CYS A 71 " pdb=" N CYS A 71 " pdb=" C CYS A 71 " pdb=" CB CYS A 71 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.33e-01 chirality pdb=" CA CYS A 192 " pdb=" N CYS A 192 " pdb=" C CYS A 192 " pdb=" CB CYS A 192 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.29e-01 ... (remaining 2472 not shown) Planarity restraints: 2670 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A 68 " 0.014 2.00e-02 2.50e+03 2.90e-02 8.40e+00 pdb=" C MET A 68 " -0.050 2.00e-02 2.50e+03 pdb=" O MET A 68 " 0.019 2.00e-02 2.50e+03 pdb=" N SER A 69 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 66 " -0.012 2.00e-02 2.50e+03 2.33e-02 5.41e+00 pdb=" C SER A 66 " 0.040 2.00e-02 2.50e+03 pdb=" O SER A 66 " -0.015 2.00e-02 2.50e+03 pdb=" N ASN A 67 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS H 23 " 0.009 2.00e-02 2.50e+03 1.89e-02 3.55e+00 pdb=" C LYS H 23 " -0.033 2.00e-02 2.50e+03 pdb=" O LYS H 23 " 0.012 2.00e-02 2.50e+03 pdb=" N ALA H 24 " 0.011 2.00e-02 2.50e+03 ... (remaining 2667 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 442 2.70 - 3.25: 14981 3.25 - 3.80: 25731 3.80 - 4.35: 34521 4.35 - 4.90: 57512 Nonbonded interactions: 133187 Sorted by model distance: nonbonded pdb=" OG SER B 50 " pdb=" OG1 THR B 286 " model vdw 2.156 3.040 nonbonded pdb=" O ASP H 50 " pdb=" OG1 THR H 57 " model vdw 2.242 3.040 nonbonded pdb=" NZ LYS D 148 " pdb=" OD2 ASP D 270 " model vdw 2.252 3.120 nonbonded pdb=" O MET B 61 " pdb=" OH TYR B 79 " model vdw 2.264 3.040 nonbonded pdb=" O MET A 61 " pdb=" OH TYR A 79 " model vdw 2.273 3.040 ... (remaining 133182 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'L' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.000 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: 0.270 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.750 Find NCS groups from input model: 0.270 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: 0.010 Load rotamer database and sin/cos tables:6.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 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 0.035 15570 Z= 0.142 Angle : 0.567 6.970 21153 Z= 0.308 Chirality : 0.045 0.237 2475 Planarity : 0.004 0.044 2670 Dihedral : 12.649 89.751 5637 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.06 % Allowed : 0.17 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.19), residues: 1959 helix: 0.47 (0.23), residues: 462 sheet: -0.31 (0.21), residues: 636 loop : 0.18 (0.21), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 375 TYR 0.031 0.002 TYR C 52 PHE 0.012 0.001 PHE F 11 TRP 0.016 0.002 TRP F 96 HIS 0.003 0.001 HIS B 372 Details of bonding type rmsd covalent geometry : bond 0.00326 (15546) covalent geometry : angle 0.56565 (21105) SS BOND : bond 0.00297 ( 24) SS BOND : angle 0.90528 ( 48) hydrogen bonds : bond 0.13592 ( 615) hydrogen bonds : angle 7.18830 ( 1668) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 291 time to evaluate : 0.672 Fit side-chains REVERT: D 209 ASP cc_start: 0.8023 (m-30) cc_final: 0.7716 (m-30) REVERT: L 27 GLU cc_start: 0.7645 (pt0) cc_final: 0.7289 (pt0) REVERT: F 27 GLU cc_start: 0.7638 (pt0) cc_final: 0.7233 (pt0) REVERT: B 415 THR cc_start: 0.8220 (p) cc_final: 0.7989 (p) outliers start: 1 outliers final: 0 residues processed: 291 average time/residue: 0.5667 time to fit residues: 182.4177 Evaluate side-chains 224 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 64 ASN D 351 ASN L 6 GLN L 38 GLN A 64 ASN A 305 ASN A 341 ASN F 6 GLN B 64 ASN B 217 ASN B 351 ASN G 6 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.131801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.109120 restraints weight = 16117.317| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.40 r_work: 0.3093 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15570 Z= 0.177 Angle : 0.568 6.735 21153 Z= 0.298 Chirality : 0.046 0.147 2475 Planarity : 0.004 0.044 2670 Dihedral : 5.093 24.833 2121 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.62 % Allowed : 8.90 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.19), residues: 1959 helix: 1.04 (0.24), residues: 465 sheet: -0.39 (0.22), residues: 588 loop : 0.07 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 244 TYR 0.040 0.002 TYR C 52 PHE 0.012 0.002 PHE D 235 TRP 0.019 0.002 TRP F 96 HIS 0.002 0.001 HIS B 372 Details of bonding type rmsd covalent geometry : bond 0.00434 (15546) covalent geometry : angle 0.56680 (21105) SS BOND : bond 0.00282 ( 