Starting phenix.real_space_refine on Tue Nov 18 13:50:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5u6o_8511/11_2025/5u6o_8511.cif Found real_map, /net/cci-nas-00/data/ceres_data/5u6o_8511/11_2025/5u6o_8511.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5u6o_8511/11_2025/5u6o_8511.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5u6o_8511/11_2025/5u6o_8511.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5u6o_8511/11_2025/5u6o_8511.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5u6o_8511/11_2025/5u6o_8511.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 9432 2.51 5 N 2448 2.21 5 O 2492 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14480 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3620 Classifications: {'peptide': 482} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PTRANS': 16, 'TRANS': 465} Chain breaks: 2 Unresolved non-hydrogen bonds: 333 Unresolved non-hydrogen angles: 416 Unresolved non-hydrogen dihedrals: 263 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'ARG:plan': 9, 'PHE:plan': 3, 'TRP:plan': 1, 'GLU:plan': 12, 'GLN:plan1': 1, 'ASP:plan': 11, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 166 Restraints were copied for chains: B, C, D Time building chain proxies: 3.33, per 1000 atoms: 0.23 Number of scatterers: 14480 At special positions: 0 Unit cell: (123.5, 123.5, 115.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 2492 8.00 N 2448 7.00 C 9432 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.28 Conformation dependent library (CDL) restraints added in 673.1 milliseconds 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3672 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 8 sheets defined 71.8% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 94 through 103 removed outlier: 4.104A pdb=" N PHE A 98 " --> pdb=" O MET A 94 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR A 99 " --> pdb=" O GLN A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 115 Processing helix chain 'A' and resid 116 through 128 Processing helix chain 'A' and resid 139 through 167 removed outlier: 3.724A pdb=" N GLY A 155 " --> pdb=" O ILE A 151 " (cutoff:3.500A) Proline residue: A 161 - end of helix removed outlier: 3.563A pdb=" N PHE A 167 " --> pdb=" O GLY A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 196 Processing helix chain 'A' and resid 211 through 219 Processing helix chain 'A' and resid 221 through 230 Processing helix chain 'A' and resid 231 through 242 Processing helix chain 'A' and resid 253 through 265 removed outlier: 3.687A pdb=" N ILE A 262 " --> pdb=" O ARG A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 269 through 290 removed outlier: 4.191A pdb=" N ARG A 273 " --> pdb=" O LEU A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 323 removed outlier: 3.587A pdb=" N PHE A 317 " --> pdb=" O GLY A 313 " (cutoff:3.500A) Proline residue: A 320 - end of helix Processing helix chain 'A' and resid 329 through 334 Processing helix chain 'A' and resid 340 through 358 Processing helix chain 'A' and resid 368 through 401 Processing helix chain 'A' and resid 401 through 422 Processing helix chain 'A' and resid 424 through 440 Processing helix chain 'A' and resid 445 through 453 Processing helix chain 'A' and resid 454 through 473 removed outlier: 5.694A pdb=" N LYS A 468 " --> pdb=" O PHE A 464 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N LEU A 469 " --> pdb=" O ASN A 465 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR A 472 " --> pdb=" O LYS A 468 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N MET A 473 " --> pdb=" O LEU A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 491 removed outlier: 3.503A pdb=" N LYS A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 576 removed outlier: 3.794A pdb=" N GLU A 575 " --> pdb=" O GLU A 571 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR A 576 " --> pdb=" O VAL A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 585 Processing helix chain 'B' and resid 95 through 103 removed outlier: 3.665A pdb=" N THR B 99 " --> pdb=" O GLN B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 115 Processing helix chain 'B' and resid 116 through 128 Processing helix chain 'B' and resid 139 through 167 removed outlier: 3.724A pdb=" N GLY B 155 " --> pdb=" O ILE B 151 " (cutoff:3.500A) Proline residue: B 161 - end of helix removed outlier: 3.565A pdb=" N PHE B 167 " --> pdb=" O GLY B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 196 Processing helix chain 'B' and resid 211 through 219 Processing helix chain 'B' and resid 221 through 230 Processing helix chain 'B' and resid 231 through 242 Processing helix chain 'B' and resid 253 through 265 removed outlier: 3.688A pdb=" N ILE B 262 " --> pdb=" O ARG B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 268 No H-bonds generated for 'chain 'B' and resid 266 through 268' Processing helix chain 'B' and resid 269 through 290 removed outlier: 4.191A pdb=" N ARG B 273 " --> pdb=" O LEU B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 323 removed outlier: 3.584A pdb=" N PHE B 317 " --> pdb=" O GLY B 313 " (cutoff:3.500A) Proline residue: B 320 - end of helix Processing helix chain 'B' and resid 329 through 334 Processing helix chain 'B' and resid 340 through 358 Processing helix chain 'B' and resid 368 through 401 Processing helix chain 'B' and resid 401 through 422 Processing helix chain 'B' and resid 424 through 440 Processing helix chain 'B' and resid 445 through 453 Processing helix chain 'B' and resid 454 through 473 removed outlier: 5.693A pdb=" N LYS B 468 " --> pdb=" O PHE B 464 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N LEU B 469 " --> pdb=" O ASN B 465 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR B 472 " --> pdb=" O LYS B 468 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N MET B 473 " --> pdb=" O LEU B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 491 removed outlier: 3.504A pdb=" N LYS B 490 " --> pdb=" O ALA B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 576 removed outlier: 3.794A pdb=" N GLU B 575 " --> pdb=" O GLU B 571 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR B 576 " --> pdb=" O VAL B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 585 Processing helix chain 'C' and resid 95 through 103 removed outlier: 3.665A pdb=" N THR C 99 " --> pdb=" O GLN C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 115 Processing helix chain 'C' and resid 116 through 128 Processing helix chain 'C' and resid 139 through 167 removed outlier: 3.724A pdb=" N GLY C 155 " --> pdb=" O ILE C 151 " (cutoff:3.500A) Proline residue: C 161 - end of helix removed outlier: 3.565A pdb=" N PHE C 167 " --> pdb=" O GLY C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 196 Processing helix chain 'C' and resid 211 through 219 Processing helix chain 'C' and resid 221 through 230 Processing helix chain 'C' and resid 231 through 242 Processing helix chain 'C' and resid 253 through 265 removed outlier: 3.687A pdb=" N ILE C 262 " --> pdb=" O ARG C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 268 No H-bonds generated for 'chain 'C' and resid 266 through 268' Processing helix chain 'C' and resid 269 through 290 removed outlier: 4.193A pdb=" N ARG C 273 " --> pdb=" O LEU C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 323 removed outlier: 3.587A pdb=" N PHE C 317 " --> pdb=" O GLY C 313 " (cutoff:3.500A) Proline residue: C 320 - end of helix Processing helix chain 'C' and resid 329 through 334 Processing helix chain 'C' and resid 340 through 358 Processing helix chain 'C' and resid 368 through 401 Processing helix chain 'C' and resid 401 through 422 Processing helix chain 'C' and resid 424 through 440 Processing helix chain 'C' and resid 445 through 453 Processing helix chain 'C' and resid 454 through 473 removed outlier: 5.692A pdb=" N LYS C 468 " --> pdb=" O PHE C 464 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N LEU C 469 " --> pdb=" O ASN C 465 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR C 472 " --> pdb=" O LYS C 468 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N MET C 473 " --> pdb=" O LEU C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 491 removed outlier: 3.503A pdb=" N LYS C 490 " --> pdb=" O ALA C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 566 through 576 removed outlier: 3.793A pdb=" N GLU C 575 " --> pdb=" O GLU C 571 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR C 576 " --> pdb=" O VAL C 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 585 Processing helix chain 'D' and resid 95 