Starting phenix.real_space_refine on Sun Aug 24 12:31:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dzg_27797/08_2025/8dzg_27797.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dzg_27797/08_2025/8dzg_27797.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dzg_27797/08_2025/8dzg_27797.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dzg_27797/08_2025/8dzg_27797.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dzg_27797/08_2025/8dzg_27797.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dzg_27797/08_2025/8dzg_27797.map" } resolution = 3.1 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= 0.002 sd= 0.077 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: 7 Type Number sf(0) Gaussians Zn 6 6.06 5 P 12 5.49 5 Mg 6 5.21 5 S 84 5.16 5 C 12396 2.51 5 N 3486 2.21 5 O 3768 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19758 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3264 Classifications: {'peptide': 420} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 15, 'TRANS': 404} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 1, 'ASP:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2249 SG CYS A 403 91.228 129.664 31.801 1.00 76.41 S ATOM 2269 SG CYS A 406 94.765 130.815 30.837 1.00 85.65 S ATOM 2553 SG CYS A 445 92.667 132.874 33.325 1.00 94.65 S ATOM 2559 SG CYS A 446 94.089 129.607 34.341 1.00 90.08 S Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 2.35, per 1000 atoms: 0.12 Number of scatterers: 19758 At special positions: 0 Unit cell: (147.96, 143.64, 81, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 6 29.99 S 84 16.00 P 12 15.00 Mg 6 11.99 O 3768 8.00 N 3486 7.00 C 12396 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.62 Conformation dependent library (CDL) restraints added in 836.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 603 " pdb="ZN ZN A 603 " - pdb=" SG CYS A 446 " pdb="ZN ZN A 603 " - pdb=" SG CYS A 445 " pdb="ZN ZN A 603 " - pdb=" SG CYS A 406 " pdb="ZN ZN A 603 " - pdb=" SG CYS A 403 " pdb=" ZN B 603 " pdb="ZN ZN B 603 " - pdb=" SG CYS B 446 " pdb="ZN ZN B 603 " - pdb=" SG CYS B 445 " pdb="ZN ZN B 603 " - pdb=" SG CYS B 406 " pdb="ZN ZN B 603 " - pdb=" SG CYS B 403 " pdb=" ZN C 603 " pdb="ZN ZN C 603 " - pdb=" SG CYS C 446 " pdb="ZN ZN C 603 " - pdb=" SG CYS C 445 " pdb="ZN ZN C 603 " - pdb=" SG CYS C 406 " pdb="ZN ZN C 603 " - pdb=" SG CYS C 403 " pdb=" ZN D 603 " pdb="ZN ZN D 603 " - pdb=" SG CYS D 446 " pdb="ZN ZN D 603 " - pdb=" SG CYS D 445 " pdb="ZN ZN D 603 " - pdb=" SG CYS D 406 " pdb="ZN ZN D 603 " - pdb=" SG CYS D 403 " pdb=" ZN E 603 " pdb="ZN ZN E 603 " - pdb=" SG CYS E 446 " pdb="ZN ZN E 603 " - pdb=" SG CYS E 445 " pdb="ZN ZN E 603 " - pdb=" SG CYS E 406 " pdb="ZN ZN E 603 " - pdb=" SG CYS E 403 " pdb=" ZN F 603 " pdb="ZN ZN F 603 " - pdb=" SG CYS F 446 " pdb="ZN ZN F 603 " - pdb=" SG CYS F 445 " pdb="ZN ZN F 603 " - pdb=" SG CYS F 406 " pdb="ZN ZN F 603 " - pdb=" SG CYS F 403 " Number of angles added : 36 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4740 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 12 sheets defined 44.6% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 107 through 122 removed outlier: 3.644A pdb=" N ALA A 111 " --> pdb=" O VAL A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 166 Processing helix chain 'A' and resid 238 through 251 Processing helix chain 'A' and resid 265 through 281 removed outlier: 3.545A pdb=" N THR A 269 " --> pdb=" O GLY A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 328 Processing helix chain 'A' and resid 341 through 353 Processing helix chain 'A' and resid 369 through 378 Processing helix chain 'A' and resid 380 through 386 removed outlier: 3.616A pdb=" N LEU A 384 " --> pdb=" O ASP A 380 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASP A 386 " --> pdb=" O PHE A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 417 Processing helix chain 'A' and resid 421 through 429 Processing helix chain 'A' and resid 463 through 472 Processing helix chain 'A' and resid 474 through 485 Processing helix chain 'A' and resid 490 through 502 Processing helix chain 'A' and resid 505 through 513 Processing helix chain 'A' and resid 515 through 519 removed outlier: 3.513A pdb=" N ILE A 519 " --> pdb=" O ILE A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 534 Processing helix chain 'B' and resid 108 through 122 Processing helix chain 'B' and resid 153 through 166 Processing helix chain 'B' and resid 238 through 251 Processing helix chain 'B' and resid 265 through 281 removed outlier: 3.544A pdb=" N THR B 269 " --> pdb=" O GLY B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 328 Processing helix chain 'B' and resid 341 through 353 Processing helix chain 'B' and resid 369 through 378 Processing helix chain 'B' and resid 380 through 386 removed outlier: 3.615A pdb=" N LEU B 384 " --> pdb=" O ASP B 380 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASP B 386 " --> pdb=" O PHE B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 417 Processing helix chain 'B' and resid 421 through 429 Processing helix chain 'B' and resid 463 through 472 Processing helix chain 'B' and resid 474 through 485 Processing helix chain 'B' and resid 490 through 502 Processing helix chain 'B' and resid 505 through 513 Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.512A pdb=" N ILE B 519 " --> pdb=" O ILE B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 534 Processing helix chain 'C' and resid 108 through 122 Processing helix chain 'C' and resid 153 through 166 Processing helix chain 'C' and resid 238 through 251 Processing helix chain 'C' and resid 265 through 281 removed outlier: 3.545A pdb=" N THR C 269 " --> pdb=" O GLY C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 328 Processing helix chain 'C' and resid 341 through 353 Processing helix chain 'C' and resid 369 through 378 Processing helix chain 'C' and resid 380 through 386 removed outlier: 3.616A pdb=" N LEU C 384 " --> pdb=" O ASP C 380 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASP C 386 " --> pdb=" O PHE C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 417 Processing helix chain 'C' and resid 421 through 429 Processing helix chain 'C' and resid 463 through 472 Processing helix chain 'C' and resid 474 through 485 Processing helix chain 'C' and resid 490 through 502 Processing helix chain 'C' and resid 505 through 513 Processing helix chain 'C' and resid 515 through 519 removed outlier: 3.512A pdb=" N ILE C 519 " --> pdb=" O ILE C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 534 Processing helix chain 'D' and resid 108 through 122 Processing helix chain 'D' and resid 153 through 166 Processing helix chain 'D' and resid 238 through 251 Processing helix chain 'D' and resid 265 through 281 removed outlier: 3.545A pdb=" N THR D 269 " --> pdb=" O GLY D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 328 Processing helix chain 'D' and resid 341 through 353 Processing helix chain 'D' and resid 369 through 378 Processing helix chain 'D' and resid 380 through 386 removed outlier: 3.616A pdb=" N LEU D 384 " --> pdb=" O ASP D 380 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASP D 386 " --> pdb=" O PHE D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 417 Processing helix chain 'D' and resid 421 through 429 Processing helix chain 'D' and resid 463 through 472 Processing helix chain 'D' and resid 474 through 485 Processing helix chain 'D' and resid 490 through 502 Processing helix chain 'D' and resid 505 through 513 Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.513A