24) SS BOND : angle 0.93888 ( 48) hydrogen bonds : bond 0.03860 ( 615) hydrogen bonds : angle 5.47271 ( 1668) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 248 time to evaluate : 0.485 Fit side-chains REVERT: D 209 ASP cc_start: 0.8222 (m-30) cc_final: 0.7789 (m-30) REVERT: D 251 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7530 (pt0) REVERT: D 380 ASN cc_start: 0.8563 (m-40) cc_final: 0.8357 (m-40) REVERT: D 406 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7226 (pt0) REVERT: H 40 ARG cc_start: 0.8339 (mtp180) cc_final: 0.8075 (mtp180) REVERT: A 156 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7775 (mp0) REVERT: A 388 ILE cc_start: 0.8685 (mm) cc_final: 0.8472 (mm) REVERT: A 406 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7306 (pt0) REVERT: C 58 ASN cc_start: 0.8279 (t0) cc_final: 0.8069 (t0) REVERT: B 139 LYS cc_start: 0.7976 (pttt) cc_final: 0.7338 (pptt) REVERT: B 258 GLU cc_start: 0.7415 (mm-30) cc_final: 0.7169 (mp0) REVERT: B 406 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7174 (pt0) REVERT: B 415 THR cc_start: 0.8581 (p) cc_final: 0.8321 (p) outliers start: 28 outliers final: 11 residues processed: 262 average time/residue: 0.5397 time to fit residues: 157.1113 Evaluate side-chains 234 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 218 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 406 GLU Chi-restraints excluded: chain D residue 440 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain G residue 9 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 159 optimal weight: 1.9990 chunk 143 optimal weight: 0.7980 chunk 139 optimal weight: 0.9980 chunk 160 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 chunk 190 optimal weight: 2.9990 chunk 184 optimal weight: 4.9990 chunk 149 optimal weight: 0.4980 chunk 93 optimal weight: 0.9980 chunk 161 optimal weight: 0.0570 chunk 82 optimal weight: 0.3980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.143140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.121111 restraints weight = 15533.764| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.56 r_work: 0.3232 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15570 Z= 0.114 Angle : 0.489 5.697 21153 Z= 0.257 Chirality : 0.044 0.142 2475 Planarity : 0.003 0.039 2670 Dihedral : 4.740 21.878 2121 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.08 % Allowed : 10.98 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.19), residues: 1959 helix: 1.38 (0.24), residues: 465 sheet: -0.39 (0.21), residues: 606 loop : 0.14 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 244 TYR 0.021 0.001 TYR H 52 PHE 0.010 0.001 PHE E 29 TRP 0.015 0.001 TRP F 96 HIS 0.002 0.000 HIS A 102 Details of bonding type rmsd covalent geometry : bond 0.00268 (15546) covalent geometry : angle 0.48878 (21105) SS BOND : bond 0.00167 ( 24) SS BOND : angle 0.69929 ( 48) hydrogen bonds : bond 0.03196 ( 615) hydrogen bonds : angle 5.10544 ( 1668) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 230 time to evaluate : 0.511 Fit side-chains revert: symmetry clash REVERT: D 209 ASP cc_start: 0.8290 (m-30) cc_final: 0.7876 (m-30) REVERT: D 406 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7395 (pt0) REVERT: H 40 ARG cc_start: 0.8222 (mtp180) cc_final: 0.7908 (mtp180) REVERT: A 156 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7752 (mp0) REVERT: A 406 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7430 (pt0) REVERT: C 80 MET cc_start: 0.9028 (OUTLIER) cc_final: 0.8792 (ttm) REVERT: B 153 SER cc_start: 0.8147 (m) cc_final: 0.7926 (p) REVERT: B 258 GLU cc_start: 0.7445 (mm-30) cc_final: 0.7217 (mp0) REVERT: B 375 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.6717 (mpp-170) REVERT: B 406 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7252 (pt0) outliers start: 36 outliers final: 10 residues processed: 254 average time/residue: 0.5715 time to fit residues: 160.4539 Evaluate side-chains 224 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 208 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 393 GLN Chi-restraints excluded: chain D residue 406 GLU Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 375 ARG Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 12 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 140 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 151 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 chunk 71 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 