Starting phenix.real_space_refine on Tue Jun 17 11:47:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dzg_27797/06_2025/8dzg_27797.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dzg_27797/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8dzg_27797/06_2025/8dzg_27797.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dzg_27797/06_2025/8dzg_27797.map" model { file = "/net/cci-nas-00/data/ceres_data/8dzg_27797/06_2025/8dzg_27797.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dzg_27797/06_2025/8dzg_27797.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP: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: C, B, E, D, F Time building chain proxies: 8.06, per 1000 atoms: 0.41 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: 5.41 Conformation dependent library (CDL) restraints added in 2.7 seconds 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: 2.51 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: 7.31 Time building geometry restraints manager: 6.21 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: 0.18 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' 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: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.750 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 48.200 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.060 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.660 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (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 TRP 0.010 0.001 TRP F 359 HIS 0.004 0.001 HIS E 127 PHE 0.010 0.001 PHE D 382 TYR 0.038 0.001 TYR F 526 ARG 0.002 0.000 ARG B 212 Details of bonding type rmsd hydrogen bonds : bond 0.15413 ( 960) hydrogen bonds : angle 4.82172 ( 2808) metal coordination : bond 0.00292 ( 24) metal coordination : angle 2.10083 ( 36) covalent geometry : bond 0.00772 (20088) covalent geometry : angle 0.73309 (27210) *********************** 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 : 2.208 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: 0.3600 time to fit residues: 88.1458 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 : 2.097 ------------------------------------------------------------------------------- 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 212 optimal weight: 8.9990 chunk 191 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 128 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 120 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 chunk 228 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 = 0.150327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.114619 restraints weight = 21396.471| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.16 r_work: 0.3266 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (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 TRP 0.005 0.001 TRP A 359 HIS 0.004 0.001 HIS F 239 PHE 0.010 0.001 PHE F 204 TYR 0.016 0.001 TYR C 526 ARG 0.003 0.000 ARG E 315 Details of bonding type rmsd hydrogen bonds : bond 0.04003 ( 960) hydrogen bonds : angle 3.92201 ( 2808) metal coordination : bond 0.00582 ( 24) metal coordination : angle 3.19926 ( 36) covalent geometry : bond 0.00445 (20088) covalent geometry : angle 0.61578 (27210) *********************** 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 : 2.283 Fit side-chains REVERT: A 526 TYR cc_start: 0.7972 (t80) cc_final: 0.7632 (t80) REVERT: B 166 ASN cc_start: 0.7847 (m-40) cc_final: 0.7479 (m110) REVERT: B 500 ILE cc_start: 0.8422 (OUTLIER) cc_final: 0.8169 (mp) REVERT: C 166 ASN cc_start: 0.7540 (m-40) cc_final: 0.7304 (m-40) REVERT: C 318 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7831 (mp0) REVERT: C 507 MET cc_start: 0.7505 (mpp) cc_final: 0.7258 (mpp) REVERT: D 113 MET cc_start: 0.6743 (mmm) cc_final: 0.6512 (mtm) REVERT: D 346 ASN cc_start: 0.7460 (m-40) cc_final: 0.7254 (m-40) REVERT: D 526 TYR cc_start: 0.8007 (t80) cc_final: 0.7646 (t80) REVERT: E 166 ASN cc_start: 0.7851 (m-40) cc_final: 0.7485 (m110) REVERT: E 500 ILE cc_start: 0.8440 (OUTLIER) cc_final: 0.8175 (mp) REVERT: F 166 ASN cc_start: 0.7502 (m-40) cc_final: 0.7264 (m-40) REVERT: F 318 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7800 (mp0) REVERT: F 507 MET cc_start: 0.7509 (mpp) cc_final: 0.7257 (mpp) outliers start: 50 outliers final: 30 residues processed: 190 average time/residue: 0.2962 time to fit residues: 89.8329 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 : 2.276 ------------------------------------------------------------------------------- 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 177 optimal weight: 5.9990 chunk 150 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 232 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 228 optimal weight: 0.0370 chunk 113 optimal weight: 0.9990 chunk 176 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 157 optimal weight: 10.0000 overall best weight: 2.2066 ------------------------------------------------------------------------------- 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 = 0.3468 r_free = 0.3468 target = 0.135736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.100649 restraints weight = 20975.014| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.99 r_work: 0.2886 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 20112 Z= 0.212 Angle : 0.657 8.541 27246 Z= 0.322 Chirality : 0.047 0.165 3120 Planarity : 0.005 0.087 3486 Dihedral : 10.442 159.090 2820 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.77 % Favored : 93.99 % Rotamer: Outliers : 2.79 % Allowed : 14.79 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.44 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.17), residues: 2496 helix: 1.64 (0.16), residues: 1116 sheet: 0.97 (0.21), residues: 546 loop : -2.38 (0.17), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 359 HIS 0.005 0.001 HIS C 239 PHE 0.012 0.002 PHE F 204 TYR 0.011 0.001 TYR B 213 ARG 0.003 0.000 ARG B 140 Details of bonding type rmsd hydrogen bonds : bond 0.04347 ( 960) hydrogen bonds : angle 4.03779 ( 2808) metal coordination : bond 0.00745 ( 24) metal coordination : angle 3.91510 ( 36) covalent geometry : bond 0.00536 (20088) covalent geometry : angle 0.64217 (27210) *********************** 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 222 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 164 time to evaluate : 2.179 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.8693 (tt0) cc_final: 0.8476 (tt0) REVERT: A 526 TYR cc_start: 0.8177 (t80) cc_final: 0.7673 (t80) REVERT: B 166 ASN cc_start: 0.7723 (m-40) cc_final: 0.7435 (m110) REVERT: B 262 THR cc_start: 0.8973 (t) cc_final: 0.8688 (t) REVERT: B 500 ILE cc_start: 0.8522 (OUTLIER) cc_final: 0.8219 (mp) REVERT: C 166 ASN cc_start: 0.7503 (m-40) cc_final: 0.7161 (m-40) REVERT: C 476 GLU cc_start: 0.7273 (tt0) cc_final: 0.7055 (pt0) REVERT: C 507 MET cc_start: 0.7485 (mpp) cc_final: 0.7205 (mpp) REVERT: D 526 TYR cc_start: 0.8176 (t80) cc_final: 0.7687 (t80) REVERT: E 166 ASN cc_start: 0.7747 (m-40) cc_final: 0.7449 (m110) REVERT: E 262 THR cc_start: 0.8981 (t) cc_final: 0.8701 (t) REVERT: E 500 ILE cc_start: 0.8523 (OUTLIER) cc_final: 0.8200 (mp) REVERT: F 166 ASN cc_start: 0.7527 (m-40) cc_final: 0.7213 (m-40) REVERT: F 507 MET cc_start: 0.7477 (mpp) cc_final: 0.7193 (mpp) outliers start: 58 outliers final: 43 residues processed: 212 average time/residue: 0.2975 time to fit residues: 101.9011 Evaluate side-chains 199 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 154 time to evaluate : 2.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ASN 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 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 500 ILE 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 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 E residue 500 ILE 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 501 SER Chi-restraints excluded: chain F residue 513 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 98 optimal weight: 0.2980 chunk 159 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 chunk 152 optimal weight: 1.9990 chunk 131 optimal weight: 6.9990 chunk 219 optimal weight: 4.9990 chunk 235 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 133 optimal weight: 5.9990 chunk 192 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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** B 396 GLN ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 GLN E 198 GLN ** E 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 