Starting phenix.real_space_refine on Sun Sep 13 02:22:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6u8a_20686/09_2026/6u8a_20686.cif Found real_map, /net/cci-nas-00/data/ceres_data/6u8a_20686/09_2026/6u8a_20686.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6u8a_20686/09_2026/6u8a_20686.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6u8a_20686/09_2026/6u8a_20686.map" model { file = "/net/cci-nas-00/data/ceres_data/6u8a_20686/09_2026/6u8a_20686.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6u8a_20686/09_2026/6u8a_20686.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6u8a_20686/09_2026/6u8a_20686.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6u8a_20686/09_2026/6u8a_20686.cif" } resolution = 3.4 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= 0.005 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 116 5.16 5 C 13172 2.51 5 N 3324 2.21 5 O 3420 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 100 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20032 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 617, 4985 Classifications: {'peptide': 617} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 594} Chain breaks: 4 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'GLU:plan': 4, 'ASP:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 48 Chain: "B" Number of atoms: 4985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 617, 4985 Classifications: {'peptide': 617} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 594} Chain breaks: 4 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'GLU:plan': 4, 'ASP:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 48 Chain: "C" Number of atoms: 4985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 617, 4985 Classifications: {'peptide': 617} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 594} Chain breaks: 4 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'GLU:plan': 4, 'ASP:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 48 Chain: "D" Number of atoms: 4985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 617, 4985 Classifications: {'peptide': 617} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 594} Chain breaks: 4 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'GLU:plan': 4, 'ASP:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 48 Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Unusual residues: {'P0T': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'P0T': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'P0T': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.99, per 1000 atoms: 0.20 Number of scatterers: 20032 At special positions: 0 Unit cell: (126.14, 126.14, 111.3, 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 116 16.00 O 3420 8.00 N 3324 7.00 C 13172 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: 1.65 Conformation dependent library (CDL) restraints added in 659.1 milliseconds 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4672 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 4 sheets defined 61.6% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 76 through 87 Processing helix chain 'A' and resid 95 through 102 removed outlier: 3.576A pdb=" N ARG A 100 " --> pdb=" O LEU A 96 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ASN A 102 " --> pdb=" O TYR A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 112 removed outlier: 3.618A pdb=" N THR A 112 " --> pdb=" O SER A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 135 through 145 Processing helix chain 'A' and resid 167 through 174 Processing helix chain 'A' and resid 176 through 185 Processing helix chain 'A' and resid 196 through 200 Processing helix chain 'A' and resid 212 through 219 Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 248 through 256 Processing helix chain 'A' and resid 260 through 282 Processing helix chain 'A' and resid 286 through 290 removed outlier: 3.566A pdb=" N ILE A 290 " --> pdb=" O LEU A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 305 Processing helix chain 'A' and resid 307 through 316 removed outlier: 3.624A pdb=" N PHE A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 324 removed outlier: 4.363A pdb=" N TYR A 323 " --> pdb=" O SER A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 363 Processing helix chain 'A' and resid 368 through 372 Processing helix chain 'A' and resid 377 through 413 removed outlier: 5.328A pdb=" N SER A 391 " --> pdb=" O ASP A 387 