pdb=" N ILE D 519 " --> pdb=" O ILE D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 534 Processing helix chain 'E' and resid 108 through 122 Processing helix chain 'E' and resid 153 through 166 Processing helix chain 'E' and resid 238 through 251 Processing helix chain 'E' and resid 265 through 281 removed outlier: 3.545A pdb=" N THR E 269 " --> pdb=" O GLY E 265 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 328 Processing helix chain 'E' and resid 341 through 353 Processing helix chain 'E' and resid 369 through 378 Processing helix chain 'E' and resid 380 through 386 removed outlier: 3.616A pdb=" N LEU E 384 " --> pdb=" O ASP E 380 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASP E 386 " --> pdb=" O PHE E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 417 Processing helix chain 'E' and resid 421 through 429 Processing helix chain 'E' and resid 463 through 472 Processing helix chain 'E' and resid 474 through 485 Processing helix chain 'E' and resid 490 through 502 Processing helix chain 'E' and resid 505 through 513 Processing helix chain 'E' and resid 515 through 519 removed outlier: 3.512A pdb=" N ILE E 519 " --> pdb=" O ILE E 516 " (cutoff:3.500A) Processing helix chain 'E' and resid 520 through 534 Processing helix chain 'F' and resid 108 through 122 Processing helix chain 'F' and resid 153 through 166 Processing helix chain 'F' and resid 238 through 251 Processing helix chain 'F' and resid 265 through 281 removed outlier: 3.545A pdb=" N THR F 269 " --> pdb=" O GLY F 265 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 328 Processing helix chain 'F' and resid 341 through 353 Processing helix chain 'F' and resid 369 through 378 Processing helix chain 'F' and resid 380 through 386 removed outlier: 3.615A pdb=" N LEU F 384 " --> pdb=" O ASP F 380 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASP F 386 " --> pdb=" O PHE F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 409 through 417 Processing helix chain 'F' and resid 421 through 429 Processing helix chain 'F' and resid 463 through 472 Processing helix chain 'F' and resid 474 through 485 Processing helix chain 'F' and resid 490 through 502 Processing helix chain 'F' and resid 505 through 513 Processing helix chain 'F' and resid 515 through 519 removed outlier: 3.512A pdb=" N ILE F 519 " --> pdb=" O ILE F 516 " (cutoff:3.500A) Processing helix chain 'F' and resid 520 through 534 Processing sheet with id=AA1, first strand: chain 'A' and resid 144 through 152 removed outlier: 6.711A pdb=" N ILE A 137 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLN A 150 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ALA A 135 " --> pdb=" O GLN A 150 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASP A 125 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N TYR A 213 " --> pdb=" O PHE A 204 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE A 204 " --> pdb=" O TYR A 213 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE A 215 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU A 202 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ARG A 217 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VAL A 200 " --> pdb=" O ARG A 217 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU A 219 " --> pdb=" O GLN A 198 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 303 through 304 removed outlier: 8.194A pdb=" N LEU A 304 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N SER A 289 " --> pdb=" O LEU A 304 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N SER A 361 " --> pdb=" O PRO A 336 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLY A 254 " --> pdb=" O VAL A 358 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N THR A 360 " --> pdb=" O GLY A 254 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASN A 256 " --> pdb=" O THR A 360 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N LEU A 362 " --> pdb=" O ASN A 256 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ILE A 258 " --> pdb=" O LEU A 362 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ILE A 255 " --> pdb=" O ILE A 390 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY A 392 " --> pdb=" O ILE A 255 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 144 through 152 removed outlier: 6.712A pdb=" N ILE B 137 " --> pdb=" O LEU B 148 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLN B 150 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ALA B 135 " --> pdb=" O GLN B 150 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASP B 125 " --> pdb=" O ARG B 140 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N TYR B 213 " --> pdb=" O PHE B 204 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE B 204 " --> pdb=" O TYR B 213 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE B 215 " --> pdb=" O LEU B 202 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU B 202 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ARG B 217 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL B 200 " --> pdb=" O ARG B 217 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU B 219 " --> pdb=" O GLN B 198 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 303 through 304 removed outlier: 8.194A pdb=" N LEU B 304 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N SER B 289 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N SER B 361 " --> pdb=" O PRO B 336 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLY B 254 " --> pdb=" O VAL B 358 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N THR B 360 " --> pdb=" O GLY B 254 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASN B 256 " --> pdb=" O THR B 360 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N LEU B 362 " --> pdb=" O ASN B 256 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ILE B 258 " --> pdb=" O LEU B 362 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ILE B 255 " --> pdb=" O ILE B 390 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY B 392 " --> pdb=" O ILE B 255 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 144 through 152 removed outlier: 6.712A pdb=" N ILE C 137 " --> pdb=" O LEU C 148 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLN C 150 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ALA C 135 " --> pdb=" O GLN C 150 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASP C 125 " --> pdb=" O ARG C 140 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N TYR C 213 " --> pdb=" O PHE C 204 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N PHE C 204 " --> pdb=" O TYR C 213 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE C 215 " --> pdb=" O LEU C 202 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU C 202 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ARG C 217 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VAL C 200 " --> pdb=" O ARG C 217 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LEU C 219 " --> pdb=" O GLN C 198 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 303 through 304 removed outlier: 8.194A pdb=" N LEU C 304 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N SER C 289 " --> pdb=" O LEU C 304 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N SER C 361 " --> pdb=" O PRO C 336 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLY C 254 " --> pdb=" O VAL C 358 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N THR C 360 " --> pdb=" O GLY C 254 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASN C 256 " --> pdb=" O THR C 360 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N LEU C 362 " --> pdb=" O ASN