through 103 removed outlier: 3.664A pdb=" N THR D 99 " --> pdb=" O GLN D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 128 Processing helix chain 'D' and resid 139 through 167 removed outlier: 3.724A pdb=" N GLY D 155 " --> pdb=" O ILE D 151 " (cutoff:3.500A) Proline residue: D 161 - end of helix removed outlier: 3.564A pdb=" N PHE D 167 " --> pdb=" O GLY D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 196 Processing helix chain 'D' and resid 211 through 219 Processing helix chain 'D' and resid 221 through 230 Processing helix chain 'D' and resid 231 through 242 Processing helix chain 'D' and resid 253 through 265 removed outlier: 3.687A pdb=" N ILE D 262 " --> pdb=" O ARG D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 268 No H-bonds generated for 'chain 'D' and resid 266 through 268' Processing helix chain 'D' and resid 269 through 290 removed outlier: 4.190A pdb=" N ARG D 273 " --> pdb=" O LEU D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 323 removed outlier: 3.585A pdb=" N PHE D 317 " --> pdb=" O GLY D 313 " (cutoff:3.500A) Proline residue: D 320 - end of helix Processing helix chain 'D' and resid 329 through 334 Processing helix chain 'D' and resid 340 through 358 Processing helix chain 'D' and resid 368 through 401 Processing helix chain 'D' and resid 401 through 422 Processing helix chain 'D' and resid 424 through 440 Processing helix chain 'D' and resid 445 through 453 Processing helix chain 'D' and resid 454 through 473 removed outlier: 5.695A pdb=" N LYS D 468 " --> pdb=" O PHE D 464 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N LEU D 469 " --> pdb=" O ASN D 465 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR D 472 " --> pdb=" O LYS D 468 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N MET D 473 " --> pdb=" O LEU D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 491 removed outlier: 3.504A pdb=" N LYS D 490 " --> pdb=" O ALA D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 566 through 576 removed outlier: 3.794A pdb=" N GLU D 575 " --> pdb=" O GLU D 571 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR D 576 " --> pdb=" O VAL D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 576 through 585 Processing sheet with id=AA1, first strand: chain 'A' and resid 492 through 496 removed outlier: 6.602A pdb=" N ARG A 554 " --> pdb=" O VAL A 522 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N VAL A 522 " --> pdb=" O ARG A 554 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ASP A 556 " --> pdb=" O ALA A 520 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ALA A 520 " --> pdb=" O ASP A 556 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N TYR A 558 " --> pdb=" O GLY A 518 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLY A 518 " --> pdb=" O TYR A 558 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ARG A 560 " --> pdb=" O GLN A 516 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN A 516 " --> pdb=" O ARG A 560 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N MET A 530 " --> pdb=" O VAL A 522 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 501 through 503 removed outlier: 6.556A pdb=" N TYR A 501 " --> pdb=" O ALA A 555 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ALA A 555 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ARG A 554 " --> pdb=" O VAL A 522 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N VAL A 522 " --> pdb=" O ARG A 554 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ASP A 556 " --> pdb=" O ALA A 520 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ALA A 520 " --> pdb=" O ASP A 556 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N TYR A 558 " --> pdb=" O GLY A 518 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLY A 518 " --> pdb=" O TYR A 558 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ARG A 560 " --> pdb=" O GLN A 516 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN A 516 " --> pdb=" O ARG A 560 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 492 through 496 removed outlier: 6.601A pdb=" N ARG B 554 " --> pdb=" O VAL B 522 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N VAL B 522 " --> pdb=" O ARG B 554 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ASP B 556 " --> pdb=" O ALA B 520 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ALA B 520 " --> pdb=" O ASP B 556 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N TYR B 558 " --> pdb=" O GLY B 518 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLY B 518 " --> pdb=" O TYR B 558 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ARG B 560 " --> pdb=" O GLN B 516 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN B 516 " --> pdb=" O ARG B 560 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N MET B 530 " --> pdb=" O VAL B 522 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 501 through 503 removed outlier: 6.558A pdb=" N TYR B 501 " --> pdb=" O ALA B 555 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ALA B 555 " --> pdb=" O TYR B 501 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ARG B 554 " --> pdb=" O VAL B 522 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N VAL B 522 " --> pdb=" O ARG B 554 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ASP B 556 " --> pdb=" O ALA B 520 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ALA B 520 " --> pdb=" O ASP B 556 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N TYR B 558 " --> pdb=" O GLY B 518 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLY B 518 " --> pdb=" O TYR B 558 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ARG B 560 " --> pdb=" O GLN B 516 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN B 516 " --> pdb=" O ARG B 560 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 492 through 496 removed outlier: 6.602A pdb=" N ARG C 554 " --> pdb=" O VAL C 522 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N VAL C 522 " --> pdb=" O ARG C 554 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ASP C 556 " --> pdb=" O ALA C 520 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ALA C 520 " --> pdb=" O ASP C 556 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N TYR C 558 " --> pdb=" O GLY C 518 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLY C 518 " --> pdb=" O TYR C 558 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ARG C 560 " --> pdb=" O GLN C 516 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN C 516 " --> pdb=" O ARG C 560 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N MET C 530 " --> pdb=" O VAL C 522 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 501 through 503 removed outlier: 6.557A pdb=" N TYR C 501 " --> pdb=" O ALA C 555 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ALA C 555 " --> pdb=" O TYR C 501 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ARG C 554 " --> pdb=" O VAL C 522 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N VAL C 522 " --> pdb=" O ARG C 554 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ASP C 556 " --> pdb=" O ALA C 520 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ALA C 520 " --> pdb=" O ASP C 556 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N TYR C 558 " --> pdb=" O GLY C 518 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLY C 518 " --> pdb=" O TYR C 558 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ARG C 560 " --> pdb=" O GLN C 516 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN C 516 " --> pdb=" O ARG C 560 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 492 through 496 removed outlier: 6.602A pdb=" N ARG D 554 " --> pdb=" O VAL D 522 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N VAL D 522 " --> pdb=" O ARG D 554 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ASP D 556 " --> pdb=" O ALA D 520 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ALA D 520 " --> pdb=" O ASP D 556 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N TYR D 558 " --> pdb=" O GLY D 518 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLY D 518 " --> pdb=" O TYR D 558 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ARG D 560 " --> pdb=" O GLN D 516 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN D 516 " --> pdb=" O ARG D 560 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N MET D 530 " --> pdb=" O VAL D 522 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 501 through 503 removed outlier: 6.558A pdb=" N TYR D 501 " --> pdb=" O ALA D 555 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ALA D 555 " --> pdb=" O TYR D 501 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ARG D 554 " --> pdb=" O VAL D 522 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N VAL D 522 " --> pdb=" O ARG D 554 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ASP D 556 " --> pdb=" O ALA D 520 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ALA D 520 " --> pdb=" O ASP D 556 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N TYR D 558 " --> pdb=" O GLY D 518 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLY D 518 " --> pdb=" O TYR D 558 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ARG D 560 " --> pdb=" O GLN D 516 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN D 516 " --> pdb=" O ARG D 560 " (cutoff:3.500A) 1036 hydrogen bonds defined for protein. 