396 GLN ** F 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.139746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.105064 restraints weight = 21207.752| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.96 r_work: 0.2921 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 20112 Z= 0.152 Angle : 0.582 7.096 27246 Z= 0.286 Chirality : 0.044 0.154 3120 Planarity : 0.005 0.085 3486 Dihedral : 9.984 156.382 2820 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.41 % Favored : 94.35 % Rotamer: Outliers : 2.79 % Allowed : 16.38 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.17), residues: 2496 helix: 1.94 (0.16), residues: 1116 sheet: 0.89 (0.21), residues: 558 loop : -2.62 (0.17), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 496 HIS 0.006 0.001 HIS F 127 PHE 0.009 0.001 PHE C 204 TYR 0.008 0.001 TYR D 213 ARG 0.002 0.000 ARG D 212 Details of bonding type rmsd hydrogen bonds : bond 0.03451 ( 960) hydrogen bonds : angle 3.85910 ( 2808) metal coordination : bond 0.00465 ( 24) metal coordination : angle 2.52642 ( 36) covalent geometry : bond 0.00377 (20088) covalent geometry : angle 0.57490 (27210) *********************** 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 212 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 154 time to evaluate : 2.088 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.8650 (tt0) cc_final: 0.8398 (tt0) REVERT: A 526 TYR cc_start: 0.8038 (t80) cc_final: 0.7546 (t80) REVERT: B 166 ASN cc_start: 0.7641 (m-40) cc_final: 0.7426 (m110) REVERT: B 262 THR cc_start: 0.8931 (t) cc_final: 0.8628 (t) REVERT: B 428 ILE cc_start: 0.6658 (mm) cc_final: 0.6424 (mt) REVERT: B 500 ILE cc_start: 0.8455 (OUTLIER) cc_final: 0.8255 (mp) REVERT: C 166 ASN cc_start: 0.7176 (m-40) cc_final: 0.6909 (m110) REVERT: C 476 GLU cc_start: 0.7204 (tt0) cc_final: 0.6978 (pt0) REVERT: C 507 MET cc_start: 0.7316 (mpp) cc_final: 0.7039 (mpp) REVERT: C 529 SER cc_start: 0.7724 (m) cc_final: 0.7198 (p) REVERT: D 526 TYR cc_start: 0.8037 (t80) cc_final: 0.7559 (t80) REVERT: E 166 ASN cc_start: 0.7659 (m-40) cc_final: 0.7437 (m110) REVERT: E 262 THR cc_start: 0.8944 (t) cc_final: 0.8649 (t) REVERT: E 428 ILE cc_start: 0.6688 (mm) cc_final: 0.6460 (mt) REVERT: F 166 ASN cc_start: 0.7199 (m-40) cc_final: 0.6939 (m110) REVERT: F 507 MET cc_start: 0.7335 (mpp) cc_final: 0.7050 (mpp) REVERT: F 529 SER cc_start: 0.7709 (m) cc_final: 0.7190 (p) outliers start: 58 outliers final: 41 residues processed: 202 average time/residue: 0.2895 time to fit residues: 94.6287 Evaluate side-chains 193 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 151 time to evaluate : 2.355 ------------------------------------------------------------------------------- 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 500 ILE 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 500 ILE Chi-restraints excluded: chain B residue 501 SER 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 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 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 420 ILE Chi-restraints excluded: chain F residue 464 SER 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 82 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 141 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 174 optimal weight: 9.9990 chunk 33 optimal weight: 0.8980 chunk 113 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3560 r_free = 0.3560 target = 0.142757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.108159 restraints weight = 21076.484| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 1.96 r_work: 0.2987 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20112 Z= 0.112 Angle : 0.548 8.171 27246 Z= 0.269 Chirality : 0.042 0.147 3120 Planarity : 0.005 0.077 3486 Dihedral : 9.550 151.324 2820 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.29 % Favored : 94.47 % Rotamer: Outliers : 2.31 % Allowed : 17.53 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.17), residues: 2496 helix: 2.23 (0.16), residues: 1116 sheet: 1.01 (0.21), residues: 558 loop : -2.58 (0.17), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 496 HIS 0.004 0.001 HIS F 127 PHE 0.008 0.001 PHE B 382 TYR 0.015 0.001 TYR F 526 ARG 0.001 0.000 ARG F 