chunk 102 optimal weight: 0.0980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 HIS A 305 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.140915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.119678 restraints weight = 15529.131| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.49 r_work: 0.3109 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15570 Z= 0.127 Angle : 0.503 6.972 21153 Z= 0.262 Chirality : 0.044 0.143 2475 Planarity : 0.003 0.039 2670 Dihedral : 4.684 21.067 2121 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.37 % Allowed : 11.96 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.19), residues: 1959 helix: 1.57 (0.25), residues: 447 sheet: -0.35 (0.21), residues: 591 loop : 0.06 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 375 TYR 0.021 0.001 TYR H 52 PHE 0.010 0.001 PHE C 29 TRP 0.017 0.002 TRP F 96 HIS 0.003 0.001 HIS A 102 Details of bonding type rmsd covalent geometry : bond 0.00305 (15546) covalent geometry : angle 0.50155 (21105) SS BOND : bond 0.00186 ( 24) SS BOND : angle 0.82746 ( 48) hydrogen bonds : bond 0.03117 ( 615) hydrogen bonds : angle 4.90723 ( 1668) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 217 time to evaluate : 0.418 Fit side-chains revert: symmetry clash REVERT: D 209 ASP cc_start: 0.8239 (m-30) cc_final: 0.7934 (m-30) REVERT: D 251 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7524 (pt0) REVERT: D 406 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7396 (pt0) REVERT: H 40 ARG cc_start: 0.8245 (mtp180) cc_final: 0.7927 (mtp180) REVERT: H 46 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7740 (mt-10) REVERT: A 156 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7728 (mp0) REVERT: A 375 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.6631 (mpp-170) REVERT: A 388 ILE cc_start: 0.8623 (mm) cc_final: 0.8407 (mm) REVERT: A 406 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7393 (pt0) REVERT: C 80 MET cc_start: 0.9007 (OUTLIER) cc_final: 0.8771 (ttm) REVERT: B 139 LYS cc_start: 0.7843 (pttt) cc_final: 0.7149 (pptt) REVERT: B 375 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.6492 (mpp-170) REVERT: B 406 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7217 (pt0) REVERT: E 46 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7846 (mt-10) outliers start: 41 outliers final: 13 residues processed: 240 average time/residue: 0.5538 time to fit residues: 147.3004 Evaluate side-chains 231 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 208 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 392 CYS Chi-restraints excluded: chain D residue 393 GLN Chi-restraints excluded: chain D residue 406 GLU Chi-restraints excluded: chain D residue 440 SER Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 375 ARG Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 375 ARG Chi-restraints excluded: chain B residue 393 GLN Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 12 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 186 optimal weight: 3.9990 chunk 154 optimal weight: 0.7980 chunk 59 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 150 optimal weight: 0.9990 chunk 161 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 178 optimal weight: 0.0870 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 58 ASN A 102 HIS A 305 ASN B 314 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.147753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.126573 restraints weight = 15161.290| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.40 r_work: 0.3143 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15570 Z= 0.128 Angle : 0.497 5.737 21153 Z= 0.259 Chirality : 0.044 0.141 2475 Planarity : 0.003 0.042 2670 Dihedral : 4.633 20.488 2121 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.06 % Allowed : 11.79 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.19), residues: 1959 helix: 1.64 (0.25), residues: 447 sheet: -0.31 (0.21), residues: 591 loop : 0.06 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 375 TYR 0.018 0.001 TYR H 52 PHE 0.009 0.001 PHE C 29 TRP 0.016 0.002 TRP F 96 HIS 0.003 0.001 HIS A 102 Details of bonding type rmsd covalent geometry : bond 0.00308 (15546) covalent geometry : angle 0.49667 (21105) SS BOND : bond 0.00167 ( 24) SS BOND : angle 0.74722 ( 48) hydrogen bonds : bond 0.03041 ( 615) hydrogen bonds : angle 4.81602 ( 1668) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 