3096 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.55 Time building geometry restraints manager: 1.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2609 1.33 - 1.45: 3919 1.45 - 1.57: 8124 1.57 - 1.69: 0 1.69 - 1.81: 188 Bond restraints: 14840 Sorted by residual: bond pdb=" C ASN B 300 " pdb=" O ASN B 300 " ideal model delta sigma weight residual 1.236 1.273 -0.036 1.15e-02 7.56e+03 9.90e+00 bond pdb=" C ASN D 300 " pdb=" O ASN D 300 " ideal model delta sigma weight residual 1.236 1.272 -0.035 1.15e-02 7.56e+03 9.50e+00 bond pdb=" C ASN C 300 " pdb=" O ASN C 300 " ideal model delta sigma weight residual 1.236 1.271 -0.035 1.15e-02 7.56e+03 9.19e+00 bond pdb=" C ASN A 300 " pdb=" O ASN A 300 " ideal model delta sigma weight residual 1.236 1.271 -0.035 1.15e-02 7.56e+03 9.06e+00 bond pdb=" C LEU D 306 " pdb=" O LEU D 306 " ideal model delta sigma weight residual 1.236 1.269 -0.032 1.15e-02 7.56e+03 7.86e+00 ... (remaining 14835 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 14101 1.39 - 2.79: 5000 2.79 - 4.18: 948 4.18 - 5.57: 115 5.57 - 6.96: 20 Bond angle restraints: 20184 Sorted by residual: angle pdb=" O VAL C 319 " pdb=" C VAL C 319 " pdb=" N PRO C 320 " ideal model delta sigma weight residual 120.07 124.19 -4.12 7.10e-01 1.98e+00 3.37e+01 angle pdb=" O VAL B 319 " pdb=" C VAL B 319 " pdb=" N PRO B 320 " ideal model delta sigma weight residual 120.07 124.18 -4.11 7.10e-01 1.98e+00 3.35e+01 angle pdb=" O VAL A 319 " pdb=" C VAL A 319 " pdb=" N PRO A 320 " ideal model delta sigma weight residual 120.07 124.17 -4.10 7.10e-01 1.98e+00 3.34e+01 angle pdb=" O VAL D 319 " pdb=" C VAL D 319 " pdb=" N PRO D 320 " ideal model delta sigma weight residual 120.07 124.16 -4.09 7.10e-01 1.98e+00 3.31e+01 angle pdb=" O ASP D 455 " pdb=" C ASP D 455 " pdb=" N PRO D 456 " ideal model delta sigma weight residual 120.38 124.75 -4.37 7.90e-01 1.60e+00 3.06e+01 ... (remaining 20179 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.18: 8052 16.18 - 32.36: 544 32.36 - 48.54: 68 48.54 - 64.72: 16 64.72 - 80.91: 4 Dihedral angle restraints: 8684 sinusoidal: 3008 harmonic: 5676 Sorted by residual: dihedral pdb=" CA ASN D 465 " pdb=" C ASN D 465 " pdb=" N CYS D 466 " pdb=" CA CYS D 466 " ideal model delta harmonic sigma weight residual -180.00 -160.06 -19.94 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA ASN A 465 " pdb=" C ASN A 465 " pdb=" N CYS A 466 " pdb=" CA CYS A 466 " ideal model delta harmonic sigma weight residual 180.00 -160.06 -19.94 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA ASN C 465 " pdb=" C ASN C 465 " pdb=" N CYS C 466 " pdb=" CA CYS C 466 " ideal model delta harmonic sigma weight residual -180.00 -160.09 -19.91 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 8681 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1474 0.065 - 0.129: 553 0.129 - 0.194: 189 0.194 - 0.258: 39 0.258 - 0.323: 13 Chirality restraints: 2268 Sorted by residual: chirality pdb=" CA PHE D 186 " pdb=" N PHE D 186 " pdb=" C PHE D 186 " pdb=" CB PHE D 186 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CA PHE C 186 " pdb=" N PHE C 186 " pdb=" C PHE C 186 " pdb=" CB PHE C 186 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CA PHE B 186 " pdb=" N PHE B 186 " pdb=" C PHE B 186 " pdb=" CB PHE B 186 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.58e+00 ... (remaining 2265 not shown) Planarity restraints: 2564 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 319 " 0.069 5.00e-02 4.00e+02 1.04e-01 1.74e+01 pdb=" N PRO C 320 " -0.180 5.00e-02 4.00e+02 pdb=" CA PRO C 320 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO C 320 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 319 " 0.069 5.00e-02 4.00e+02 1.04e-01 1.74e+01 pdb=" N PRO B 320 " -0.180 5.00e-02 4.00e+02 pdb=" CA PRO B 320 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO B 320 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 319 " -0.069 5.00e-02 4.00e+02 1.04e-01 1.74e+01 pdb=" N PRO D 320 " 0.180 5.00e-02 4.00e+02 pdb=" CA PRO D 320 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO D 320 " -0.056 5.00e-02 4.00e+02 ... (remaining 2561 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 5244 2.88 - 3.39: 15227 3.39 - 3.89: 24506 3.89 - 4.40: 26984 4.40 - 4.90: 43744 Nonbonded interactions: 115705 Sorted by model distance: nonbonded pdb=" O VAL A 257 " pdb=" OG1 THR A 260 " model vdw 2.380 3.040 nonbonded pdb=" O VAL C 257 " pdb=" OG1 THR C 260 " model vdw 2.381 3.040 nonbonded pdb=" O VAL D 257 " pdb=" OG1 THR D 260 " model vdw 2.381 3.040 nonbonded pdb=" O VAL B 257 " pdb=" OG1 THR B 260 " model vdw 2.381 3.040 nonbonded pdb=" O LYS A 261 " pdb=" OG SER A 264 " model vdw 2.415 3.040 ... (remaining 115700 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 14.550 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6556 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 0.042 14840 Z= 0.542 Angle : 1.441 6.963 20184 Z= 1.117 Chirality : 0.077 0.323 2268 Planarity : 0.006 0.104 2564 Dihedral : 11.339 80.905 5012 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.17), residues: 1904 helix: 2.21 (0.12), residues: 1276 sheet: -3.72 (0.34), residues: 116 loop : -2.35 (0.21), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 267 TYR 0.028 0.003 TYR C 411 PHE 0.028 0.002 PHE B 186 TRP 0.030 0.003 TRP B 281 HIS 0.006 0.003 HIS A 392 Details of bonding type rmsd covalent geometry : bond 0.00752 (14840) covalent geometry : angle 1.44093 (20184) hydrogen bonds : bond 0.17180 ( 1020) hydrogen bonds : angle 6.19264 ( 3096) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 444 time to evaluate : 0.632 Fit side-chains REVERT: A 121 GLU cc_start: 0.8281 (mt-10) cc_final: 0.7985 (mm-30) REVERT: A 122 LYS cc_start: 0.9078 (tttt) cc_final: 0.8815 (tptp) REVERT: A 149 MET cc_start: 0.8434 (mmm) cc_final: 0.8140 (mmm) REVERT: A 189 ASP cc_start: 0.8732 (t0) cc_final: 0.8375 (t0) REVERT: A 283 GLU cc_start: 0.8317 (mt-10) cc_final: 0.8030 (tp30) REVERT: A 317 PHE cc_start: 0.8034 (t80) cc_final: 0.7809 (t80) REVERT: A 433 ASP cc_start: 0.8078 (m-30) cc_final: 0.7848 (m-30) REVERT: A 445 ASP cc_start: 0.6910 (t0) cc_final: 0.6664 (t0) REVERT: A 514 PHE cc_start: 0.7943 (m-80) cc_final: 0.7732 (m-80) REVERT: A 515 ILE cc_start: 0.7728 (mt) cc_final: 0.7354 (tt) REVERT: A 517 HIS cc_start: 0.6518 (t70) cc_final: 0.5785 (t-90) REVERT: B 101 MET cc_start: 0.7359 (mmm) cc_final: 0.7098 (ttm) REVERT: B 113 MET cc_start: 0.8803 (tpp) cc_final: 0.8392 (mmm) REVERT: B 121 GLU cc_start: 0.8295 (mt-10) cc_final: 0.8052 (mm-30) REVERT: B 149 MET cc_start: 0.8421 (mmm) cc_final: 0.8103 (mmm) REVERT: B 189 ASP cc_start: 0.8824 (t0) cc_final: 0.8508 (t70) REVERT: B 283 GLU cc_start: 0.8338 (mt-10) cc_final: 0.8068 (tp30) REVERT: B 287 MET cc_start: 0.6209 (mmm) cc_final: 0.5939 (tpt) REVERT: B 317 PHE cc_start: 0.7963 (t80) cc_final: 0.7749 (t80) REVERT: B 356 MET cc_start: 0.7555 (ttm) cc_final: 0.7355 (ttt) REVERT: B 433 ASP cc_start: 0.8113 (m-30) cc_final: 0.7858 (m-30) REVERT: B 445 ASP cc_start: 0.7080 (t0) cc_final: 0.6804 (t0) REVERT: B 514 PHE cc_start: 0.7964 (m-80) cc_final: 0.7761 (m-80) REVERT: B 515 ILE cc_start: 0.7720 (mt) cc_final: 0.7301 (tt) REVERT: B 517 HIS cc_start: 0.6585 (t70) cc_final: 0.5878 (t-90) REVERT: C 101 MET cc_start: 0.7412 (mmm) cc_final: 0.7144 (ttm) REVERT: C 121 GLU cc_start: 0.8307 (mt-10) cc_final: 0.8050 (mm-30) REVERT: C 122 LYS cc_start: 0.9039 (tttt) cc_final: 0.8769 (tptp) REVERT: C 149 MET cc_start: 0.8418 (mmm) cc_final: 0.8113 (mmm) REVERT: C 189 ASP cc_start: 0.8740 (t0) cc_final: 0.8451 (t70) REVERT: C 283 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7894 (tp30) REVERT: C 317 PHE cc_start: 0.7994 (t80) cc_final: 0.7762 (t80) REVERT: C 356 MET cc_start: 0.7545 (ttm) cc_final: 0.7338 (ttt) REVERT: C 433 ASP cc_start: 0.8057 (m-30) cc_final: 0.7781 (m-30) REVERT: C 445 ASP cc_start: 0.7206 (t0) cc_final: 0.6975 (t0) REVERT: C 494 GLU cc_start: 0.7583 (mt-10) cc_final: 0.6908 (mt-10) REVERT: C 515 ILE cc_start: 0.7814 (mt) cc_final: 0.7384 (tt) REVERT: C 517 HIS cc_start: 0.6459 (t70) cc_final: 0.5734 (t-90) REVERT: D 121 GLU cc_start: 0.8290 (mt-10) cc_final: 0.8025 (mm-30) REVERT: D 122 LYS cc_start: 0.9065 (tttt) cc_final: 0.8800 (tptp) REVERT: D 149 MET cc_start: 0.8419 (mmm) cc_final: 0.8133 (mmm) REVERT: D 189 ASP cc_start: 0.8718 (t0) cc_final: 0.8382 (t0) REVERT: D 278 ILE cc_start: 0.7738 (mm) cc_final: 0.7536 (mt) REVERT: D 282 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7789 (mt-10) REVERT: D 283 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7949 (tp30) REVERT: D 317 PHE cc_start: 0.8029 (t80) cc_final: 0.7778 (t80) REVERT: D 433 ASP cc_start: 0.8037 (m-30) cc_final: 0.7770 (m-30) REVERT: D 445 ASP cc_start: 0.6979 (t0) cc_final: 0.6744 (t0) REVERT: D 494 GLU cc_start: 0.7458 (mt-10) cc_final: 0.6841 (mt-10) REVERT: D 514 PHE cc_start: 0.7916 (m-80) cc_final: 0.7668 (m-80) REVERT: D 515 ILE cc_start: 0.7758 (mt) cc_final: 0.7371 (tt) REVERT: D 517 HIS cc_start: 0.6438 (t70) cc_final: 0.5714 (t-90) outliers start: 0 outliers final: 0 residues processed: 444 average time/residue: 0.1181 time to fit residues: 78.8231 Evaluate side-chains 320 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 320 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.0030 chunk 91 optimal weight: 0.0670 chunk 149 optimal weight: 0.9990 overall best weight: 0.5328 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 398 GLN A 421 HIS A 568 ASN ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 398 GLN B 421 HIS B 568 ASN C 179 ASN C 286 HIS C 398 GLN C 421 HIS C 568 ASN D 179 ASN D 286 HIS D 398 GLN D 421 HIS D 568 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.105839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.088281 restraints weight = 34105.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.088160 restraints weight = 17456.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.088654 restraints weight = 17695.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.089721 restraints weight = 12718.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.089793 restraints weight = 10831.845| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14840 Z= 0.142 Angle : 0.571 8.929 20184 Z= 0.306 Chirality : 0.041 0.163 2268 Planarity : 0.005 0.061 2564 Dihedral : 4.103 18.008 2076 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.34 % Allowed : 8.96 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.48 (0.19), residues: 1904 helix: 3.20 (0.14), residues: 1304 sheet: -2.90 (0.40), residues: 112 loop : -1.80 (0.23), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 270 TYR 0.017 0.002 TYR D 289 PHE 0.023 0.002 PHE C 514 TRP 0.012 0.001 TRP C 330 HIS 0.003 0.001 HIS A 355 Details of bonding type rmsd covalent geometry : bond 0.00282 (14840) covalent geometry : angle 0.57137 (20184) hydrogen bonds : bond 0.04980 ( 1020) hydrogen bonds : angle 4.79229 ( 3096) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 387 time to evaluate : 0.583 Fit side-chains REVERT: A 122 LYS cc_start: 0.9278 (tttt) cc_final: 0.9072 (ptmm) REVERT: A 149 MET cc_start: 0.8267 (mmm) cc_final: 0.7600 (mmm) REVERT: A 189 ASP cc_start: 0.8759 (t0) cc_final: 0.7872 (t70) REVERT: A 265 LEU cc_start: 0.9446 (mt) cc_final: 0.9229 (mm) REVERT: A 317 PHE cc_start: 0.9050 (t80) cc_final: 0.8686 (t80) REVERT: A 418 MET cc_start: 0.8712 (mtt) cc_final: 0.8489 (mtt) REVERT: A 426 ASP cc_start: 0.8570 (p0) cc_final: 0.8122 (p0) REVERT: A 427 MET cc_start: 0.8151 (ttm) cc_final: 0.7906 (ttm) REVERT: A 433 ASP cc_start: 0.8402 (m-30) cc_final: 0.8166 (m-30) REVERT: B 101 MET cc_start: 0.7810 (mmm) cc_final: 0.7547 (ttm) REVERT: B 122 LYS cc_start: 0.9252 (OUTLIER) cc_final: 0.9042 (ttmm) REVERT: B 149 MET cc_start: 0.8296 (mmm) cc_final: 0.7580 (mmm) REVERT: B 189 ASP cc_start: 0.8704 (t0) cc_final: 0.7752 (t70) REVERT: B 317 PHE cc_start: 0.9023 (t80) cc_final: 0.8690 (t80) REVERT: B 433 ASP cc_start: 0.8469 (m-30) cc_final: 0.8232 (m-30) REVERT: C 101 MET cc_start: 0.7828 (mmm) cc_final: 0.7502 (ttm) REVERT: C 149 MET cc_start: 0.8341 (mmm) cc_final: 0.7585 (mmm) REVERT: C 189 ASP cc_start: 0.8751 (t0) cc_final: 0.7872 (t70) REVERT: C 317 PHE cc_start: 0.9036 (t80) cc_final: 0.8681 (t80) REVERT: C 386 TYR cc_start: 0.8826 (t80) cc_final: 0.8585 (t80) REVERT: C 433 ASP cc_start: 0.8516 (m-30) cc_final: 0.8266 (m-30) REVERT: C 494 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7828 (mt-10) REVERT: D 122 LYS cc_start: 0.9281 (tttt) cc_final: 0.8761 (tptp) REVERT: D 149 MET cc_start: 0.8315 (mmm) cc_final: 0.7621 (mmm) REVERT: D 189 ASP cc_start: 0.8799 (t0) cc_final: 0.7936 (t70) REVERT: D 265 LEU cc_start: 0.9444 (mt) cc_final: 0.9223 (mm) REVERT: D 317 PHE cc_start: 0.9055 (t80) cc_final: 0.8686 (t80) REVERT: D 386 TYR cc_start: 0.8800 (t80) cc_final: 0.8554 (t80) REVERT: D 426 ASP cc_start: 0.8569 (p0) cc_final: 0.8126 (p0) REVERT: D 433 ASP cc_start: 0.8401 (m-30) cc_final: 0.8169 (m-30) outliers start: 18 outliers final: 14 residues processed: 398 average time/residue: 0.1052 time to fit residues: 65.4622 Evaluate side-chains 303 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 288 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 259 PHE Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 259 PHE Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 259 PHE Chi-restraints excluded: chain D residue 443 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 110 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 142 optimal weight: 0.9990 chunk 167 optimal weight: 7.9990 chunk 174 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 135 optimal weight: 7.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 ASN B 156 ASN ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 ASN D 156 ASN D 300 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.104593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.086990 restraints weight = 34677.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.087819 restraints weight = 16630.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.088410 restraints weight = 12527.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.088796 restraints weight = 10938.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.089077 restraints weight = 10458.225| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14840 Z= 0.157 Angle : 0.543 6.612 20184 Z= 0.294 Chirality : 0.042 0.214 2268 Planarity : 0.004 0.044 2564 Dihedral : 4.024 18.086 2076 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.61 % Allowed : 11.12 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.20), residues: 1904 helix: 2.83 (0.14), residues: 1308 sheet: -2.53 (0.40), residues: 120 loop : -1.47 (0.25), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 458 TYR 0.017 0.001 TYR C 411 PHE 0.021 0.001 PHE C 514 TRP 0.010 0.002 TRP D 281 HIS 0.004 0.001 HIS C 392 Details of bonding type rmsd covalent geometry : bond 0.00347 (14840) covalent geometry : angle 0.54262 (20184) hydrogen bonds : bond 0.04587 ( 1020) hydrogen bonds : angle 4.58218 ( 3096) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 301 time to evaluate : 0.581 Fit side-chains REVERT: A 149 MET cc_start: 0.8294 (mmm) cc_final: 0.7843 (mmm) REVERT: A 189 ASP cc_start: 0.8737 (t0) cc_final: 0.7934 (t70) REVERT: A 317 PHE cc_start: 0.9016 (t80) cc_final: 0.8696 (t80) REVERT: A 426 ASP cc_start: 0.8618 (p0) cc_final: 0.8189 (p0) REVERT: A 433 ASP cc_start: 0.8363 (m-30) cc_final: 0.8108 (m-30) REVERT: B 149 MET cc_start: 0.8288 (mmm) cc_final: 0.7591 (mmm) REVERT: B 189 ASP cc_start: 0.8700 (t0) cc_final: 0.7841 (t70) REVERT: B 265 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8951 (mm) REVERT: B 317 PHE cc_start: 0.8918 (t80) cc_final: 0.8594 (t80) REVERT: B 418 MET cc_start: 0.9008 (mtt) cc_final: 0.8808 (mtt) REVERT: B 426 ASP cc_start: 0.8671 (p0) cc_final: 0.8245 (p0) REVERT: B 433 ASP cc_start: 0.8448 (m-30) cc_final: 0.8173 (m-30) REVERT: C 101 MET cc_start: 0.7735 (mmm) cc_final: 0.7523 (ttm) REVERT: C 112 ARG cc_start: 0.7875 (mtp180) cc_final: 0.7559 (ttm110) REVERT: C 149 MET cc_start: 0.8344 (mmm) cc_final: 0.7633 (mmm) REVERT: C 189 ASP cc_start: 0.8787 (t0) cc_final: 0.7961 (t70) REVERT: C 265 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8984 (mm) REVERT: C 317 PHE cc_start: 0.8994 (t80) cc_final: 0.8643 (t80) REVERT: C 426 ASP cc_start: 0.8603 (p0) cc_final: 0.8204 (p0) REVERT: C 433 ASP cc_start: 0.8496 (m-30) cc_final: 0.8226 (m-30) REVERT: C 494 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7806 (mt-10) REVERT: D 122 LYS cc_start: 0.9265 (tttt) cc_final: 0.8762 (tptp) REVERT: D 149 MET cc_start: 0.8359 (mmm) cc_final: 0.7856 (mmm) REVERT: D 189 ASP cc_start: 0.8782 (t0) cc_final: 0.8024 (t70) REVERT: D 317 PHE cc_start: 0.9020 (t80) cc_final: 0.8673 (t80) REVERT: D 426 ASP cc_start: 0.8600 (p0) cc_final: 0.8158 (p0) REVERT: D 433 ASP cc_start: 0.8369 (m-30) cc_final: 0.8119 (m-30) outliers start: 35 outliers final: 26 residues processed: 325 average time/residue: 0.1049 time to fit residues: 53.3430 Evaluate side-chains 308 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 280 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 259 PHE Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 466 CYS Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 435 TYR Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 466 CYS Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 259 PHE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 466 CYS Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 259 PHE Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 466 CYS Chi-restraints excluded: chain D residue 561 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 144 optimal weight: 10.0000 chunk 120 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 160 optimal weight: 0.9980 chunk 109 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 177 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 180 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 300 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.105766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.088330 restraints weight = 34645.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.088216 restraints weight = 17523.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.088691 restraints weight = 17571.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.089802 restraints weight = 12755.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.089821 restraints weight = 10916.664| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14840 Z= 0.123 Angle : 0.492 5.294 20184 Z= 0.265 Chirality : 0.040 0.261 2268 Planarity : 0.003 0.038 2564 Dihedral : 3.897 17.811 2076 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.46 % Allowed : 11.12 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.20), residues: 1904 helix: 2.72 (0.14), residues: 1308 sheet: -2.07 (0.42), residues: 120 loop : -1.25 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 492 TYR 0.016 0.001 TYR D 411 PHE 0.016 0.001 PHE C 514 TRP 0.008 0.001 TRP D 281 HIS 0.002 0.001 HIS B 286 Details of bonding type rmsd covalent geometry : bond 0.00262 (14840) covalent geometry : angle 0.49208 (20184) hydrogen bonds : bond 0.03996 ( 1020) hydrogen bonds : angle 4.37481 ( 3096) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 332 time to evaluate : 0.584 Fit side-chains REVERT: A 121 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7811 (mt-10) REVERT: A 149 MET cc_start: 0.8172 (mmm) cc_final: 0.7715 (mmm) REVERT: A 189 ASP cc_start: 0.8737 (t0) cc_final: 0.8038 (t70) REVERT: A 265 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8921 (mm) REVERT: A 317 PHE cc_start: 0.8991 (t80) cc_final: 0.8684 (t80) REVERT: A 433 ASP cc_start: 0.8339 (m-30) cc_final: 0.8078 (m-30) REVERT: B 144 TYR cc_start: 0.7903 (m-80) cc_final: 0.7635 (m-80) REVERT: B 149 MET cc_start: 0.8229 (mmm) cc_final: 0.7730 (mmm) REVERT: B 189 ASP cc_start: 0.8728 (t0) cc_final: 0.7958 (t70) REVERT: B 265 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8882 (mm) REVERT: B 317 PHE cc_start: 0.8883 (t80) cc_final: 0.8558 (t80) REVERT: B 356 MET cc_start: 0.8243 (tpp) cc_final: 0.7426 (ttm) REVERT: B 386 TYR cc_start: 0.8923 (t80) cc_final: 0.8611 (t80) REVERT: B 433 ASP cc_start: 0.8446 (m-30) cc_final: 0.8193 (m-30) REVERT: C 112 ARG cc_start: 0.7787 (mtp180) cc_final: 0.7550 (ttm110) REVERT: C 140 ASP cc_start: 0.7409 (t70) cc_final: 0.6951 (t70) REVERT: C 144 TYR cc_start: 0.7873 (m-80) cc_final: 0.7579 (m-80) REVERT: C 149 MET cc_start: 0.8280 (mmm) cc_final: 0.7753 (mmm) REVERT: C 189 ASP cc_start: 0.8765 (t0) cc_final: 0.8007 (t70) REVERT: C 265 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8876 (mm) REVERT: C 317 PHE cc_start: 0.8919 (t80) cc_final: 0.8582 (t80) REVERT: C 433 ASP cc_start: 0.8496 (m-30) cc_final: 0.8218 (m-30) REVERT: C 494 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7696 (mt-10) REVERT: D 122 LYS cc_start: 0.9299 (tttt) cc_final: 0.8777 (tptp) REVERT: D 149 MET cc_start: 0.8244 (mmm) cc_final: 0.7778 (mmm) REVERT: D 189 ASP cc_start: 0.8765 (t0) cc_final: 0.8054 (t70) REVERT: D 265 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8928 (mm) REVERT: D 282 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7883 (mt-10) REVERT: D 317 PHE cc_start: 0.8952 (t80) cc_final: 0.8675 (t80) REVERT: D 433 ASP cc_start: 0.8344 (m-30) cc_final: 0.8099 (m-30) outliers start: 33 outliers final: 15 residues processed: 349 average time/residue: 0.1030 time to fit residues: 56.5942 Evaluate side-chains 315 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 296 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 435 TYR Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 466 CYS Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 466 CYS Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 443 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 113 optimal weight: 1.9990 chunk 153 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 chunk 151 optimal weight: 0.9990 chunk 137 optimal weight: 9.9990 chunk 78 optimal weight: 0.6980 chunk 117 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 ASN ** B 179 ASN ** 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 = 0.3522 r_free = 0.3522 target = 0.105192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.087828 restraints weight = 34995.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.087769 restraints weight = 17568.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.088694 restraints weight = 14126.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.088836 restraints weight = 11990.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.089162 restraints weight = 11621.369| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14840 Z= 0.142 Angle : 0.504 5.610 20184 Z= 0.271 Chirality : 0.040 0.241 2268 Planarity : 0.003 0.039 2564 Dihedral : 3.831 17.445 2076 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.46 % Allowed : 15.15 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.19), residues: 1904 helix: 2.58 (0.14), residues: 1312 sheet: -1.88 (0.42), residues: 120 loop : -1.11 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 492 TYR 0.024 0.001 TYR C 289 PHE 0.023 0.001 PHE D 514 TRP 0.009 0.002 TRP C 281 HIS 0.004 0.001 HIS C 392 Details of bonding type rmsd covalent geometry : bond 0.00314 (14840) covalent geometry : angle 0.50396 (20184) hydrogen bonds : bond 0.04027 ( 1020) hydrogen bonds : angle 4.35161 ( 3096) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 311 time to evaluate : 0.616 Fit side-chains REVERT: A 112 ARG cc_start: 0.7792 (mtp180) cc_final: 0.7580 (ttm110) REVERT: A 149 MET cc_start: 0.8265 (mmm) cc_final: 0.7814 (mmm) REVERT: A 189 ASP cc_start: 0.8785 (t0) cc_final: 0.8057 (t70) REVERT: A 265 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8853 (mm) REVERT: A 317 PHE cc_start: 0.8939 (t80) cc_final: 0.8658 (t80) REVERT: A 433 ASP cc_start: 0.8328 (m-30) cc_final: 0.8090 (m-30) REVERT: B 122 LYS cc_start: 0.9293 (OUTLIER) cc_final: 0.9080 (ttmm) REVERT: B 144 TYR cc_start: 0.7835 (m-80) cc_final: 0.7569 (m-80) REVERT: B 149 MET cc_start: 0.8277 (mmm) cc_final: 0.7773 (mmm) REVERT: B 189 ASP cc_start: 0.8787 (t0) cc_final: 0.7992 (t70) REVERT: B 265 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8858 (mm) REVERT: B 317 PHE cc_start: 0.8825 (t80) cc_final: 0.8537 (t80) REVERT: B 356 MET cc_start: 0.8174 (tpp) cc_final: 0.7357 (ttm) REVERT: B 369 MET cc_start: 0.7927 (mmm) cc_final: 0.7720 (mmm) REVERT: B 415 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7885 (mt-10) REVERT: B 433 ASP cc_start: 0.8438 (m-30) cc_final: 0.8181 (m-30) REVERT: B 435 TYR cc_start: 0.8907 (OUTLIER) cc_final: 0.7698 (t80) REVERT: C 112 ARG cc_start: 0.7528 (mtp180) cc_final: 0.7265 (mmm160) REVERT: C 144 TYR cc_start: 0.7884 (m-80) cc_final: 0.7618 (m-80) REVERT: C 149 MET cc_start: 0.8407 (mmm) cc_final: 0.7658 (mmm) REVERT: C 189 ASP cc_start: 0.8823 (t0) cc_final: 0.7970 (t70) REVERT: C 265 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8884 (mm) REVERT: C 317 PHE cc_start: 0.8849 (t80) cc_final: 0.8521 (t80) REVERT: C 369 MET cc_start: 0.7896 (mmm) cc_final: 0.7671 (mmm) REVERT: C 433 ASP cc_start: 0.8494 (m-30) cc_final: 0.8213 (m-30) REVERT: C 494 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7755 (mt-10) REVERT: D 122 LYS cc_start: 0.9287 (tttt) cc_final: 0.8801 (tptp) REVERT: D 125 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7490 (mm-30) REVERT: D 149 MET cc_start: 0.8305 (mmm) cc_final: 0.7784 (tpp) REVERT: D 189 ASP cc_start: 0.8828 (t0) cc_final: 0.7572 (t70) REVERT: D 265 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8863 (mm) REVERT: D 282 GLU cc_start: 0.8290 (mt-10) cc_final: 0.8013 (mt-10) REVERT: D 317 PHE cc_start: 0.8940 (t80) cc_final: 0.8662 (t80) REVERT: D 369 MET cc_start: 0.7993 (mmm) cc_final: 0.7764 (mmm) REVERT: D 433 ASP cc_start: 0.8463 (m-30) cc_final: 0.8205 (m-30) outliers start: 33 outliers final: 20 residues processed: 331 average time/residue: 0.1028 time to fit residues: 53.6171 Evaluate side-chains 306 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 280 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 466 CYS Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 435 TYR Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 466 CYS Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 466 CYS Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 435 TYR Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 466 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 7.9990 chunk 111 optimal weight: 0.6980 chunk 157 optimal weight: 0.6980 chunk 92 optimal weight: 0.4980 chunk 186 optimal weight: 20.0000 chunk 74 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 153 optimal weight: 0.9990 chunk 142 optimal weight: 4.9990 chunk 90 optimal weight: 20.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 ASN ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 286 HIS D 300 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.105664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.088315 restraints weight = 35087.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.088558 restraints weight = 17774.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.089083 restraints weight = 14749.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.089346 restraints weight = 12247.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.089562 restraints weight = 10880.060| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14840 Z= 0.113 Angle : 0.489 7.801 20184 Z= 0.261 Chirality : 0.040 0.224 2268 Planarity : 0.004 0.065 2564 Dihedral : 3.770 17.750 2076 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.46 % Allowed : 15.67 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.13 (0.19), residues: 1904 helix: 2.51 (0.14), residues: 1312 sheet: -1.66 (0.43), residues: 120 loop : -0.98 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 267 TYR 0.029 0.001 TYR C 289 PHE 0.026 0.001 PHE B 514 TRP 0.011 0.001 TRP A 373 HIS 0.002 0.001 HIS D 517 Details of bonding type rmsd covalent geometry : bond 0.00236 (14840) covalent geometry : angle 0.48894 (20184) hydrogen bonds : bond 0.03775 ( 1020) hydrogen bonds : angle 4.24795 ( 3096) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 316 time to evaluate : 0.568 Fit side-chains REVERT: A 112 ARG cc_start: 0.7497 (mtp180) cc_final: 0.6602 (ttm110) REVERT: A 149 MET cc_start: 0.8127 (mmm) cc_final: 0.7675 (tpp) REVERT: A 189 ASP cc_start: 0.8789 (t0) cc_final: 0.7582 (t70) REVERT: A 265 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8863 (mm) REVERT: A 317 PHE cc_start: 0.8856 (t80) cc_final: 0.8533 (t80) REVERT: A 433 ASP cc_start: 0.8360 (m-30) cc_final: 0.8100 (m-30) REVERT: A 484 VAL cc_start: 0.8992 (t) cc_final: 0.8776 (t) REVERT: B 122 LYS cc_start: 0.9308 (OUTLIER) cc_final: 0.9090 (ttmm) REVERT: B 140 ASP cc_start: 0.7300 (t70) cc_final: 0.6707 (t70) REVERT: B 144 TYR cc_start: 0.7813 (m-80) cc_final: 0.7489 (m-80) REVERT: B 149 MET cc_start: 0.8250 (mmm) cc_final: 0.7821 (tpp) REVERT: B 189 ASP cc_start: 0.8771 (t0) cc_final: 0.7483 (t70) REVERT: B 265 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8788 (mm) REVERT: B 289 TYR cc_start: 0.7472 (m-10) cc_final: 0.7176 (m-10) REVERT: B 317 PHE cc_start: 0.8816 (t80) cc_final: 0.8505 (t80) REVERT: B 356 MET cc_start: 0.8161 (tpp) cc_final: 0.7406 (ttm) REVERT: B 369 MET cc_start: 0.8049 (mmm) cc_final: 0.7819 (mmm) REVERT: B 433 ASP cc_start: 0.8433 (m-30) cc_final: 0.8204 (m-30) REVERT: B 435 TYR cc_start: 0.8667 (OUTLIER) cc_final: 0.7658 (t80) REVERT: C 144 TYR cc_start: 0.7890 (m-80) cc_final: 0.7654 (m-80) REVERT: C 149 MET cc_start: 0.8285 (mmm) cc_final: 0.7523 (mmm) REVERT: C 189 ASP cc_start: 0.8785 (t0) cc_final: 0.7944 (t70) REVERT: C 265 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8812 (mm) REVERT: C 289 TYR cc_start: 0.7459 (m-10) cc_final: 0.7240 (m-10) REVERT: C 317 PHE cc_start: 0.8819 (t80) cc_final: 0.8507 (t80) REVERT: C 369 MET cc_start: 0.8016 (mmm) cc_final: 0.7759 (mmm) REVERT: C 433 ASP cc_start: 0.8391 (m-30) cc_final: 0.8106 (m-30) REVERT: C 494 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7846 (mt-10) REVERT: D 121 GLU cc_start: 0.8460 (mm-30) cc_final: 0.8254 (mm-30) REVERT: D 122 LYS cc_start: 0.9339 (tttt) cc_final: 0.8900 (tptp) REVERT: D 149 MET cc_start: 0.8237 (mmm) cc_final: 0.7510 (mmm) REVERT: D 186 PHE cc_start: 0.8740 (m-80) cc_final: 0.8492 (m-10) REVERT: D 189 ASP cc_start: 0.8781 (t0) cc_final: 0.7945 (t70) REVERT: D 265 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8857 (mm) REVERT: D 282 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7818 (mt-10) REVERT: D 317 PHE cc_start: 0.8901 (t80) cc_final: 0.8610 (t80) REVERT: D 433 ASP cc_start: 0.8343 (m-30) cc_final: 0.8098 (m-30) REVERT: D 435 TYR cc_start: 0.9001 (OUTLIER) cc_final: 0.7855 (t80) REVERT: D 484 VAL cc_start: 0.9059 (t) cc_final: 0.8852 (t) outliers start: 33 outliers final: 20 residues processed: 333 average time/residue: 0.1032 time to fit residues: 54.1662 Evaluate side-chains 314 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 287 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 466 CYS Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 435 TYR Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 466 CYS Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 435 TYR Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 466 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 140 optimal weight: 30.0000 chunk 162 optimal weight: 0.0670 chunk 117 optimal weight: 0.7980 chunk 168 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 48 optimal weight: 10.0000 chunk 137 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 overall best weight: 1.5724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 HIS A 300 ASN A 406 GLN ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 300 ASN C 300 ASN D 179 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.106040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.088243 restraints weight = 34936.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.088463 restraints weight = 16770.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.088843 restraints weight = 17326.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.089799 restraints weight = 12501.