C 256 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ILE C 258 " --> pdb=" O LEU C 362 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ILE C 255 " --> pdb=" O ILE C 390 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY C 392 " --> pdb=" O ILE C 255 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 144 through 152 removed outlier: 6.711A pdb=" N ILE D 137 " --> pdb=" O LEU D 148 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLN D 150 " --> pdb=" O ALA D 135 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ALA D 135 " --> pdb=" O GLN D 150 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASP D 125 " --> pdb=" O ARG D 140 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N TYR D 213 " --> pdb=" O PHE D 204 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N PHE D 204 " --> pdb=" O TYR D 213 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE D 215 " --> pdb=" O LEU D 202 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU D 202 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ARG D 217 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VAL D 200 " --> pdb=" O ARG D 217 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU D 219 " --> pdb=" O GLN D 198 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 303 through 304 removed outlier: 8.194A pdb=" N LEU D 304 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N SER D 289 " --> pdb=" O LEU D 304 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N SER D 361 " --> pdb=" O PRO D 336 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLY D 254 " --> pdb=" O VAL D 358 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N THR D 360 " --> pdb=" O GLY D 254 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ASN D 256 " --> pdb=" O THR D 360 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N LEU D 362 " --> pdb=" O ASN D 256 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ILE D 258 " --> pdb=" O LEU D 362 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ILE D 255 " --> pdb=" O ILE D 390 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY D 392 " --> pdb=" O ILE D 255 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 144 through 152 removed outlier: 6.712A pdb=" N ILE E 137 " --> pdb=" O LEU E 148 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLN E 150 " --> pdb=" O ALA E 135 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ALA E 135 " --> pdb=" O GLN E 150 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASP E 125 " --> pdb=" O ARG E 140 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N TYR E 213 " --> pdb=" O PHE E 204 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE E 204 " --> pdb=" O TYR E 213 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE E 215 " --> pdb=" O LEU E 202 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU E 202 " --> pdb=" O ILE E 215 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ARG E 217 " --> pdb=" O VAL E 200 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N VAL E 200 " --> pdb=" O ARG E 217 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU E 219 " --> pdb=" O GLN E 198 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 303 through 304 removed outlier: 8.194A pdb=" N LEU E 304 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N SER E 289 " --> pdb=" O LEU E 304 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N SER E 361 " --> pdb=" O PRO E 336 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLY E 254 " --> pdb=" O VAL E 358 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N THR E 360 " --> pdb=" O GLY E 254 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASN E 256 " --> pdb=" O THR E 360 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N LEU E 362 " --> pdb=" O ASN E 256 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ILE E 258 " --> pdb=" O LEU E 362 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ILE E 255 " --> pdb=" O ILE E 390 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY E 392 " --> pdb=" O ILE E 255 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 144 through 152 removed outlier: 6.712A pdb=" N ILE F 137 " --> pdb=" O LEU F 148 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLN F 150 " --> pdb=" O ALA F 135 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ALA F 135 " --> pdb=" O GLN F 150 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASP F 125 " --> pdb=" O ARG F 140 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N TYR F 213 " --> pdb=" O PHE F 204 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE F 204 " --> pdb=" O TYR F 213 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE F 215 " --> pdb=" O LEU F 202 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU F 202 " --> pdb=" O ILE F 215 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ARG F 217 " --> pdb=" O VAL F 200 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N VAL F 200 " --> pdb=" O ARG F 217 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU F 219 " --> pdb=" O GLN F 198 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 303 through 304 removed outlier: 8.194A pdb=" N LEU F 304 " --> pdb=" O ILE F 287 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N SER F 289 " --> pdb=" O LEU F 304 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N SER F 361 " --> pdb=" O PRO F 336 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLY F 254 " --> pdb=" O VAL F 358 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N THR F 360 " --> pdb=" O GLY F 254 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASN F 256 " --> pdb=" O THR F 360 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N LEU F 362 " --> pdb=" O ASN F 256 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ILE F 258 " --> pdb=" O LEU F 362 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ILE F 255 " --> pdb=" O ILE F 390 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY F 392 " --> pdb=" O ILE F 255 " (cutoff:3.500A) 960 hydrogen bonds defined for protein. 2808 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.63 Time building geometry restraints manager: 2.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6624 1.34 - 1.46: 3258 1.46 - 1.58: 10050 1.58 - 1.69: 24 1.69 - 1.81: 132 Bond restraints: 20088 Sorted by residual: bond pdb=" C1' ADP F 602 " pdb=" C2' ADP F 602 " ideal model delta sigma weight residual 1.524 1.289 0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" C1' ADP D 602 " pdb=" C2' ADP D 602 " ideal model delta sigma weight residual 1.524 1.289 0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" C1' ADP E 602 " pdb=" C2' ADP E 602 " ideal model delta sigma weight residual 1.524 1.289 0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" C1' ADP B 602 " pdb=" C2' ADP B 602 " ideal model delta sigma weight residual 1.524 1.289 0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" C1' ADP A 602 " pdb=" C2' ADP A 602 " ideal model delta sigma weight residual 1.524 1.290 0.234 2.00e-02 2.50e+03 1.37e+02 ... (remaining 20083 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 26861 2.38 - 4.77: 247 4.77 - 7.15: 48 7.15 - 9.53: 18 9.53 - 11.91: 36 Bond angle restraints: 27210 Sorted by residual: angle pdb=" C SER E 170 " pdb=" N ASP E 171 " pdb=" CA ASP E 171 " ideal model delta sigma weight residual 121.54 130.53 -8.99 1.91e+00 2.74e-01 2.22e+01 angle pdb=" C SER B 170 " pdb=" N ASP B 171 " pdb=" CA ASP B 171 " ideal model delta sigma weight residual 121.54 130.53 -8.99 1.91e+00 2.74e-01 2.21e+01 angle pdb=" C SER C 170 " pdb=" N ASP C 171 " pdb=" CA ASP C 