214 time to evaluate : 0.642 Fit side-chains revert: symmetry clash REVERT: D 209 ASP cc_start: 0.8185 (m-30) cc_final: 0.7860 (m-30) REVERT: D 251 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7573 (pt0) REVERT: D 375 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.6468 (mpp-170) REVERT: D 406 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7381 (pt0) REVERT: H 40 ARG cc_start: 0.8230 (mtp180) cc_final: 0.7905 (mtp180) REVERT: H 46 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7703 (mt-10) REVERT: A 156 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7723 (mp0) REVERT: A 293 ILE cc_start: 0.9011 (OUTLIER) cc_final: 0.8722 (mm) REVERT: A 375 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.6589 (mpp-170) REVERT: A 388 ILE cc_start: 0.8606 (mm) cc_final: 0.8385 (mm) REVERT: A 406 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7326 (pt0) REVERT: C 46 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7829 (mt-10) REVERT: C 80 MET cc_start: 0.9005 (OUTLIER) cc_final: 0.8772 (ttm) REVERT: B 139 LYS cc_start: 0.7835 (pttt) cc_final: 0.7134 (pptt) REVERT: B 212 PHE cc_start: 0.7805 (m-80) cc_final: 0.7248 (t80) REVERT: B 293 ILE cc_start: 0.9038 (OUTLIER) cc_final: 0.8769 (mm) REVERT: B 375 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.6558 (mpp-170) REVERT: B 406 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7270 (pt0) REVERT: E 46 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7785 (mt-10) outliers start: 53 outliers final: 22 residues processed: 245 average time/residue: 0.5486 time to fit residues: 149.2685 Evaluate side-chains 244 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 208 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 375 ARG Chi-restraints excluded: chain D residue 392 CYS Chi-restraints excluded: chain D residue 393 GLN Chi-restraints excluded: chain D residue 406 GLU Chi-restraints excluded: chain D residue 440 SER Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 375 ARG Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 375 ARG Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 20 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 129 optimal weight: 0.5980 chunk 161 optimal weight: 1.9990 chunk 183 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 131 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 22 optimal weight: 0.3980 chunk 111 optimal weight: 0.0970 chunk 80 optimal weight: 3.9990 chunk 172 optimal weight: 0.0980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 HIS A 305 ASN B 51 ASN B 314 ASN G 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.149768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.128041 restraints weight = 15139.160| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.57 r_work: 0.3175 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 15570 Z= 0.103 Angle : 0.470 5.565 21153 Z= 0.244 Chirality : 0.043 0.141 2475 Planarity : 0.003 0.039 2670 Dihedral : 4.466 19.612 2121 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.60 % Allowed : 13.06 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.19), residues: 1959 helix: 1.68 (0.24), residues: 447 sheet: -0.27 (0.21), residues: 591 loop : 0.13 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 244 TYR 0.015 0.001 TYR F 91 PHE 0.009 0.001 PHE H 29 TRP 0.015 0.001 TRP F 96 HIS 0.002 0.000 HIS A 102 Details of bonding type rmsd covalent geometry : bond 0.00242 (15546) covalent geometry : angle 0.46904 (21105) SS BOND : bond 0.00282 ( 24) SS BOND : angle 0.66229 ( 48) hydrogen bonds : bond 0.02819 ( 615) hydrogen bonds : angle 4.65881 ( 1668) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 223 time to evaluate : 0.482 Fit side-chains revert: symmetry clash REVERT: D 251 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7595 (pt0) REVERT: D 293 ILE cc_start: 0.8974 (OUTLIER) cc_final: 0.8762 (mm) REVERT: D 406 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7406 (pt0) REVERT: H 40 ARG cc_start: 0.8145 (mtp180) cc_final: 0.7823 (mtp180) REVERT: A 156 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7675 (mp0) REVERT: A 388 ILE cc_start: 0.8587 (mm) cc_final: 0.8374 (mm) REVERT: A 406 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7359 (pt0) REVERT: C 46 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7831 (mt-10) REVERT: C 80 MET cc_start: 0.8993 (OUTLIER) cc_final: 0.8756 (ttm) REVERT: B 212 PHE cc_start: 0.7796 (m-80) cc_final: 0.7204 (t80) REVERT: B 422 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8372 (mt) REVERT: E 46 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7770 (mt-10) REVERT: G 38 GLN cc_start: 0.8696 (OUTLIER) cc_final: 0.8489 (tt0) REVERT: G 45 ARG cc_start: 0.8502 (ptm-80) cc_final: 0.8293 (ptt180) outliers start: 45 outliers final: 18 residues processed: 252 average time/residue: 0.5468 time to fit residues: 152.8437 Evaluate side-chains 241 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 213 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 293 ILE Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 392 CYS Chi-restraints excluded: chain D residue 393 GLN Chi-restraints excluded: chain D residue 406 GLU Chi-restraints excluded: chain D residue 440 SER Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 38 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 15 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 168 optimal weight: 3.9990 chunk 160 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 146 optimal weight: 1.9990 chunk 167 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 HIS A 305 ASN B 314 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.145068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.124021 restraints weight = 15076.201| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.39 r_work: 0.3144 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15570 Z= 0.157 Angle : 0.521 6.025 21153 Z= 0.270 Chirality : 0.045 0.142 2475 Planarity : 0.003 0.041 2670 Dihedral : 4.684 19.621 2121 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.24 % Allowed : 12.77 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.19), residues: 1959 helix: 1.61 (0.25), residues: 447 sheet: -0.28 (0.21), residues: 591 loop : 0.07 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 244 TYR 0.019 0.002 TYR H 52 PHE 0.010 0.001 PHE E 29 TRP 0.017 0.002 TRP F 96 HIS 0.003 0.001 HIS A 102 Details of bonding type rmsd covalent geometry : bond 0.00384 (15546) covalent geometry : angle 0.51992 (21105) SS BOND : bond 0.00258 ( 24) SS BOND : angle 0.99439 ( 48) hydrogen bonds : bond 0.03162 ( 615) hydrogen bonds : angle 4.80475 ( 1668) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 225 time to evaluate : 0.690 Fit side-chains revert: symmetry clash REVERT: D 152 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7278 (tt0) REVERT: D 209 ASP cc_start: 0.8186 (m-30) cc_final: 0.7854 (m-30) REVERT: D 251 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7669 (pt0) REVERT: D 293 ILE cc_start: 0.9066 (OUTLIER) cc_final: 0.8790 (mm) REVERT: D 375 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.6564 (mpp-170) REVERT: D 406 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7362 (pt0) REVERT: H 40 ARG cc_start: 0.8222 (mtp180) cc_final: 0.7898 (mtp180) REVERT: H 46 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7706 (mt-10) REVERT: L 45 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.8425 (ptt90) REVERT: A 156 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7633 (mp0) REVERT: A 293 ILE cc_start: 0.9019 (OUTLIER) cc_final: 0.8722 (mm) REVERT: A 373 VAL cc_start: 0.7765 (m) cc_final: 0.7428 (p) REVERT: A 388 ILE cc_start: 0.8641 (mm) cc_final: 0.8423 (mm) REVERT: A 406 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7363 (pt0) REVERT: C 46 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7833 (mt-10) REVERT: C 80 MET cc_start: 0.8993 (OUTLIER) cc_final: 0.8713 (ttm) REVERT: B 139 LYS cc_start: 0.7815 (pttt) cc_final: 0.7135 (pptt) REVERT: B 212 PHE cc_start: 0.7793 (m-80) cc_final: 0.7310 (t80) REVERT: B 293 ILE cc_start: 0.9048 (OUTLIER) cc_final: 0.8755 (mm) REVERT: B 406 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7304 (pt0) REVERT: E 46 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7759 (mt-10) REVERT: G 45 ARG cc_start: 0.8501 (ptm-80) cc_final: 0.8252 (ptt180) outliers start: 56 outliers final: 25 residues processed: 260 average time/residue: 0.5297 time to fit residues: 153.4110 Evaluate side-chains 254 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 215 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 293 ILE Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 375 ARG Chi-restraints excluded: chain D residue 392 CYS Chi-restraints excluded: chain D residue 393 GLN Chi-restraints excluded: chain D residue 406 GLU Chi-restraints excluded: chain D residue 440 