201 Details of bonding type rmsd hydrogen bonds : bond 0.02819 ( 960) hydrogen bonds : angle 3.63016 ( 2808) metal coordination : bond 0.00333 ( 24) metal coordination : angle 2.12866 ( 36) covalent geometry : bond 0.00263 (20088) covalent geometry : angle 0.54333 (27210) *********************** 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 205 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 157 time to evaluate : 2.074 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.8609 (tt0) cc_final: 0.8381 (tt0) REVERT: A 526 TYR cc_start: 0.8086 (t80) cc_final: 0.7619 (t80) REVERT: B 166 ASN cc_start: 0.7706 (m-40) cc_final: 0.7503 (m-40) REVERT: B 262 THR cc_start: 0.8879 (t) cc_final: 0.8600 (t) REVERT: C 130 VAL cc_start: 0.8464 (t) cc_final: 0.8244 (t) REVERT: C 166 ASN cc_start: 0.7122 (m-40) cc_final: 0.6830 (m110) REVERT: C 529 SER cc_start: 0.7901 (m) cc_final: 0.7326 (p) REVERT: D 526 TYR cc_start: 0.8081 (t80) cc_final: 0.7619 (t80) REVERT: E 166 ASN cc_start: 0.7714 (m-40) cc_final: 0.7508 (m-40) REVERT: E 262 THR cc_start: 0.8886 (t) cc_final: 0.8611 (t) REVERT: F 130 VAL cc_start: 0.8456 (t) cc_final: 0.8235 (t) REVERT: F 166 ASN cc_start: 0.7133 (m-40) cc_final: 0.6839 (m110) REVERT: F 526 TYR cc_start: 0.8102 (t80) cc_final: 0.7876 (t80) REVERT: F 529 SER cc_start: 0.7892 (m) cc_final: 0.7336 (p) outliers start: 48 outliers final: 41 residues processed: 198 average time/residue: 0.2768 time to fit residues: 88.6902 Evaluate side-chains 195 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 154 time to evaluate : 1.988 ------------------------------------------------------------------------------- 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 500 ILE Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 219 LEU 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 464 SER Chi-restraints excluded: chain C residue 500 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 E residue 145 MET Chi-restraints excluded: chain E residue 154 ASN Chi-restraints excluded: chain E residue 163 LEU 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 132 optimal weight: 9.9990 chunk 17 optimal weight: 0.6980 chunk 51 optimal weight: 0.0010 chunk 171 optimal weight: 6.9990 chunk 234 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 174 optimal weight: 9.9990 chunk 130 optimal weight: 4.9990 chunk 219 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 overall best weight: 2.3392 ------------------------------------------------------------------------------- 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** E 439 ASN ** 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 = 0.3636 r_free = 0.3636 target = 0.144634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.109738 restraints weight = 21634.947| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.10 r_work: 0.3181 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 20112 Z= 0.220 Angle : 0.645 8.214 27246 Z= 0.315 Chirality : 0.046 0.161 3120 Planarity : 0.005 0.072 3486 Dihedral : 10.045 157.131 2820 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.85 % Favored : 93.91 % Rotamer: Outliers : 3.17 % Allowed : 17.20 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.44 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.17), residues: 2496 helix: 1.99 (0.16), residues: 1116 sheet: 0.76 (0.21), residues: 552 loop : -2.81 (0.17), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 359 HIS 0.004 0.001 HIS F 239 PHE 0.013 0.002 PHE B 204 TYR 0.017 0.001 TYR C 526 ARG 0.002 0.000 ARG C 201 Details of bonding type rmsd hydrogen bonds : bond 0.04243 ( 960) hydrogen bonds : angle 3.99552 ( 2808) metal coordination : bond 0.00717 ( 24) metal coordination : angle 3.53901 ( 36) covalent geometry : bond 0.00554 (20088) covalent geometry : angle 0.63261 (27210) *********************** 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 229 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 163 time to evaluate : 3.025 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.8705 (tt0) cc_final: 0.8444 (tt0) REVERT: A 346 ASN cc_start: 0.7544 (OUTLIER) cc_final: 0.7229 (m110) REVERT: A 464 SER cc_start: 0.7870 (OUTLIER) cc_final: 0.7567 (p) REVERT: A 526 TYR cc_start: 0.8071 (t80) cc_final: 0.7607 (t80) REVERT: C 166 ASN cc_start: 0.7365 (m-40) cc_final: 0.7143 (m110) REVERT: C 476 GLU cc_start: 0.7245 (tt0) cc_final: 0.6954 (pt0) REVERT: C 507 MET cc_start: 0.7538 (mpp) cc_final: 0.7242 (mpp) REVERT: D 346 ASN cc_start: 0.7526 (OUTLIER) cc_final: 0.7213 (m110) REVERT: D 464 SER cc_start: 0.7864 (OUTLIER) cc_final: 0.7557 (p) REVERT: D 493 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.8381 (mt-10) REVERT: D 526 TYR cc_start: 0.8103 (t80) cc_final: 0.7616 (t80) REVERT: E 262 THR cc_start: 0.9016 (t) cc_final: 0.8708 (t) REVERT: E 500 ILE cc_start: 0.8488 (OUTLIER) cc_final: 0.8248 (mp) REVERT: F 166 ASN cc_start: 0.7379 (m-40) cc_final: 0.7154 (m110) REVERT: F 507 MET cc_start: 0.7533 (mpp) cc_final: 0.7240 (mpp) outliers start: 66 outliers final: 50 residues processed: 218 average time/residue: 0.3535 time to fit residues: 124.3886 Evaluate side-chains 210 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 154 time to evaluate : 2.761 ------------------------------------------------------------------------------- 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 420 ILE Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 501 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 455 ILE 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 346 ASN 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 493 GLU 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 500 ILE Chi-restraints excluded: chain E residue 501 SER 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 455 ILE Chi-restraints excluded: chain F residue 464 SER Chi-restraints excluded: chain F residue 476 GLU 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 0 optimal weight: 10.0000 chunk 231 optimal weight: 2.9990 chunk 248 optimal weight: 4.9990 chunk 208 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 161 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 149 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 GLN B 166 ASN ** 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 166 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.138509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.104137 restraints weight = 21106.446| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 1.94 r_work: 0.2940 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 20112 Z= 0.127 Angle : 0.566 6.494 27246 Z= 0.279 Chirality : 0.043 0.148 3120 Planarity : 0.005 0.066 3486 Dihedral : 9.610 152.614 2820 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.57 % Favored : 94.19 % Rotamer: Outliers : 2.93 % Allowed : 18.97 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.17), residues: 2496 helix: 2.23 (0.16), residues: 1116 sheet: 0.86 (0.21), residues: 558 loop : -2.73 (0.17), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 496 HIS 0.005 0.001 HIS D 127 PHE 0.007 0.001 PHE B 382 TYR 0.016 0.001 TYR E 526 ARG 0.004 0.000 ARG C 149 Details of bonding type rmsd hydrogen bonds : bond 0.03063 ( 960) hydrogen bonds : angle 3.75923 ( 2808) metal coordination : bond 0.00345 ( 24) metal coordination : angle 1.88016 ( 36) covalent geometry : bond 0.00308 (20088) covalent geometry : angle 0.56203 (27210) *********************** 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 217 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 156 time to evaluate : 2.650 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.8669 (tt0) cc_final: 0.8428 (tt0) REVERT: A 346 ASN cc_start: 0.7484 (OUTLIER) cc_final: 0.7148 (m110) REVERT: A 526 TYR cc_start: 0.8152 (t80) cc_final: 0.7736 (t80) REVERT: C 130 VAL cc_start: 0.8518 (t) cc_final: 0.8307 (t) REVERT: C 138 TYR cc_start: 0.8594 (m-80) cc_final: 0.7987 (m-80) REVERT: C 507 MET cc_start: 0.7429 (mpp) cc_final: 0.7167 (mpp) REVERT: D 526 TYR cc_start: 0.8144 (t80) cc_final: 0.7730 (t80) REVERT: E 262 THR cc_start: 0.8925 (t) cc_final: 0.8639 (t) REVERT: F 166 ASN cc_start: 0.7200 (m-40) cc_final: 0.6980 (m110) REVERT: F 507 MET cc_start: 0.7440 (mpp) cc_final: 0.7179 (mpp) outliers start: 61 outliers final: 49 residues processed: 204 average time/residue: 0.3103 time to fit residues: 102.3177 Evaluate side-chains 200 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 150 time to evaluate : 2.