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.089875 restraints weight = 10658.042| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14840 Z= 0.155 Angle : 0.516 7.111 20184 Z= 0.275 Chirality : 0.040 0.204 2268 Planarity : 0.004 0.056 2564 Dihedral : 3.790 17.862 2076 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.76 % Allowed : 16.19 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.19), residues: 1904 helix: 2.42 (0.14), residues: 1312 sheet: -1.48 (0.43), residues: 120 loop : -0.87 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 112 TYR 0.036 0.001 TYR D 289 PHE 0.024 0.001 PHE B 514 TRP 0.011 0.001 TRP A 281 HIS 0.004 0.001 HIS C 392 Details of bonding type rmsd covalent geometry : bond 0.00348 (14840) covalent geometry : angle 0.51567 (20184) hydrogen bonds : bond 0.03950 ( 1020) hydrogen bonds : angle 4.26934 ( 3096) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 285 time to evaluate : 0.583 Fit side-chains REVERT: A 149 MET cc_start: 0.8262 (mmm) cc_final: 0.7747 (tpp) REVERT: A 189 ASP cc_start: 0.8842 (t0) cc_final: 0.7566 (t70) REVERT: A 265 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8844 (mm) REVERT: A 289 TYR cc_start: 0.7390 (m-10) cc_final: 0.7067 (m-10) REVERT: A 317 PHE cc_start: 0.8907 (t80) cc_final: 0.8593 (t80) REVERT: A 433 ASP cc_start: 0.8407 (m-30) cc_final: 0.8127 (m-30) REVERT: A 484 VAL cc_start: 0.9018 (t) cc_final: 0.8813 (t) REVERT: B 122 LYS cc_start: 0.9330 (OUTLIER) cc_final: 0.9121 (ttmm) REVERT: B 144 TYR cc_start: 0.7885 (m-80) cc_final: 0.7628 (m-80) REVERT: B 149 MET cc_start: 0.8368 (mmm) cc_final: 0.7865 (tpp) REVERT: B 189 ASP cc_start: 0.8862 (t0) cc_final: 0.7522 (t70) REVERT: B 265 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8793 (mm) REVERT: B 317 PHE cc_start: 0.8911 (t80) cc_final: 0.8610 (t80) REVERT: B 356 MET cc_start: 0.8247 (tpp) cc_final: 0.7424 (ttm) REVERT: B 433 ASP cc_start: 0.8542 (m-30) cc_final: 0.8209 (m-30) REVERT: B 435 TYR cc_start: 0.8786 (OUTLIER) cc_final: 0.7577 (t80) REVERT: C 149 MET cc_start: 0.8431 (mmm) cc_final: 0.7672 (mmm) REVERT: C 189 ASP cc_start: 0.8821 (t0) cc_final: 0.7955 (t70) REVERT: C 317 PHE cc_start: 0.8921 (t80) cc_final: 0.8614 (t80) REVERT: C 433 ASP cc_start: 0.8526 (m-30) cc_final: 0.8209 (m-30) REVERT: C 494 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7949 (mt-10) REVERT: D 122 LYS cc_start: 0.9363 (tttt) cc_final: 0.8907 (tptp) REVERT: D 149 MET cc_start: 0.8439 (mmm) cc_final: 0.7886 (mmm) REVERT: D 189 ASP cc_start: 0.8884 (t0) cc_final: 0.8040 (t70) REVERT: D 265 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8851 (mm) REVERT: D 317 PHE cc_start: 0.8902 (t80) cc_final: 0.8603 (t80) REVERT: D 369 MET cc_start: 0.8070 (mmm) cc_final: 0.7819 (mmm) REVERT: D 433 ASP cc_start: 0.8537 (m-30) cc_final: 0.8208 (m-30) REVERT: D 435 TYR cc_start: 0.8612 (OUTLIER) cc_final: 0.7835 (t80) REVERT: D 484 VAL cc_start: 0.9024 (t) cc_final: 0.8819 (t) outliers start: 37 outliers final: 27 residues processed: 302 average time/residue: 0.0996 time to fit residues: 47.9142 Evaluate side-chains 309 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 276 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 466 CYS Chi-restraints excluded: chain A residue 517 HIS Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 435 TYR Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 466 CYS Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 466 CYS Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 435 TYR Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 466 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 142 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 177 optimal weight: 3.9990 chunk 134 optimal weight: 6.9990 chunk 185 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 99 optimal weight: 9.9990 chunk 113 optimal weight: 5.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN B 179 ASN D 300 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.105573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.088242 restraints weight = 34787.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.087832 restraints weight = 17249.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.088687 restraints weight = 15787.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.089253 restraints weight = 11858.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.089416 restraints weight = 11024.650| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14840 Z= 0.121 Angle : 0.507 7.304 20184 Z= 0.270 Chirality : 0.040 0.192 2268 Planarity : 0.003 0.032 2564 Dihedral : 3.753 19.093 2076 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.46 % Allowed : 17.31 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.19), residues: 1904 helix: 2.43 (0.14), residues: 1308 sheet: -1.30 (0.43), residues: 120 loop : -0.70 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 492 TYR 0.038 0.001 TYR D 289 PHE 0.031 0.001 PHE B 514 TRP 0.011 0.001 TRP C 281 HIS 0.002 0.001 HIS A 437 Details of bonding type rmsd covalent geometry : bond 0.00260 (14840) covalent geometry : angle 0.50656 (20184) hydrogen bonds : bond 0.03760 ( 1020) hydrogen bonds : angle 4.25702 ( 3096) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 289 time to evaluate : 0.615 Fit side-chains REVERT: A 149 MET cc_start: 0.8205 (mmm) cc_final: 0.7759 (tpp) REVERT: A 189 ASP cc_start: 0.8770 (t0) cc_final: 0.7518 (t70) REVERT: A 265 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8881 (mm) REVERT: A 317 PHE cc_start: 0.8851 (t80) cc_final: 0.8555 (t80) REVERT: A 433 ASP cc_start: 0.8356 (m-30) cc_final: 0.8094 (m-30) REVERT: A 484 VAL cc_start: 0.9027 (t) cc_final: 0.8817 (t) REVERT: B 122 LYS cc_start: 0.9329 (OUTLIER) cc_final: 0.9117 (ttmm) REVERT: B 144 TYR cc_start: 0.7774 (m-80) cc_final: 0.7533 (m-80) REVERT: B 265 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8796 (mm) REVERT: B 317 PHE cc_start: 0.8857 (t80) cc_final: 0.8555 (t80) REVERT: B 356 MET cc_start: 0.8203 (tpp) cc_final: 0.7417 (ttm) REVERT: B 369 MET cc_start: 0.8023 (mmm) cc_final: 0.7676 (ptt) REVERT: B 433 ASP cc_start: 0.8519 (m-30) cc_final: 0.8164 (m-30) REVERT: B 435 TYR cc_start: 0.8730 (OUTLIER) cc_final: 0.7608 (t80) REVERT: C 149 MET cc_start: 0.8319 (mmm) cc_final: 0.7574 (mmm) REVERT: C 189 ASP cc_start: 0.8762 (t0) cc_final: 0.7876 (t70) REVERT: C 265 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8817 (mm) REVERT: C 287 MET cc_start: 0.8128 (tpt) cc_final: 0.7842 (tpt) REVERT: C 317 PHE cc_start: 0.8875 (t80) cc_final: 0.8567 (t80) REVERT: C 369 MET cc_start: 0.8016 (mmm) cc_final: 0.7689 (ptt) REVERT: C 433 ASP cc_start: 0.8397 (m-30) cc_final: 0.8110 (m-30) REVERT: C 494 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7908 (mt-10) REVERT: D 122 LYS cc_start: 0.9362 (tttt) cc_final: 0.8897 (tptp) REVERT: D 149 MET cc_start: 0.8312 (mmm) cc_final: 0.7587 (tpp) REVERT: D 186 PHE cc_start: 0.8729 (m-80) cc_final: 0.8503 (m-10) REVERT: D 189 ASP cc_start: 0.8815 (t0) cc_final: 0.7429 (t70) REVERT: D 265 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.8882 (mm) REVERT: D 317 PHE cc_start: 0.8839 (t80) cc_final: 0.8524 (t80) REVERT: D 369 MET cc_start: 0.8096 (mmm) cc_final: 0.7830 (mmm) REVERT: D 433 ASP cc_start: 0.8492 (m-30) cc_final: 0.8179 (m-30) REVERT: D 435 TYR cc_start: 0.8634 (OUTLIER) cc_final: 0.7940 (t80) outliers start: 33 outliers final: 23 residues processed: 305 average time/residue: 0.0989 time to fit residues: 49.1234 Evaluate side-chains 301 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 271 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 466 CYS Chi-restraints excluded: chain A residue 517 HIS Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 435 TYR Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 466 CYS Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 435 TYR Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 466 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 51 optimal weight: 0.9980 chunk 174 optimal weight: 4.9990 chunk 164 optimal weight: 3.9990 chunk 96 optimal weight: 20.0000 chunk 6 optimal weight: 4.9990 chunk 94 optimal weight: 8.9990 chunk 97 optimal weight: 0.9990 chunk 170 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 154 optimal weight: 7.9990 chunk 73 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN B 103 GLN D 300 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.103697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.086235 restraints weight = 35172.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.086107 restraints weight = 18006.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.086531 restraints weight = 18662.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.087601 restraints weight = 13528.