SER Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 45 ARG Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 393 GLN Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 20 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 31 optimal weight: 1.9990 chunk 177 optimal weight: 0.8980 chunk 68 optimal weight: 0.3980 chunk 7 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 chunk 139 optimal weight: 1.9990 chunk 187 optimal weight: 0.0270 chunk 59 optimal weight: 0.0050 chunk 11 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 overall best weight: 0.4652 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 ASN B 51 ASN B 314 ASN G 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.146312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.125978 restraints weight = 15297.583| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.37 r_work: 0.3211 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15570 Z= 0.110 Angle : 0.478 5.847 21153 Z= 0.248 Chirality : 0.043 0.144 2475 Planarity : 0.003 0.039 2670 Dihedral : 4.498 19.904 2121 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.72 % Allowed : 13.34 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.19), residues: 1959 helix: 1.65 (0.25), residues: 447 sheet: -0.24 (0.21), residues: 591 loop : 0.14 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 244 TYR 0.016 0.001 TYR F 91 PHE 0.009 0.001 PHE H 29 TRP 0.021 0.001 TRP F 96 HIS 0.002 0.001 HIS A 102 Details of bonding type rmsd covalent geometry : bond 0.00260 (15546) covalent geometry : angle 0.47688 (21105) SS BOND : bond 0.00197 ( 24) SS BOND : angle 0.71912 ( 48) hydrogen bonds : bond 0.02845 ( 615) hydrogen bonds : angle 4.67965 ( 1668) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 220 time to evaluate : 0.418 Fit side-chains revert: symmetry clash REVERT: D 152 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7351 (tt0) REVERT: D 209 ASP cc_start: 0.8240 (m-30) cc_final: 0.7899 (m-30) REVERT: D 251 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7487 (pt0) REVERT: D 293 ILE cc_start: 0.9025 (OUTLIER) cc_final: 0.8793 (mm) REVERT: D 375 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.6540 (mpp-170) REVERT: D 406 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7446 (pt0) REVERT: H 40 ARG cc_start: 0.8190 (mtp180) cc_final: 0.7908 (mtp180) REVERT: H 46 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7708 (mt-10) REVERT: A 156 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7585 (mp0) REVERT: A 293 ILE cc_start: 0.9016 (OUTLIER) cc_final: 0.8728 (mm) REVERT: A 388 ILE cc_start: 0.8690 (mm) cc_final: 0.8475 (mm) REVERT: A 393 GLN cc_start: 0.7991 (OUTLIER) cc_final: 0.7657 (tt0) REVERT: A 406 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7411 (pt0) REVERT: C 46 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7803 (mt-10) REVERT: C 80 MET cc_start: 0.8954 (OUTLIER) cc_final: 0.8723 (ttm) REVERT: B 212 PHE cc_start: 0.7807 (m-80) cc_final: 0.7395 (t80) REVERT: B 293 ILE cc_start: 0.9051 (OUTLIER) cc_final: 0.8786 (mm) REVERT: B 406 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7376 (pt0) REVERT: E 46 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7763 (mt-10) REVERT: G 38 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.8454 (tt0) REVERT: G 45 ARG cc_start: 0.8491 (ptm-80) cc_final: 0.8272 (ptt180) outliers start: 47 outliers final: 22 residues processed: 250 average time/residue: 0.5543 time to fit residues: 153.3367 Evaluate side-chains 245 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 208 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 293 ILE Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 375 ARG Chi-restraints excluded: chain D residue 392 CYS Chi-restraints excluded: chain D residue 406 GLU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 393 GLN Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 38 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 124 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 168 optimal weight: 0.0980 chunk 14 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 165 optimal weight: 0.5980 chunk 180 optimal weight: 0.8980 chunk 189 optimal weight: 6.9990 chunk 146 optimal weight: 0.8980 chunk 100 optimal weight: 0.3980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 ASN B 314 ASN G 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.148594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.126753 