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU 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 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 277 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 513 ILE Chi-restraints excluded: chain D residue 126 LEU 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 277 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 58 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 chunk 47 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 chunk 232 optimal weight: 3.9990 chunk 247 optimal weight: 3.9990 chunk 240 optimal weight: 8.9990 chunk 84 optimal weight: 10.0000 overall best weight: 2.5386 ------------------------------------------------------------------------------- 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** B 439 ASN C 166 ASN ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 ASN ** 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** F 439 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.143114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.108232 restraints weight = 21795.526| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.10 r_work: 0.3188 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 20112 Z= 0.235 Angle : 0.665 8.255 27246 Z= 0.325 Chirality : 0.047 0.159 3120 Planarity : 0.006 0.069 3486 Dihedral : 10.012 157.769 2820 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.93 % Favored : 93.83 % Rotamer: Outliers : 3.46 % Allowed : 18.64 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.44 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.17), residues: 2496 helix: 1.95 (0.16), residues: 1116 sheet: 0.69 (0.21), residues: 546 loop : -2.65 (0.17), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 359 HIS 0.005 0.001 HIS C 239 PHE 0.014 0.002 PHE E 204 TYR 0.018 0.002 TYR F 526 ARG 0.004 0.000 ARG F 149 Details of bonding type rmsd hydrogen bonds : bond 0.04367 ( 960) hydrogen bonds : angle 4.04897 ( 2808) metal coordination : bond 0.00736 ( 24) metal coordination : angle 3.40648 ( 36) covalent geometry : bond 0.00593 (20088) covalent geometry : angle 0.65383 (27210) *********************** 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 222 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 150 time to evaluate : 2.799 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.8741 (tt0) cc_final: 0.8475 (tt0) REVERT: A 346 ASN cc_start: 0.7562 (OUTLIER) cc_final: 0.7253 (m110) REVERT: A 464 SER cc_start: 0.7871 (OUTLIER) cc_final: 0.7566 (p) REVERT: A 526 TYR cc_start: 0.8118 (t80) cc_final: 0.7646 (t80) REVERT: C 476 GLU cc_start: 0.7260 (tt0) cc_final: 0.6886 (pt0) REVERT: C 507 MET cc_start: 0.7528 (mpp) cc_final: 0.7226 (mpp) REVERT: D 346 ASN cc_start: 0.7553 (OUTLIER) cc_final: 0.7241 (m110) REVERT: D 464 SER cc_start: 0.7856 (OUTLIER) cc_final: 0.7549 (p) REVERT: D 493 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.8373 (mt-10) REVERT: D 526 TYR cc_start: 0.8102 (t80) cc_final: 0.7629 (t80) REVERT: E 500 ILE cc_start: 0.8459 (OUTLIER) cc_final: 0.8210 (mp) REVERT: F 507 MET cc_start: 0.7542 (mpp) cc_final: 0.7244 (mpp) outliers start: 72 outliers final: 59 residues processed: 209 average time/residue: 0.4085 time to fit residues: 142.9175 Evaluate side-chains 208 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 143 time to evaluate : 3.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU 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 277 LEU Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 450 TYR Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 277 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 126 LEU 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 346 ASN 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 493 GLU 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 277 LEU Chi-restraints excluded: chain E residue 411 THR Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 450 TYR 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 154 ASN Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 277 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 144 optimal weight: 7.9990 chunk 243 optimal weight: 0.0170 chunk 241 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 201 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 118 