171 " ideal model delta sigma weight residual 121.54 130.52 -8.98 1.91e+00 2.74e-01 2.21e+01 angle pdb=" C SER F 170 " pdb=" N ASP F 171 " pdb=" CA ASP F 171 " ideal model delta sigma weight residual 121.54 130.52 -8.98 1.91e+00 2.74e-01 2.21e+01 angle pdb=" C SER A 170 " pdb=" N ASP A 171 " pdb=" CA ASP A 171 " ideal model delta sigma weight residual 121.54 130.51 -8.97 1.91e+00 2.74e-01 2.20e+01 ... (remaining 27205 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.91: 11774 32.91 - 65.82: 436 65.82 - 98.73: 24 98.73 - 131.64: 6 131.64 - 164.54: 6 Dihedral angle restraints: 12246 sinusoidal: 4914 harmonic: 7332 Sorted by residual: dihedral pdb=" C2' ADP F 602 " pdb=" C1' ADP F 602 " pdb=" N9 ADP F 602 " pdb=" C4 ADP F 602 " ideal model delta sinusoidal sigma weight residual 91.55 -73.00 164.54 1 2.00e+01 2.50e-03 4.71e+01 dihedral pdb=" C2' ADP E 602 " pdb=" C1' ADP E 602 " pdb=" N9 ADP E 602 " pdb=" C4 ADP E 602 " ideal model delta sinusoidal sigma weight residual 91.55 -72.99 164.53 1 2.00e+01 2.50e-03 4.71e+01 dihedral pdb=" C2' ADP C 602 " pdb=" C1' ADP C 602 " pdb=" N9 ADP C 602 " pdb=" C4 ADP C 602 " ideal model delta sinusoidal sigma weight residual 91.55 -72.98 164.52 1 2.00e+01 2.50e-03 4.71e+01 ... (remaining 12243 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1790 0.027 - 0.055: 758 0.055 - 0.082: 320 0.082 - 0.110: 133 0.110 - 0.137: 119 Chirality restraints: 3120 Sorted by residual: chirality pdb=" CA ILE E 258 " pdb=" N ILE E 258 " pdb=" C ILE E 258 " pdb=" CB ILE E 258 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.70e-01 chirality pdb=" CA ILE B 258 " pdb=" N ILE B 258 " pdb=" C ILE B 258 " pdb=" CB ILE B 258 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.47e-01 chirality pdb=" CA ILE A 258 " pdb=" N ILE A 258 " pdb=" C ILE A 258 " pdb=" CB ILE A 258 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.45e-01 ... (remaining 3117 not shown) Planarity restraints: 3486 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 526 " -0.012 2.00e-02 2.50e+03 1.55e-02 4.82e+00 pdb=" CG TYR F 526 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR F 526 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR F 526 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR F 526 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR F 526 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR F 526 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR F 526 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 193 " -0.036 5.00e-02 4.00e+02 5.44e-02 4.74e+00 pdb=" N PRO D 194 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO D 194 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 194 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 526 " -0.011 2.00e-02 2.50e+03 1.54e-02 4.74e+00 pdb=" CG TYR E 526 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR E 526 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR E 526 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR E 526 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR E 526 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR E 526 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR E 526 " 0.001 2.00e-02 2.50e+03 ... (remaining 3483 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 162 2.64 - 3.21: 16546 3.21 - 3.77: 28979 3.77 - 4.34: 39696 4.34 - 4.90: 68339 Nonbonded interactions: 153722 Sorted by model distance: nonbonded pdb="MG MG D 601 " pdb=" O2B ADP D 602 " model vdw 2.076 2.170 nonbonded pdb="MG MG C 601 " pdb=" O2B ADP C 602 " model vdw 2.076 2.170 nonbonded pdb="MG MG A 601 " pdb=" O2B ADP A 602 " model vdw 2.076 2.170 nonbonded pdb="MG MG B 601 " pdb=" O2B ADP B 602 " model vdw 2.076 2.170 nonbonded pdb="MG MG E 601 " pdb=" O2B ADP E 602 " model vdw 2.076 2.170 ... (remaining 153717 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.560 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 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 : 0.008 0.235 20112 Z= 0.386 Angle : 0.737 11.913 27246 Z= 0.355 Chirality : 0.044 0.137 3120 Planarity : 0.005 0.054 3486 Dihedral : 16.805 164.544 7506 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.81 % Favored : 94.95 % Rotamer: Outliers : 0.29 % Allowed : 12.39 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.16), residues: 2496 helix: 0.78 (0.15), residues: 1104 sheet: 1.42 (0.21), residues: 546 loop : -2.41 (0.17), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 212 TYR 0.038 0.001 TYR F 526 PHE 0.010 0.001 PHE D 382 TRP 0.010 0.001 TRP F 359 HIS 0.004 0.001 HIS E 127 Details of bonding type rmsd covalent geometry : bond 0.00772 (20088) covalent geometry : angle 0.73309 (27210) hydrogen bonds : bond 0.15413 ( 960) hydrogen bonds : angle 4.82172 ( 2808) metal coordination : bond 0.00292 ( 24) metal coordination : angle 2.10083 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 161 time to evaluate : 0.756 Fit side-chains REVERT: A 463 ASP cc_start: 0.7240 (m-30) cc_final: 0.6944 (m-30) REVERT: C 338 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7415 (mm-30) REVERT: C 489 MET cc_start: 0.8396 (ttp) cc_final: 0.8130 (ttp) REVERT: D 463 ASP cc_start: 0.7313 (m-30) cc_final: 0.6964 (m-30) REVERT: F 489 MET cc_start: 0.8395 (ttp) cc_final: 0.8134 (ttp) outliers start: 6 outliers final: 0 residues processed: 161 average time/residue: 0.1455 time to fit residues: 35.5969 Evaluate side-chains 137 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 136 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 338 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 8.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 247 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 ASN A 363 HIS B 205 ASN B 363 HIS C 205 ASN D 205 ASN D 363 HIS E 205 ASN E 363 HIS F 205 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.150350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.114589 restraints weight = 21457.403| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.16 r_work: 0.3267 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20112 Z= 0.181 Angle : 0.626 7.610 27246 Z= 0.304 Chirality : 0.045 0.154 3120 Planarity : 0.005 0.047 3486 Dihedral : 10.742 162.264 2823 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.97 % Favored : 94.79 % Rotamer: Outliers : 2.40 % Allowed : 12.87 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.16), residues: 2496 helix: 1.51 (0.16), residues: 1110 sheet: 1.31 (0.21), residues: 546 loop : -2.52 (0.17), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 315 TYR 0.016 0.001 TYR C 526 PHE 0.010 0.001 PHE F 204 TRP 0.005 0.001 TRP A 359 HIS 0.004 0.001 HIS F 239 Details of bonding type rmsd covalent geometry : bond 0.00445 (20088) covalent geometry : angle 0.61578 (27210) hydrogen bonds : bond 0.04003 ( 960) hydrogen bonds : angle 3.92201 ( 2808) metal coordination : bond 0.00582 ( 24) metal coordination : angle 3.19926 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 153 time to evaluate : 0.895 Fit side-chains REVERT: A 526 TYR cc_start: 0.7994 (t80) cc_final: 0.7656 (t80) REVERT: B 166 ASN cc_start: 0.7871 (m-40) cc_final: 0.7507 (m110) REVERT: B 500 ILE cc_start: 0.8444 (OUTLIER) cc_final: 0.8192 (mp) REVERT: C 166 ASN cc_start: 0.7566 (m-40) cc_final: 0.7329 (m-40) REVERT: C 318 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7852 (mp0) REVERT: C 507 MET cc_start: 0.7546 (mpp) cc_final: 0.7301 (mpp) REVERT: D 113 MET cc_start: 0.6754 (mmm) cc_final: 0.6526 (mtm) REVERT: D 346 ASN cc_start: 0.7480 (m-40) cc_final: 0.7278 (m-40) REVERT: D 526 TYR cc_start: 0.8029 (t80) cc_final: 0.7670 (t80) REVERT: E 166 ASN cc_start: 0.7877 (m-40) cc_final: 0.7514 (m110) REVERT: E 500 ILE cc_start: 0.8459 (OUTLIER) cc_final: 0.8196 (mp) REVERT: F 166 ASN cc_start: 0.7529 (m-40) cc_final: 0.7289 (m-40) REVERT: F 318 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7822 (mp0) REVERT: F 507 MET cc_start: 0.7551 (mpp) cc_final: 0.7299 (mpp) outliers start: 50 outliers final: 30 residues processed: 190 average time/residue: 0.1250 time to fit residues: 37.9094 Evaluate side-chains 170 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 136 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 501 SER Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 455 ILE Chi-restraints excluded: chain D residue 464 SER Chi-restraints excluded: chain D residue 500 ILE Chi-restraints excluded: chain D residue 513 ILE Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 464 SER Chi-restraints excluded: chain E residue 500 ILE Chi-restraints excluded: chain E residue 501 SER Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 318 GLU Chi-restraints excluded: chain F residue 420 ILE Chi-restraints excluded: chain F residue 501 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 36 optimal weight: 0.6980 chunk 137 optimal weight: 5.9990 chunk 209 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 213 optimal weight: 0.0770 chunk 6 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 143 optimal weight: 5.9990 chunk 60 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 overall best weight: 1.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 ASN ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 198 GLN ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 439 ASN ** E 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 198 GLN ** F 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.142148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.106355 restraints weight = 21056.237| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.06 r_work: 0.2971 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20112 Z= 0.134 Angle : 0.574 9.185 27246 Z= 0.282 Chirality : 0.043 0.152 3120 Planarity : 0.005 0.075 3486 Dihedral : 10.118 156.908 2820 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.69 % Favored : 95.07 % Rotamer: Outliers : 1.92 % Allowed : 15.08 % Favored : 83.00 % 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 aren not related in a simple way. whole: 0.61 (0.17), residues: 2496 helix: 1.96 (0.16), residues: 1110 sheet: 1.20 (0.21), residues: 552 loop : -2.48 (0.17), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 212 TYR 0.008 0.001 TYR B 213 PHE 0.008 0.001 PHE B 382 TRP 0.005 0.001 TRP C 496 HIS 0.003 0.001 HIS D 127 Details of bonding type rmsd covalent geometry : bond 0.00325 (20088) covalent geometry : angle 0.56705 (27210) hydrogen bonds : bond 0.03305 ( 960) hydrogen bonds : angle 3.74467 ( 2808) metal coordination : bond 0.00432 ( 24) metal coordination : angle 2.53465 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 152 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.8607 (tt0) cc_final: 0.8390 (tt0) REVERT: A 526 TYR cc_start: 0.8102 (t80) cc_final: 0.7606 (t80) REVERT: B 166 ASN cc_start: 0.7666 (m-40) cc_final: 0.7259 (m110) REVERT: C 166 ASN cc_start: 0.7408 (m-40) cc_final: 0.7112 (m110) REVERT: C 507 MET cc_start: 0.7330 (mpp) cc_final: 0.7066 (mpp) REVERT: C 526 TYR cc_start: 0.8099 (t80) cc_final: 0.7811 (t80) REVERT: D 526 TYR cc_start: 0.8096 (t80) cc_final: 0.7602 (t80) REVERT: E 166 ASN cc_start: 0.7678 (m-40) cc_final: 0.7273 (m110) REVERT: E 198 GLN cc_start: 0.6882 (mt0) cc_final: 0.6682 (mt0) REVERT: E 262 THR cc_start: 0.8927 (t) cc_final: 0.8664 (t) REVERT: F 166 ASN cc_start: 0.7436 (m-40) cc_final: 0.7214 (m-40) REVERT: F 507 MET cc_start: 0.7345 (mpp) cc_final: 0.7081 (mpp) REVERT: F 526 TYR cc_start: 0.8106 (t80) cc_final: 0.7824 (t80) outliers start: 40 outliers final: 30 residues processed: 182 average time/residue: 0.1095 time to fit residues: 32.1659 Evaluate side-chains 175 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 145 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 464 SER Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 455 ILE Chi-restraints excluded: chain D residue 464 SER Chi-restraints excluded: chain D residue 501 SER Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain E residue 154 ASN Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 464 SER Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 420 ILE Chi-restraints excluded: chain F residue 464 SER Chi-restraints excluded: chain F residue 476 GLU Chi-restraints excluded: chain F residue 501 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 121 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 236 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 86 optimal weight: 6.9990 chunk 251 optimal weight: 4.9990 chunk 138 optimal weight: 0.9990 chunk 117 optimal weight: 0.5980 chunk 165 optimal weight: 2.9990 chunk 196 optimal weight: 0.6980 chunk 127 optimal weight: 7.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 GLN ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.144602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.109820 restraints weight = 20985.350| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 1.97 r_work: 0.2969 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20112 Z= 0.126 Angle : 0.554 7.116 27246 Z= 0.269 Chirality : 0.043 0.151 3120 Planarity : 0.004 0.070 3486 Dihedral : 9.714 152.897 2820 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.09 % Favored : 94.67 % Rotamer: Outliers : 2.59 % Allowed : 16.23 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.17), residues: 2496 helix: 2.17 (0.16), residues: 1110 sheet: 1.15 (0.21), residues: 552 loop : -2.51 (0.17), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 212 TYR 0.007 0.001 TYR E 213 PHE 0.008 0.001 PHE F 204 TRP 0.005 0.001 TRP F 496 HIS 0.003 0.001 HIS B 127 Details of bonding type rmsd covalent geometry : bond 0.00301 (20088) covalent geometry : angle 0.54692 (27210) hydrogen bonds : bond 0.03099 ( 960) hydrogen bonds : angle 3.63717 ( 2808) metal coordination : bond 0.00428 ( 24) metal coordination : angle 2.55551 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 150 time to evaluate : 0.653 Fit side-chains revert: symmetry clash REVERT: A 338 GLU cc_start: 0.8608 (tt0) cc_final: 0.8401 (tt0) REVERT: A 526 TYR cc_start: 0.8093 (t80) cc_final: 0.7607 (t80) REVERT: B 166 ASN cc_start: 0.7775 (m-40) cc_final: 0.7432 (m110) REVERT: B 262 THR cc_start: 0.8877 (t) cc_final: 0.8593 (t) REVERT: B 513 ILE cc_start: 0.8373 (OUTLIER) cc_final: 0.8142 (mt) REVERT: C 166 ASN cc_start: 0.7396 (m-40) cc_final: 0.7099 (m110) REVERT: C 507 MET cc_start: 0.7407 (mpp) cc_final: 0.7139 (mpp) REVERT: C 526 TYR cc_start: 0.8132 (t80) cc_final: 0.7917 (t80) REVERT: D 526 TYR cc_start: 0.8096 (t80) cc_final: 0.7619 (t80) REVERT: E 166 ASN cc_start: 0.7786 (m-40) cc_final: 0.7434 (m110) REVERT: E 262 THR cc_start: 0.8885 (t) cc_final: 0.8612 (t) REVERT: E 513 ILE cc_start: 0.8371 (OUTLIER) cc_final: 0.8140 (mt) REVERT: F 166 ASN cc_start: 0.7411 (m-40) cc_final: 0.7112 (m110) REVERT: F 507 MET cc_start: 0.7404 (mpp) cc_final: 0.7134 (mpp) REVERT: F 526 TYR cc_start: 0.8127 (t80) cc_final: 0.7915 (t80) outliers start: 54 outliers final: 40 residues processed: 194 average time/residue: 0.1118 time to fit residues: 34.9767 Evaluate side-chains 184 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 142 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 