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.087618 restraints weight = 11366.617| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14840 Z= 0.192 Angle : 0.553 7.127 20184 Z= 0.299 Chirality : 0.041 0.186 2268 Planarity : 0.004 0.059 2564 Dihedral : 3.859 18.929 2076 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.99 % Allowed : 17.01 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.19), residues: 1904 helix: 2.30 (0.14), residues: 1312 sheet: -1.28 (0.43), residues: 120 loop : -0.66 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 492 TYR 0.036 0.002 TYR C 289 PHE 0.032 0.002 PHE B 514 TRP 0.015 0.002 TRP A 281 HIS 0.005 0.001 HIS D 392 Details of bonding type rmsd covalent geometry : bond 0.00435 (14840) covalent geometry : angle 0.55297 (20184) hydrogen bonds : bond 0.04166 ( 1020) hydrogen bonds : angle 4.37137 ( 3096) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 277 time to evaluate : 0.597 Fit side-chains REVERT: A 149 MET cc_start: 0.8364 (mmm) cc_final: 0.7905 (tpp) REVERT: A 189 ASP cc_start: 0.8789 (t0) cc_final: 0.7364 (t70) REVERT: A 265 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8928 (mm) REVERT: A 287 MET cc_start: 0.8021 (tpt) cc_final: 0.7739 (tpt) REVERT: A 317 PHE cc_start: 0.8897 (t80) cc_final: 0.8588 (t80) REVERT: A 433 ASP cc_start: 0.8483 (m-30) cc_final: 0.8206 (m-30) REVERT: B 122 LYS cc_start: 0.9334 (OUTLIER) cc_final: 0.9121 (ttmm) REVERT: B 144 TYR cc_start: 0.7847 (m-80) cc_final: 0.7628 (m-10) REVERT: B 189 ASP cc_start: 0.8421 (t70) cc_final: 0.7688 (t0) REVERT: B 265 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8832 (mm) REVERT: B 317 PHE cc_start: 0.8898 (t80) cc_final: 0.8588 (t80) REVERT: B 433 ASP cc_start: 0.8512 (m-30) cc_final: 0.8210 (m-30) REVERT: B 435 TYR cc_start: 0.8813 (OUTLIER) cc_final: 0.7658 (t80) REVERT: C 149 MET cc_start: 0.8426 (mmm) cc_final: 0.7971 (mmm) REVERT: C 189 ASP cc_start: 0.8771 (t0) cc_final: 0.8068 (t70) REVERT: C 287 MET cc_start: 0.8187 (tpt) cc_final: 0.7897 (tpt) REVERT: C 317 PHE cc_start: 0.8920 (t80) cc_final: 0.8595 (t80) REVERT: C 433 ASP cc_start: 0.8504 (m-30) cc_final: 0.8206 (m-30) REVERT: C 484 VAL cc_start: 0.8978 (t) cc_final: 0.8765 (t) REVERT: D 122 LYS cc_start: 0.9369 (tttt) cc_final: 0.8892 (tptp) REVERT: D 149 MET cc_start: 0.8389 (mmm) cc_final: 0.7674 (tpp) REVERT: D 189 ASP cc_start: 0.8849 (t0) cc_final: 0.7405 (t70) REVERT: D 265 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.8926 (mm) REVERT: D 317 PHE cc_start: 0.8910 (t80) cc_final: 0.8594 (t80) REVERT: D 433 ASP cc_start: 0.8520 (m-30) cc_final: 0.8221 (m-30) REVERT: D 435 TYR cc_start: 0.8631 (OUTLIER) cc_final: 0.8085 (t80) outliers start: 40 outliers final: 32 residues processed: 297 average time/residue: 0.0984 time to fit residues: 47.0354 Evaluate side-chains 306 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 268 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 466 CYS Chi-restraints excluded: chain A residue 517 HIS Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 435 TYR Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 466 CYS Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 466 CYS Chi-restraints excluded: chain C residue 515 ILE Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 435 TYR Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 466 CYS Chi-restraints excluded: chain D residue 517 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 163 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 139 optimal weight: 6.9990 chunk 92 optimal weight: 20.0000 chunk 100 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 160 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 300 ASN D 300 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.104364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.086944 restraints weight = 35212.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.087444 restraints weight = 18840.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.087753 restraints weight = 19205.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.088456 restraints weight = 13304.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.088610 restraints weight = 11551.554| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14840 Z= 0.152 Angle : 0.543 7.579 20184 Z= 0.291 Chirality : 0.041 0.191 2268 Planarity : 0.003 0.038 2564 Dihedral : 3.860 19.590 2076 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.54 % Allowed : 17.76 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.19), residues: 1904 helix: 2.25 (0.14), residues: 1312 sheet: -1.12 (0.43), residues: 120 loop : -0.58 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 492 TYR 0.034 0.001 TYR C 289 PHE 0.034 0.001 PHE B 514 TRP 0.013 0.002 TRP A 281 HIS 0.004 0.001 HIS A 392 Details of bonding type rmsd covalent geometry : bond 0.00342 (14840) covalent geometry : angle 0.54335 (20184) hydrogen bonds : bond 0.04004 ( 1020) hydrogen bonds : angle 4.38662 ( 3096) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 274 time to evaluate : 0.521 Fit side-chains REVERT: A 149 MET cc_start: 0.8252 (mmm) cc_final: 0.7591 (tpp) REVERT: A 189 ASP cc_start: 0.8742 (t0) cc_final: 0.7443 (t70) REVERT: A 265 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8870 (mm) REVERT: A 287 MET cc_start: 0.8104 (tpt) cc_final: 0.7835 (tpt) REVERT: A 317 PHE cc_start: 0.8869 (t80) cc_final: 0.8567 (t80) REVERT: A 433 ASP cc_start: 0.8464 (m-30) cc_final: 0.8196 (m-30) REVERT: B 101 MET cc_start: 0.8539 (ttp) cc_final: 0.8216 (ttm) REVERT: B 122 LYS cc_start: 0.9307 (OUTLIER) cc_final: 0.9092 (ttmm) REVERT: B 265 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8840 (mm) REVERT: B 317 PHE cc_start: 0.8880 (t80) cc_final: 0.8570 (t80) REVERT: B 369 MET cc_start: 0.8118 (mmm) cc_final: 0.7796 (ptt) REVERT: B 433 ASP cc_start: 0.8521 (m-30) cc_final: 0.8203 (m-30) REVERT: B 435 TYR cc_start: 0.8791 (OUTLIER) cc_final: 0.7721 (t80) REVERT: B 484 VAL cc_start: 0.8966 (t) cc_final: 0.8759 (t) REVERT: C 149 MET cc_start: 0.8370 (mmm) cc_final: 0.7694 (tpp) REVERT: C 189 ASP cc_start: 0.8716 (t0) cc_final: 0.7214 (t70) REVERT: C 265 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8823 (mm) REVERT: C 287 MET cc_start: 0.8173 (tpt) cc_final: 0.7927 (tpt) REVERT: C 317 PHE cc_start: 0.8905 (t80) cc_final: 0.8589 (t80) REVERT: C 369 MET cc_start: 0.8092 (mmm) cc_final: 0.7772 (ptt) REVERT: C 433 ASP cc_start: 0.8495 (m-30) cc_final: 0.8204 (m-30) REVERT: C 484 VAL cc_start: 0.8950 (t) cc_final: 0.8744 (t) REVERT: D 122 LYS cc_start: 0.9331 (tttt) cc_final: 0.8884 (tptp) REVERT: D 149 MET cc_start: 0.8343 (mmm) cc_final: 0.7638 (tpp) REVERT: D 189 ASP cc_start: 0.8779 (t0) cc_final: 0.7170 (t70) REVERT: D 265 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.8904 (mm) REVERT: D 287 MET cc_start: 0.7978 (tpt) cc_final: 0.7579 (tpt) REVERT: D 317 PHE cc_start: 0.8901 (t80) cc_final: 0.8569 (t80) REVERT: D 369 MET cc_start: 0.8080 (mmm) cc_final: 0.7804 (ptt) REVERT: D 433 ASP cc_start: 0.8522 (m-30) cc_final: 0.8216 (m-30) REVERT: D 435 TYR cc_start: 0.8689 (OUTLIER) cc_final: 0.8187 (t80) outliers start: 34 outliers final: 27 residues processed: 290 average time/residue: 0.0951 time to fit residues: 44.9104 Evaluate side-chains 302 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 268 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 466 CYS Chi-restraints excluded: chain A residue 517 HIS Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 435 TYR Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 466 CYS Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 515 ILE Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 435 TYR Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 466 CYS Chi-restraints excluded: chain D residue 517 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 9 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 98 optimal weight: 0.0470 chunk 169 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 chunk 156 optimal weight: 0.6980 chunk 190 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 189 optimal weight: 0.4980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 156 ASN D 300 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.106881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.089436 restraints weight = 34646.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.089657 restraints weight = 17772.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.090260 restraints weight = 17233.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.090950 restraints weight = 13131.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.091165 restraints weight = 11841.618| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14840 Z= 0.112 Angle : 0.514 7.462 20184 Z= 0.273 Chirality : 0.040 0.190 2268 Planarity : 0.003 0.034 2564 Dihedral : 3.738 20.230 2076 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.87 % Allowed : 18.66 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.19), residues: 1904 helix: 2.30 (0.14), residues: 1308 sheet: -0.98 (0.43), residues: 120 loop : -0.46 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 492 TYR 0.031 0.001 TYR C 289 PHE 0.033 0.001 PHE B 514 TRP 0.014 0.001 TRP B 145 HIS 0.003 0.001 HIS C 286 Details of bonding type rmsd covalent geometry : bond 0.00236 (14840) covalent geometry : angle 0.51388 (20184) hydrogen bonds : bond 0.03582 ( 1020) hydrogen bonds : angle 4.30067 ( 3096) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2299.12 seconds wall clock time: 40 minutes 37.49 seconds (2437.49 seconds total)