optimal weight: 0.7980 chunk 174 optimal weight: 8.9990 chunk 44 optimal weight: 3.9990 chunk 228 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.9624 ------------------------------------------------------------------------------- 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 F 166 ASN ** 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 = 0.3508 r_free = 0.3508 target = 0.138715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.103865 restraints weight = 21140.752| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 1.99 r_work: 0.2936 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 20112 Z= 0.123 Angle : 0.569 6.500 27246 Z= 0.280 Chirality : 0.043 0.147 3120 Planarity : 0.005 0.063 3486 Dihedral : 9.573 153.270 2820 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.61 % Favored : 94.15 % Rotamer: Outliers : 2.79 % Allowed : 19.45 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.17), residues: 2496 helix: 2.25 (0.16), residues: 1116 sheet: 0.76 (0.21), residues: 558 loop : -2.77 (0.17), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 496 HIS 0.004 0.001 HIS D 127 PHE 0.008 0.001 PHE C 382 TYR 0.017 0.001 TYR F 526 ARG 0.003 0.000 ARG F 149 Details of bonding type rmsd hydrogen bonds : bond 0.03064 ( 960) hydrogen bonds : angle 3.77676 ( 2808) metal coordination : bond 0.00309 ( 24) metal coordination : angle 1.63989 ( 36) covalent geometry : bond 0.00296 (20088) covalent geometry : angle 0.56579 (27210) *********************** 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 207 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 149 time to evaluate : 2.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.8677 (tt0) cc_final: 0.8428 (tt0) REVERT: A 346 ASN cc_start: 0.7470 (OUTLIER) cc_final: 0.7131 (m110) REVERT: A 526 TYR cc_start: 0.8137 (t80) cc_final: 0.7722 (t80) REVERT: C 507 MET cc_start: 0.7355 (mpp) cc_final: 0.7081 (mpp) REVERT: D 493 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8348 (mt-10) REVERT: D 526 TYR cc_start: 0.8129 (t80) cc_final: 0.7720 (t80) REVERT: E 212 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.8095 (tpt170) REVERT: E 500 ILE cc_start: 0.8463 (OUTLIER) cc_final: 0.8192 (mp) REVERT: F 507 MET cc_start: 0.7376 (mpp) cc_final: 0.7102 (mpp) outliers start: 58 outliers final: 47 residues processed: 193 average time/residue: 0.2947 time to fit residues: 91.5830 Evaluate side-chains 191 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 140 time to evaluate : 2.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU 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 277 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 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 420 ILE Chi-restraints excluded: chain D residue 455 ILE Chi-restraints excluded: chain D residue 464 SER Chi-restraints excluded: chain D residue 493 GLU Chi-restraints excluded: chain D residue 500 ILE 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 212 ARG Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 277 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 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 74 optimal weight: 4.9990 chunk 150 optimal weight: 0.0670 chunk 131 optimal weight: 0.8980 chunk 197 optimal weight: 0.7980 chunk 195 optimal weight: 0.6980 chunk 214 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 162 optimal weight: 2.9990 chunk 238 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.6718 ------------------------------------------------------------------------------- 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 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.142629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.108047 restraints weight = 21040.316| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.97 r_work: 0.2972 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 20112 Z= 0.106 Angle : 0.544 6.342 27246 Z= 0.266 Chirality : 0.042 0.146 3120 Planarity : 0.005 0.062 3486 Dihedral : 9.148 146.785 2820 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.53 % Favored : 94.15 % Rotamer: Outliers : 2.45 % Allowed : 19.55 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.17), residues: 2496 helix: 2.43 (0.16), residues: 1116 sheet: 0.92 (0.22), residues: 558 loop : -2.68 (0.17), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 359 HIS 0.003 0.001 HIS C 127 PHE 0.008 0.001 PHE F 382 TYR 0.019 0.001 TYR C 526 ARG 0.003 0.000 ARG F 149 Details of bonding type rmsd hydrogen bonds : bond 0.02684 ( 960) hydrogen bonds : angle 3.58926 ( 2808) metal coordination : bond 0.00204 ( 24) metal coordination : angle 1.39698 ( 36) covalent geometry : bond 0.00247 (20088) covalent geometry : angle 0.54214 (27210) ********************** 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 195 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 144 time to evaluate : 2.136 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 346 ASN cc_start: 0.7533 (OUTLIER) cc_final: 0.7184 (m110) REVERT: A 526 TYR cc_start: 0.8075 (t80) cc_final: 0.7667 (t80) REVERT: C 130 VAL cc_start: 0.8446 (t) cc_final: 0.8234 (t) REVERT: C 212 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.8418 (tpt170) REVERT: C 526 TYR cc_start: 0.8017 (t80) cc_final: 0.7735 (t80) REVERT: D 121 MET cc_start: 0.7683 (mtp) cc_final: 0.7449 (mtp) REVERT: D 493 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8212 (mt-10) REVERT: D 526 TYR cc_start: 0.8108 (t80) cc_final: 0.7716 (t80) REVERT: E 212 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.8001 (tpt170) REVERT: E 500 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.8196 (mp) REVERT: F 130 VAL cc_start: 0.8435 (t) cc_final: 0.8227 (t) REVERT: F 212 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.8066 (tpt170) outliers start: 51 outliers final: 41 residues processed: 188 average time/residue: 0.3125 time to fit residues: 92.8467 Evaluate side-chains 186 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 139 time to evaluate : 2.118 ------------------------------------------------------------------------------- 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 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 277 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 212 ARG Chi-restraints excluded: chain C residue 420 ILE 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 420 ILE Chi-restraints excluded: chain D residue 455 ILE Chi-restraints excluded: chain D residue 464 SER Chi-restraints excluded: chain D residue 493 GLU 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 212 ARG Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 277 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 F residue 212 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 47 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 199 optimal weight: 4.9990 chunk 246 optimal weight: 0.9990 chunk 165 optimal weight: 0.9980 chunk 192 optimal weight: 0.0470 chunk 209 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 197 optimal weight: 0.9990 chunk 113 optimal weight: 0.8980 chunk 179 optimal weight: 6.9990 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 HIS ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 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 = 0.3555 r_free = 0.3555 target = 0.142590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.107797 restraints weight = 21229.221| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 1.99 r_work: 0.2962 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20112 Z= 0.109 Angle : 0.547 6.368 27246 Z= 0.267 Chirality : 0.042 0.145 3120 Planarity : 0.005 0.060 3486 Dihedral : 9.061 146.117 2820 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.57 % Favored : 94.11 % Rotamer: Outliers : 2.45 % Allowed : 19.60 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.17), residues: 2496 helix: 2.52 (0.16), residues: 1116 sheet: 0.95 (0.21), residues: 558 loop : -2.63 (0.17), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 359 HIS 0.003 0.001 HIS C 127 PHE 0.008 0.001 PHE C 382 TYR 0.019 0.001 TYR F 526 ARG 0.003 0.000 ARG C 149 Details of bonding type rmsd hydrogen bonds : bond 0.02740 ( 960) hydrogen bonds : angle 3.56908 ( 2808) metal coordination : bond 0.00244 ( 24) metal coordination : angle 1.48269 ( 36) covalent geometry : bond 0.00257 (20088) covalent geometry : angle 0.54480 (27210) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9808.76 seconds wall clock time: 173 minutes 11.57 seconds (10391.57 seconds total)