421 SER Chi-restraints excluded: chain C residue 464 SER Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 455 ILE Chi-restraints excluded: chain D residue 464 SER Chi-restraints excluded: chain D residue 501 SER Chi-restraints excluded: chain D residue 513 ILE Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 411 THR Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 464 SER Chi-restraints excluded: chain E residue 513 ILE Chi-restraints excluded: chain F residue 154 ASN Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 411 THR Chi-restraints excluded: chain F residue 420 ILE Chi-restraints excluded: chain F residue 464 SER Chi-restraints excluded: chain F residue 476 GLU Chi-restraints excluded: chain F residue 513 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 124 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 53 optimal weight: 6.9990 chunk 105 optimal weight: 0.5980 chunk 143 optimal weight: 0.6980 chunk 205 optimal weight: 4.9990 chunk 240 optimal weight: 0.3980 chunk 40 optimal weight: 0.9980 chunk 70 optimal weight: 0.4980 chunk 146 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 396 GLN ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 GLN ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.147524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.112906 restraints weight = 20922.163| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 1.97 r_work: 0.3017 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 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 : 0.002 0.060 20112 Z= 0.100 Angle : 0.532 8.243 27246 Z= 0.259 Chirality : 0.042 0.144 3120 Planarity : 0.004 0.083 3486 Dihedral : 9.306 147.393 2820 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.09 % Favored : 94.67 % Rotamer: Outliers : 2.16 % Allowed : 16.71 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.17), residues: 2496 helix: 2.38 (0.16), residues: 1110 sheet: 1.27 (0.21), residues: 552 loop : -2.47 (0.17), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 212 TYR 0.015 0.001 TYR E 526 PHE 0.007 0.001 PHE E 382 TRP 0.005 0.001 TRP D 359 HIS 0.003 0.001 HIS A 127 Details of bonding type rmsd covalent geometry : bond 0.00230 (20088) covalent geometry : angle 0.52601 (27210) hydrogen bonds : bond 0.02591 ( 960) hydrogen bonds : angle 3.51067 ( 2808) metal coordination : bond 0.00316 ( 24) metal coordination : angle 2.16572 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 152 time to evaluate : 0.785 Fit side-chains REVERT: A 338 GLU cc_start: 0.8582 (tt0) cc_final: 0.8358 (tt0) REVERT: A 526 TYR cc_start: 0.8082 (t80) cc_final: 0.7625 (t80) REVERT: B 166 ASN cc_start: 0.7727 (m-40) cc_final: 0.7443 (m-40) REVERT: B 513 ILE cc_start: 0.8288 (OUTLIER) cc_final: 0.8079 (mt) REVERT: C 166 ASN cc_start: 0.7277 (m-40) cc_final: 0.6990 (m110) REVERT: D 346 ASN cc_start: 0.7497 (m-40) cc_final: 0.7290 (m-40) REVERT: D 526 TYR cc_start: 0.8075 (t80) cc_final: 0.7634 (t80) REVERT: E 166 ASN cc_start: 0.7755 (m-40) cc_final: 0.7472 (m-40) REVERT: E 513 ILE cc_start: 0.8278 (OUTLIER) cc_final: 0.8070 (mt) REVERT: F 166 ASN cc_start: 0.7388 (m-40) cc_final: 0.7094 (m110) outliers start: 45 outliers final: 35 residues processed: 192 average time/residue: 0.1281 time to fit residues: 39.7386 Evaluate side-chains 179 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 142 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 421 SER Chi-restraints excluded: chain C residue 464 SER Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 464 SER Chi-restraints excluded: chain D residue 500 ILE Chi-restraints excluded: chain D residue 501 SER Chi-restraints excluded: chain D residue 513 ILE Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain E residue 154 ASN Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 411 THR Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 464 SER Chi-restraints excluded: chain E residue 513 ILE Chi-restraints excluded: chain F residue 154 ASN Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 420 ILE Chi-restraints excluded: chain F residue 464 SER Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 513 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 87 optimal weight: 0.3980 chunk 211 optimal weight: 2.9990 chunk 186 optimal weight: 0.9990 chunk 232 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 130 optimal weight: 6.9990 chunk 234 optimal weight: 1.9990 chunk 214 optimal weight: 6.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.139675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.104439 restraints weight = 21047.234| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.99 r_work: 0.2943 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 20112 Z= 0.156 Angle : 0.586 7.097 27246 Z= 0.286 Chirality : 0.044 0.155 3120 Planarity : 0.005 0.082 3486 Dihedral : 9.528 151.947 2820 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.45 % Favored : 94.31 % Rotamer: Outliers : 2.83 % Allowed : 17.58 % Favored : 79.59 % 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 aren not related in a simple way. whole: 0.73 (0.17), residues: 2496 helix: 2.23 (0.16), residues: 1116 sheet: 1.07 (0.21), residues: 552 loop : -2.59 (0.17), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 212 TYR 0.026 0.001 TYR F 526 PHE 0.010 0.001 PHE B 204 TRP 0.007 0.001 TRP D 359 HIS 0.004 0.001 HIS E 127 Details of bonding type rmsd covalent geometry : bond 0.00385 (20088) covalent geometry : angle 0.57656 (27210) hydrogen bonds : bond 0.03482 ( 960) hydrogen bonds : angle 3.76605 ( 2808) metal coordination : bond 0.00545 ( 24) metal coordination : angle 2.98833 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 146 time to evaluate : 0.720 Fit side-chains REVERT: A 338 GLU cc_start: 0.8641 (tt0) cc_final: 0.8389 (tt0) REVERT: A 526 TYR cc_start: 0.8107 (t80) cc_final: 0.7652 (t80) REVERT: B 262 THR cc_start: 0.8889 (t) cc_final: 0.8601 (t) REVERT: C 166 ASN cc_start: 0.7341 (m-40) cc_final: 0.6972 (m110) REVERT: C 507 MET cc_start: 0.7405 (mpp) cc_final: 0.7157 (mpp) REVERT: C 529 SER cc_start: 0.7778 (m) cc_final: 0.7279 (p) REVERT: D 526 TYR cc_start: 0.8117 (t80) cc_final: 0.7667 (t80) REVERT: E 262 THR cc_start: 0.8892 (t) cc_final: 0.8603 (t) REVERT: F 166 ASN cc_start: 0.7358 (m-40) cc_final: 0.6986 (m110) REVERT: F 507 MET cc_start: 0.7400 (mpp) cc_final: 0.7145 (mpp) outliers start: 59 outliers final: 46 residues processed: 195 average time/residue: 0.1306 time to fit residues: 41.1903 Evaluate side-chains 191 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 145 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 421 SER Chi-restraints excluded: chain C residue 464 SER Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 501 SER Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 455 ILE Chi-restraints excluded: chain D residue 464 SER Chi-restraints excluded: chain D residue 500 ILE Chi-restraints excluded: chain D residue 501 SER Chi-restraints excluded: chain D residue 513 ILE Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 411 THR Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 464 SER Chi-restraints excluded: chain F residue 154 ASN Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 420 ILE Chi-restraints excluded: chain F residue 464 SER Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 513 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 227 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 96 optimal weight: 0.8980 chunk 149 optimal weight: 0.9990 chunk 166 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 