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ARG A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 459 Processing helix chain 'A' and resid 471 through 492 removed outlier: 3.968A pdb=" N LEU A 475 " --> pdb=" O TYR A 471 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU A 477 " --> pdb=" O GLU A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 512 removed outlier: 4.266A pdb=" N LEU A 500 " --> pdb=" O TRP A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 518 removed outlier: 3.836A pdb=" N THR A 516 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG A 517 " --> pdb=" O TYR A 514 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY A 518 " --> pdb=" O TYR A 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 513 through 518' Processing helix chain 'A' and resid 519 through 529 Processing helix chain 'A' and resid 533 through 559 removed outlier: 3.706A pdb=" N PHE A 540 " --> pdb=" O ASP A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 602 Processing helix chain 'A' and resid 618 through 649 Processing helix chain 'A' and resid 655 through 672 Processing helix chain 'A' and resid 711 through 718 Processing helix chain 'B' and resid 76 through 87 Processing helix chain 'B' and resid 95 through 102 removed outlier: 3.576A pdb=" N ARG B 100 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ASN B 102 " --> pdb=" O TYR B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 112 removed outlier: 3.618A pdb=" N THR B 112 " --> pdb=" O SER B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 Processing helix chain 'B' and resid 135 through 145 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 176 through 185 Processing helix chain 'B' and resid 196 through 200 Processing helix chain 'B' and resid 212 through 219 Processing helix chain 'B' and resid 222 through 231 Processing helix chain 'B' and resid 248 through 256 Processing helix chain 'B' and resid 260 through 282 Processing helix chain 'B' and resid 286 through 290 removed outlier: 3.566A pdb=" N ILE B 290 " --> pdb=" O LEU B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 305 Processing helix chain 'B' and resid 307 through 316 removed outlier: 3.624A pdb=" N PHE B 311 " --> pdb=" O LYS B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 324 removed outlier: 4.363A pdb=" N TYR B 323 " --> pdb=" O SER B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 363 Processing helix chain 'B' and resid 368 through 372 Processing helix chain 'B' and resid 377 through 413 removed outlier: 5.328A pdb=" N SER B 391 " --> pdb=" O ASP B 387 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ARG B 392 " --> pdb=" O ARG B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 459 Processing helix chain 'B' and resid 471 through 492 removed outlier: 3.968A pdb=" N LEU B 475 " --> pdb=" O TYR B 471 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU B 477 " --> pdb=" O GLU B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 512 removed outlier: 4.266A pdb=" N LEU B 500 " --> pdb=" O TRP B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 518 removed outlier: 3.836A pdb=" N THR B 516 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG B 517 " --> pdb=" O TYR B 514 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY B 518 " --> pdb=" O TYR B 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 513 through 518' Processing helix chain 'B' and resid 519 through 529 Processing helix chain 'B' and resid 533 through 559 removed outlier: 3.706A pdb=" N PHE B 540 " --> pdb=" O ASP B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 602 Processing helix chain 'B' and resid 618 through 649 Processing helix chain 'B' and resid 655 through 672 Processing helix chain 'B' and resid 711 through 718 Processing helix chain 'C' and resid 76 through 87 Processing helix chain 'C' and resid 95 through 102 removed outlier: 3.577A pdb=" N ARG C 100 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASN C 102 " --> pdb=" O TYR C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 112 removed outlier: 3.619A pdb=" N THR C 112 " --> pdb=" O SER C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 Processing helix chain 'C' and resid 135 through 145 Processing helix chain 'C' and resid 166 through 174 removed outlier: 4.037A pdb=" N ILE C 170 " --> pdb=" O SER C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 185 Processing helix chain 'C' and resid 196 through 200 Processing helix chain 'C' and resid 