restraints weight = 15024.931| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.53 r_work: 0.3182 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15570 Z= 0.115 Angle : 0.486 5.702 21153 Z= 0.252 Chirality : 0.043 0.142 2475 Planarity : 0.003 0.054 2670 Dihedral : 4.486 19.824 2121 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.37 % Allowed : 13.75 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.19), residues: 1959 helix: 1.67 (0.24), residues: 447 sheet: -0.24 (0.21), residues: 591 loop : 0.15 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 13 TYR 0.016 0.001 TYR F 91 PHE 0.009 0.001 PHE H 29 TRP 0.021 0.001 TRP F 96 HIS 0.003 0.001 HIS A 102 Details of bonding type rmsd covalent geometry : bond 0.00275 (15546) covalent geometry : angle 0.48510 (21105) SS BOND : bond 0.00199 ( 24) SS BOND : angle 0.69379 ( 48) hydrogen bonds : bond 0.02880 ( 615) hydrogen bonds : angle 4.65542 ( 1668) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 216 time to evaluate : 0.636 Fit side-chains revert: symmetry clash REVERT: D 152 GLU cc_start: 0.7495 (mt-10) cc_final: 0.7247 (tt0) REVERT: D 156 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7797 (tp30) REVERT: D 244 ARG cc_start: 0.8676 (ttm110) cc_final: 0.8432 (ttp-110) REVERT: D 251 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7472 (pt0) REVERT: D 293 ILE cc_start: 0.9009 (OUTLIER) cc_final: 0.8778 (mm) REVERT: D 375 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.6511 (mpp-170) REVERT: D 406 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7380 (pt0) REVERT: H 40 ARG cc_start: 0.8122 (mtp180) cc_final: 0.7816 (mtp180) REVERT: H 46 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7663 (mt-10) REVERT: L 45 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.8417 (ptt90) REVERT: A 156 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7500 (mp0) REVERT: A 293 ILE cc_start: 0.9001 (OUTLIER) cc_final: 0.8705 (mm) REVERT: A 388 ILE cc_start: 0.8605 (mm) cc_final: 0.8388 (mm) REVERT: A 393 GLN cc_start: 0.7870 (tt0) cc_final: 0.7516 (tt0) REVERT: A 406 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7333 (pt0) REVERT: C 80 MET cc_start: 0.8980 (OUTLIER) cc_final: 0.8742 (ttm) REVERT: B 212 PHE cc_start: 0.7787 (m-80) cc_final: 0.7259 (t80) REVERT: B 293 ILE cc_start: 0.9033 (OUTLIER) cc_final: 0.8756 (mm) REVERT: B 406 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7319 (pt0) REVERT: E 46 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7745 (mt-10) REVERT: G 38 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.8448 (tt0) REVERT: G 45 ARG cc_start: 0.8500 (ptm-80) cc_final: 0.8280 (ptt180) REVERT: G 61 ARG cc_start: 0.8528 (ptt-90) cc_final: 0.8263 (ptt-90) outliers start: 41 outliers final: 23 residues processed: 244 average time/residue: 0.5685 time to fit residues: 153.3130 Evaluate side-chains 245 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 208 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 293 ILE Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 375 ARG Chi-restraints excluded: chain D residue 392 CYS Chi-restraints excluded: chain D residue 406 GLU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 45 ARG Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 393 GLN Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 38 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 47 optimal weight: 0.0970 chunk 43 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 132 optimal weight: 0.9990 chunk 156 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 108 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 125 optimal weight: 0.8980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 ASN B 314 ASN G 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.147404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.125425 restraints weight = 15196.788| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.55 r_work: 0.3161 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15570 Z= 0.134 Angle : 0.505 6.186 21153 Z= 0.261 Chirality : 0.044 0.142 2475 Planarity : 0.003 0.059 2670 Dihedral : 4.548 19.733 2121 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.60 % Allowed : 13.69 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.19), residues: 1959 helix: 1.64 (0.25), residues: 447 sheet: -0.26 (0.21), residues: 591 loop : 0.12 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 13 TYR 0.016 0.002 TYR L 