199 optimal weight: 7.9990 chunk 210 optimal weight: 10.0000 chunk 160 optimal weight: 1.9990 chunk 182 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 GLN ** E 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.139577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.104193 restraints weight = 21114.624| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.02 r_work: 0.2967 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 20112 Z= 0.149 Angle : 0.580 6.920 27246 Z= 0.284 Chirality : 0.044 0.152 3120 Planarity : 0.005 0.096 3486 Dihedral : 9.499 151.816 2820 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.57 % Favored : 94.19 % Rotamer: Outliers : 2.64 % Allowed : 17.82 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.17), residues: 2496 helix: 2.23 (0.16), residues: 1116 sheet: 1.02 (0.21), residues: 552 loop : -2.65 (0.17), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 212 TYR 0.027 0.001 TYR F 526 PHE 0.009 0.001 PHE F 204 TRP 0.005 0.001 TRP F 359 HIS 0.003 0.001 HIS C 239 Details of bonding type rmsd covalent geometry : bond 0.00367 (20088) covalent geometry : angle 0.57287 (27210) hydrogen bonds : bond 0.03369 ( 960) hydrogen bonds : angle 3.76874 ( 2808) metal coordination : bond 0.00470 ( 24) metal coordination : angle 2.58868 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 140 time to evaluate : 0.768 Fit side-chains REVERT: A 338 GLU cc_start: 0.8703 (tt0) cc_final: 0.8451 (tt0) REVERT: A 346 ASN cc_start: 0.7457 (OUTLIER) cc_final: 0.7119 (m110) REVERT: A 526 TYR cc_start: 0.8129 (t80) cc_final: 0.7676 (t80) REVERT: B 121 MET cc_start: 0.8068 (mtp) cc_final: 0.7858 (mtp) REVERT: B 262 THR cc_start: 0.8899 (t) cc_final: 0.8604 (t) REVERT: C 166 ASN cc_start: 0.7182 (m-40) cc_final: 0.6875 (m110) REVERT: C 507 MET cc_start: 0.7376 (mpp) cc_final: 0.7099 (mpp) REVERT: D 450 TYR cc_start: 0.7948 (OUTLIER) cc_final: 0.7737 (m-80) REVERT: D 526 TYR cc_start: 0.8139 (t80) cc_final: 0.7689 (t80) REVERT: E 121 MET cc_start: 0.8055 (mtp) cc_final: 0.7846 (mtp) REVERT: E 262 THR cc_start: 0.8914 (t) cc_final: 0.8628 (t) REVERT: F 166 ASN cc_start: 0.7211 (m-40) cc_final: 0.6879 (m110) REVERT: F 507 MET cc_start: 0.7387 (mpp) cc_final: 0.7110 (mpp) outliers start: 55 outliers final: 44 residues processed: 185 average time/residue: 0.1160 time to fit residues: 34.7940 Evaluate side-chains 182 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 136 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 346 ASN Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 421 SER Chi-restraints excluded: chain C residue 464 SER Chi-restraints excluded: chain C residue 501 SER Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 450 TYR Chi-restraints excluded: chain D residue 455 ILE Chi-restraints excluded: chain D residue 464 SER Chi-restraints excluded: chain D residue 500 ILE Chi-restraints excluded: chain D residue 501 SER Chi-restraints excluded: chain D residue 513 ILE Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 411 THR Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 464 SER Chi-restraints excluded: chain E residue 501 SER Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 411 THR Chi-restraints excluded: chain F residue 420 ILE Chi-restraints excluded: chain F residue 464 SER Chi-restraints excluded: chain F residue 513 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 43 optimal weight: 7.9990 chunk 119 optimal weight: 0.9980 chunk 158 optimal weight: 4.9990 chunk 168 optimal weight: 10.0000 chunk 243 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 40 optimal weight: 6.9990 chunk 178 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.137162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.101979 restraints weight = 21073.309| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.00 r_work: 0.2920 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 20112 Z= 0.177 Angle : 0.608 7.383 27246 Z= 0.297 Chirality : 0.045 0.155 3120 Planarity : 0.005 0.096 3486 Dihedral : 9.613 154.315 2820 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.73 % Favored : 94.03 % Rotamer: Outliers : 2.74 % Allowed : 17.96 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.17), residues: 2496 helix: 2.17 (0.16), residues: 1116 sheet: 0.88 (0.21), residues: 552 loop : -2.74 (0.17), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 212 TYR 0.029 0.001 TYR C 526 PHE 0.011 0.001 PHE B 204 TRP 0.007 0.001 TRP D 359 HIS 0.004 0.001 HIS C 239 Details of bonding type rmsd covalent geometry : bond 0.00441 (20088) covalent geometry : angle 0.59774 (27210) hydrogen bonds : bond 0.03740 ( 960) hydrogen bonds : angle 3.86973 ( 2808) metal coordination : bond 0.00598 ( 24) metal coordination : angle 3.09611 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 146 time to evaluate : 0.765 Fit side-chains REVERT: A 338 GLU cc_start: 0.8681 (tt0) cc_final: 0.8433 (tt0) REVERT: A 346 ASN cc_start: 0.7488 (OUTLIER) cc_final: 0.7169 (m110) REVERT: A 526 TYR cc_start: 0.8142 (t80) cc_final: 0.7701 (t80) REVERT: B 262 THR cc_start: 0.8939 (t) cc_final: 0.8640 (t) REVERT: C 166 ASN cc_start: 0.7295 (m-40) cc_final: 0.7049 (m110) REVERT: C 507 MET cc_start: 0.7501 (mpp) cc_final: 0.7202 (mpp) REVERT: D 526 TYR cc_start: 0.8139 (t80) cc_final: 0.7701 (t80) REVERT: E 262 THR cc_start: 0.8952 (t) cc_final: 0.8652 (t) REVERT: F 166 ASN cc_start: 0.7291 (m-40) cc_final: 0.7041 (m110) REVERT: F 507 MET cc_start: 0.7508 (mpp) cc_final: 0.7206 (mpp) outliers start: 57 outliers final: 50 residues processed: 192 average time/residue: 0.1266 time to fit residues: 39.3481 Evaluate side-chains 195 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 144 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 346 ASN Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 455 ILE Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 421 SER Chi-restraints excluded: chain C residue 464 SER Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 501 SER Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 455 ILE Chi-restraints excluded: chain D residue 464 SER Chi-restraints excluded: chain D residue 500 ILE Chi-restraints excluded: chain D residue 501 SER Chi-restraints excluded: chain D residue 513 ILE Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain E residue 154 ASN Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 411 THR Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 464 SER Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 411 THR Chi-restraints excluded: chain F residue 420 ILE Chi-restraints excluded: chain F residue 464 SER Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 513 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 251 optimal weight: 1.9990 chunk 169 optimal weight: 4.9990 chunk 129 optimal weight: 6.9990 chunk 231 optimal weight: 0.3980 chunk 109 optimal weight: 3.9990 chunk 40 optimal weight: 0.1980 chunk 7 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 182 optimal weight: 3.9990 chunk 189 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.145283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.111361 restraints weight = 20899.555| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 1.91 r_work: 0.2969 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 20112 Z= 0.117 Angle : 0.560 6.855 27246 Z= 0.276 Chirality : 0.042 0.146 3120 Planarity : 0.005 0.086 3486 Dihedral : 9.303 149.758 2820 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.49 % Favored : 94.19 % Rotamer: Outliers : 2.40 % Allowed : 18.78 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.17), residues: 