212 through 219 Processing helix chain 'C' and resid 222 through 231 Processing helix chain 'C' and resid 248 through 256 Processing helix chain 'C' and resid 260 through 282 Processing helix chain 'C' and resid 286 through 290 removed outlier: 3.566A pdb=" N ILE C 290 " --> pdb=" O LEU C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 305 Processing helix chain 'C' and resid 307 through 316 removed outlier: 3.624A pdb=" N PHE C 311 " --> pdb=" O LYS C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 324 removed outlier: 4.363A pdb=" N TYR C 323 " --> pdb=" O SER C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 363 Processing helix chain 'C' and resid 368 through 372 Processing helix chain 'C' and resid 377 through 413 removed outlier: 5.329A pdb=" N SER C 391 " --> pdb=" O ASP C 387 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ARG C 392 " --> pdb=" O ARG C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 459 Processing helix chain 'C' and resid 471 through 492 removed outlier: 3.968A pdb=" N LEU C 475 " --> pdb=" O TYR C 471 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU C 477 " --> pdb=" O GLU C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 512 removed outlier: 4.266A pdb=" N LEU C 500 " --> pdb=" O TRP C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 518 removed outlier: 3.837A pdb=" N THR C 516 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG C 517 " --> pdb=" O TYR C 514 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY C 518 " --> pdb=" O TYR C 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 513 through 518' Processing helix chain 'C' and resid 519 through 529 Processing helix chain 'C' and resid 533 through 559 removed outlier: 3.705A pdb=" N PHE C 540 " --> pdb=" O ASP C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 602 Processing helix chain 'C' and resid 618 through 649 Processing helix chain 'C' and resid 655 through 672 Processing helix chain 'C' and resid 711 through 718 Processing helix chain 'D' and resid 76 through 87 Processing helix chain 'D' and resid 95 through 102 removed outlier: 3.577A pdb=" N ARG D 100 " --> pdb=" O LEU D 96 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ASN D 102 " --> pdb=" O TYR D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 112 removed outlier: 3.618A pdb=" N THR D 112 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 Processing helix chain 'D' and resid 135 through 145 Processing helix chain 'D' and resid 167 through 174 Processing helix chain 'D' and resid 176 through 185 Processing helix chain 'D' and resid 196 through 200 Processing helix chain 'D' and resid 212 through 219 Processing helix chain 'D' and resid 222 through 231 Processing helix chain 'D' and resid 248 through 256 Processing helix chain 'D' and resid 260 through 282 Processing helix chain 'D' and resid 286 through 290 removed outlier: 3.566A pdb=" N ILE D 290 " --> pdb=" O LEU D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 305 Processing helix chain 'D' and resid 307 through 316 removed outlier: 3.623A pdb=" N PHE D 311 " --> pdb=" O LYS D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 324 removed outlier: 4.363A pdb=" N TYR D 323 " --> pdb=" O SER D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 363 Processing helix chain 'D' and resid 368 through 372 Processing helix chain 'D' and resid 377 through 413 removed outlier: 5.328A pdb=" N SER D 391 " --> pdb=" O ASP D 387 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N ARG D 392 " --> pdb=" O ARG D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 459 Processing helix chain 'D' and resid 471 through 492 removed outlier: 3.968A pdb=" N LEU D 475 " --> pdb=" O TYR D 471 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU D 477 " --> pdb=" O GLU D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 512 removed outlier: 4.266A pdb=" N LEU D 500 " --> pdb=" O TRP D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 518 removed outlier: 3.836A pdb=" N THR D 516 " --> pdb=" O LEU D 513 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG D 517 " --> pdb=" O TYR D 514 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY D 518 " --> pdb=" O TYR D 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 513 through 518' Processing helix chain 'D' and resid 519 through 529 Processing helix chain 'D' and resid 533 through 559 removed outlier: 3.706A pdb=" N PHE D 540 " --> pdb=" O ASP