91 PHE 0.009 0.001 PHE E 29 TRP 0.025 0.002 TRP F 96 HIS 0.003 0.001 HIS A 102 Details of bonding type rmsd covalent geometry : bond 0.00325 (15546) covalent geometry : angle 0.50389 (21105) SS BOND : bond 0.00217 ( 24) SS BOND : angle 0.74868 ( 48) hydrogen bonds : bond 0.02981 ( 615) hydrogen bonds : angle 4.69478 ( 1668) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 211 time to evaluate : 0.462 Fit side-chains revert: symmetry clash REVERT: D 152 GLU cc_start: 0.7508 (mt-10) cc_final: 0.7263 (tt0) REVERT: D 209 ASP cc_start: 0.8210 (m-30) cc_final: 0.7900 (m-30) REVERT: D 244 ARG cc_start: 0.8686 (ttm110) cc_final: 0.8448 (ttp-110) REVERT: D 251 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7494 (pt0) REVERT: D 293 ILE cc_start: 0.9025 (OUTLIER) cc_final: 0.8770 (mm) REVERT: D 375 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.6710 (mpp-170) REVERT: D 406 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7390 (pt0) REVERT: H 40 ARG cc_start: 0.8154 (mtp180) cc_final: 0.7847 (mtp180) REVERT: H 46 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7696 (mt-10) REVERT: L 45 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.8416 (ptt90) REVERT: A 156 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7525 (mp0) REVERT: A 293 ILE cc_start: 0.9007 (OUTLIER) cc_final: 0.8730 (mm) REVERT: A 373 VAL cc_start: 0.7611 (m) cc_final: 0.7258 (p) REVERT: A 388 ILE cc_start: 0.8613 (mm) cc_final: 0.8392 (mm) REVERT: A 393 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.7573 (tt0) REVERT: A 406 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7341 (pt0) REVERT: C 46 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7802 (mt-10) REVERT: C 80 MET cc_start: 0.8988 (OUTLIER) cc_final: 0.8761 (ttm) REVERT: B 212 PHE cc_start: 0.7792 (m-80) cc_final: 0.7265 (t80) REVERT: B 293 ILE cc_start: 0.9017 (OUTLIER) cc_final: 0.8736 (mm) REVERT: B 406 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7329 (pt0) REVERT: E 46 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7782 (mt-10) REVERT: G 38 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.8499 (tt0) REVERT: G 45 ARG cc_start: 0.8521 (ptm-80) cc_final: 0.8287 (ptt180) REVERT: G 61 ARG cc_start: 0.8542 (ptt-90) cc_final: 0.8329 (ptt-90) outliers start: 45 outliers final: 26 residues processed: 242 average time/residue: 0.5956 time to fit residues: 159.1916 Evaluate side-chains 250 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 208 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 293 ILE Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 375 ARG Chi-restraints excluded: chain D residue 392 CYS Chi-restraints excluded: chain D residue 393 GLN Chi-restraints excluded: chain D residue 406 GLU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 45 ARG Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 393 GLN Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 38 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 58 optimal weight: 0.4980 chunk 69 optimal weight: 0.9990 chunk 139 optimal weight: 1.9990 chunk 174 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 158 optimal weight: 0.8980 chunk 2 optimal weight: 0.4980 chunk 37 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 HIS A 305 ASN B 314 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.146766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.124798 restraints weight = 15050.881| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.54 r_work: 0.3139 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15570 Z= 0.143 Angle : 0.515 6.605 21153 Z= 0.266 Chirality : 0.044 0.142 2475 Planarity : 0.003 0.055 2670 Dihedral : 4.603 19.779 2121 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.48 % Allowed : 13.92 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.19), residues: 1959 helix: 1.62 (0.25), residues: 447 sheet: -0.28 (0.21), residues: 591 loop : 0.10 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 13 TYR 0.017 0.002 TYR G 91 PHE 0.009 0.001 PHE C 29 TRP 0.023 0.002 TRP F 96 HIS 0.003 0.001 HIS A 102 Details of bonding type rmsd covalent geometry : bond 0.00348 (15546) covalent geometry : angle 0.51413 (21105) SS BOND : bond 0.00222 ( 24) SS BOND : angle 0.75966 ( 48) hydrogen bonds : bond 0.03046 ( 615) hydrogen bonds : angle 4.73433 ( 1668) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5312.10 seconds wall clock time: 91 minutes 18.48 seconds (5478.48 seconds total)