2496 helix: 2.33 (0.16), residues: 1116 sheet: 1.04 (0.21), residues: 552 loop : -2.67 (0.17), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 212 TYR 0.025 0.001 TYR C 526 PHE 0.008 0.001 PHE E 382 TRP 0.005 0.001 TRP D 496 HIS 0.003 0.001 HIS A 127 Details of bonding type rmsd covalent geometry : bond 0.00282 (20088) covalent geometry : angle 0.55580 (27210) hydrogen bonds : bond 0.02907 ( 960) hydrogen bonds : angle 3.70978 ( 2808) metal coordination : bond 0.00324 ( 24) metal coordination : angle 1.90236 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 145 time to evaluate : 0.765 Fit side-chains REVERT: A 338 GLU cc_start: 0.8653 (tt0) cc_final: 0.8392 (tt0) REVERT: A 526 TYR cc_start: 0.8079 (t80) cc_final: 0.7662 (t80) REVERT: B 262 THR cc_start: 0.8902 (t) cc_final: 0.8605 (t) REVERT: C 166 ASN cc_start: 0.7089 (m-40) cc_final: 0.6868 (m110) REVERT: C 507 MET cc_start: 0.7305 (mpp) cc_final: 0.7027 (mpp) REVERT: D 526 TYR cc_start: 0.8080 (t80) cc_final: 0.7660 (t80) REVERT: E 262 THR cc_start: 0.8910 (t) cc_final: 0.8622 (t) REVERT: F 166 ASN cc_start: 0.7093 (m-40) cc_final: 0.6871 (m110) REVERT: F 507 MET cc_start: 0.7312 (mpp) cc_final: 0.7030 (mpp) outliers start: 50 outliers final: 46 residues processed: 187 average time/residue: 0.1255 time to fit residues: 37.9848 Evaluate side-chains 184 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 138 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 421 SER Chi-restraints excluded: chain C residue 464 SER Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 455 ILE Chi-restraints excluded: chain D residue 464 SER Chi-restraints excluded: chain D residue 500 ILE Chi-restraints excluded: chain D residue 501 SER Chi-restraints excluded: chain D residue 513 ILE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain E residue 154 ASN Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 411 THR Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 464 SER Chi-restraints excluded: chain E residue 501 SER Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 411 THR Chi-restraints excluded: chain F residue 420 ILE Chi-restraints excluded: chain F residue 464 SER Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 501 SER Chi-restraints excluded: chain F residue 513 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 97 optimal weight: 2.9990 chunk 134 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 43 optimal weight: 8.9990 chunk 200 optimal weight: 0.4980 chunk 137 optimal weight: 6.9990 chunk 227 optimal weight: 0.6980 chunk 115 optimal weight: 7.9990 chunk 204 optimal weight: 5.9990 chunk 141 optimal weight: 1.9990 chunk 224 optimal weight: 0.5980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.139010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.103896 restraints weight = 21007.626| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.00 r_work: 0.2934 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 20112 Z= 0.149 Angle : 0.588 7.005 27246 Z= 0.290 Chirality : 0.044 0.151 3120 Planarity : 0.005 0.089 3486 Dihedral : 9.364 151.350 2820 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.61 % Favored : 94.07 % Rotamer: Outliers : 2.69 % Allowed : 18.68 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.17), residues: 2496 helix: 2.30 (0.16), residues: 1116 sheet: 0.94 (0.21), residues: 552 loop : -2.70 (0.17), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 212 TYR 0.019 0.001 TYR F 526 PHE 0.009 0.001 PHE F 204 TRP 0.006 0.001 TRP F 359 HIS 0.006 0.001 HIS F 127 Details of bonding type rmsd covalent geometry : bond 0.00371 (20088) covalent geometry : angle 0.58181 (27210) hydrogen bonds : bond 0.03345 ( 960) hydrogen bonds : angle 3.79045 ( 2808) metal coordination : bond 0.00429 ( 24) metal coordination : angle 2.32841 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 141 time to evaluate : 0.747 Fit side-chains REVERT: A 338 GLU cc_start: 0.8678 (tt0) cc_final: 0.8441 (tt0) REVERT: A 526 TYR cc_start: 0.8142 (t80) cc_final: 0.7720 (t80) REVERT: B 262 THR cc_start: 0.8910 (t) cc_final: 0.8608 (t) REVERT: C 166 ASN cc_start: 0.7262 (m-40) cc_final: 0.7014 (m110) REVERT: C 507 MET cc_start: 0.7392 (mpp) cc_final: 0.7109 (mpp) REVERT: D 526 TYR cc_start: 0.8139 (t80) cc_final: 0.7724 (t80) REVERT: E 262 THR cc_start: 0.8929 (t) cc_final: 0.8637 (t) REVERT: F 166 ASN cc_start: 0.7264 (m-40) cc_final: 0.7018 (m110) REVERT: F 507 MET cc_start: 0.7406 (mpp) cc_final: 0.7118 (mpp) outliers start: 56 outliers final: 49 residues processed: 189 average time/residue: 0.1147 time to fit residues: 35.2089 Evaluate side-chains 190 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 141 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 421 SER Chi-restraints excluded: chain C residue 464 SER Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 501 SER Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 455 ILE Chi-restraints excluded: chain D residue 464 SER Chi-restraints excluded: chain D residue 500 ILE Chi-restraints excluded: chain D residue 501 SER Chi-restraints excluded: chain D residue 513 ILE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain E residue 154 ASN Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 411 THR Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 464 SER Chi-restraints excluded: chain E residue 501 SER Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 411 THR Chi-restraints excluded: chain F residue 420 ILE Chi-restraints excluded: chain F residue 464 SER Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 501 SER Chi-restraints excluded: chain F residue 513 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 143 optimal weight: 0.6980 chunk 83 optimal weight: 5.9990 chunk 166 optimal weight: 0.3980 chunk 73 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 135 optimal weight: 0.9990 chunk 188 optimal weight: 1.9990 chunk 82 optimal weight: 0.3980 chunk 35 optimal weight: 0.9990 chunk 151 optimal weight: 0.1980 chunk 214 optimal weight: 2.9990 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 396 GLN D 396 GLN ** E 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 396 GLN ** F 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 439 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.144375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.109800 restraints weight = 21181.325| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.99 r_work: 0.3014 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 20112 Z= 0.102 Angle : 0.543 6.804 27246 Z= 0.269 Chirality : 0.042 0.143 3120 Planarity : 0.004 0.082 3486 Dihedral : 9.016 145.922 2820 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.25 % Favored : 94.35 % Rotamer: Outliers : 2.02 % Allowed : 19.31 % Favored : 78.67 % 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 aren not related in a simple way. whole: 0.93 (0.17), residues: 2496 helix: 2.52 (0.16), residues: 1116 sheet: 1.11 (0.21), residues: 552 loop : -2.62 (0.17), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 201 TYR 0.018 0.001 TYR F 526 PHE 0.008 0.001 PHE E 382 TRP 0.005 0.001 TRP A 359 HIS 0.003 0.001 HIS E 127 Details of bonding type rmsd covalent geometry : bond 0.00239 (20088) covalent geometry : angle 0.54021 (27210) hydrogen bonds : bond 0.02526 ( 960) hydrogen bonds : angle 3.56426 ( 2808) metal coordination : bond 0.00240 ( 24) metal coordination : angle 1.49772 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3919.44 seconds wall clock time: 67 minutes 58.41 seconds (4078.41 seconds total)