D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 602 Processing helix chain 'D' and resid 618 through 649 Processing helix chain 'D' and resid 655 through 672 Processing helix chain 'D' and resid 711 through 718 Processing sheet with id=AA1, first strand: chain 'A' and resid 330 through 335 removed outlier: 6.660A pdb=" N VAL A 340 " --> pdb=" O GLU A 332 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N CYS A 334 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL A 338 " --> pdb=" O CYS A 334 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 330 through 335 removed outlier: 6.660A pdb=" N VAL B 340 " --> pdb=" O GLU B 332 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N CYS B 334 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL B 338 " --> pdb=" O CYS B 334 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 330 through 335 removed outlier: 6.661A pdb=" N VAL C 340 " --> pdb=" O GLU C 332 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N CYS C 334 " --> pdb=" O VAL C 338 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL C 338 " --> pdb=" O CYS C 334 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 330 through 335 removed outlier: 6.659A pdb=" N VAL D 340 " --> pdb=" O GLU D 332 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N CYS D 334 " --> pdb=" O VAL D 338 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL D 338 " --> pdb=" O CYS D 334 " (cutoff:3.500A) 1072 hydrogen bonds defined for protein. 3108 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.21 Time building geometry restraints manager: 2.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6137 1.34 - 1.46: 5115 1.46 - 1.58: 9112 1.58 - 1.71: 0 1.71 - 1.83: 180 Bond restraints: 20544 Sorted by residual: bond pdb=" C12 P0T C1001 " pdb=" O02 P0T C1001 " ideal model delta sigma weight residual 1.352 1.404 -0.052 2.00e-02 2.50e+03 6.69e+00 bond pdb=" C12 P0T A1002 " pdb=" O02 P0T A1002 " ideal model delta sigma weight residual 1.352 1.404 -0.052 2.00e-02 2.50e+03 6.69e+00 bond pdb=" C12 P0T D1001 " pdb=" O02 P0T D1001 " ideal model delta sigma weight residual 1.352 1.404 -0.052 2.00e-02 2.50e+03 6.64e+00 bond pdb=" C12 P0T A1001 " pdb=" O02 P0T A1001 " ideal model delta sigma weight residual 1.352 1.404 -0.052 2.00e-02 2.50e+03 6.63e+00 bond pdb=" C11 P0T A1001 " pdb=" O01 P0T A1001 " ideal model delta sigma weight residual 1.352 1.403 -0.051 2.00e-02 2.50e+03 6.41e+00 ... (remaining 20539 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 26945 2.34 - 4.67: 796 4.67 - 7.01: 83 7.01 - 9.34: 36 9.34 - 11.68: 16 Bond angle restraints: 27876 Sorted by residual: angle pdb=" N ILE D 529 " pdb=" CA ILE D 529 " pdb=" C ILE D 529 " ideal model delta sigma weight residual 111.91 108.09 3.82 8.90e-01 1.26e+00 1.84e+01 angle pdb=" N ILE B 529 " pdb=" CA ILE B 529 " pdb=" C ILE B 529 " ideal model delta sigma weight residual 111.91 108.11 3.80 8.90e-01 1.26e+00 1.83e+01 angle pdb=" N ILE C 529 " pdb=" CA ILE C 529 " pdb=" C ILE C 529 " ideal model delta sigma weight residual 111.91 108.11 3.80 8.90e-01 1.26e+00 1.82e+01 angle pdb=" N ILE A 529 " pdb=" CA ILE A 529 " pdb=" C ILE A 529 " ideal model delta sigma weight residual 111.91 108.11 3.80 8.90e-01 1.26e+00 1.82e+01 angle pdb=" C03 P0T A1001 " pdb=" C04 P0T A1001 " pdb=" C08 P0T A1001 " ideal model delta sigma weight residual 111.12 122.80 -11.68 3.00e+00 1.11e-01 1.52e+01 ... (remaining 27871 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.27: 10817 19.27 - 38.53: 1003 38.53 - 57.80: 176 57.80 - 77.07: 28 77.07 - 96.33: 12 Dihedral angle restraints: 12036 sinusoidal: 4816 harmonic: 7220 Sorted by residual: dihedral pdb=" CA ASN C 655 " pdb=" C ASN C 655 " pdb=" N SER C 656 " pdb=" CA SER C 656 " ideal model delta harmonic sigma weight residual -180.00 -160.78 -19.22 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA ASN A 655 " pdb=" C ASN A 655 " pdb=" N SER A 656 " pdb=" CA SER A 656 " ideal model delta harmonic sigma weight residual 180.00 -160.81 -19.19 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA ASN B 655 " pdb=" C ASN B 655 " pdb=" N SER B 656 " pdb=" CA SER B 656 " ideal model delta harmonic sigma weight residual -180.00 -160.82 -19.18 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 12033 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1999 0.045 - 0.090: 861 0.090 - 0.135: 212 0.135 - 0.180: 68 0.180 - 0.225: 8 Chirality restraints: 3148 Sorted by residual: chirality pdb=" C03 P0T A1002 " pdb=" C04 P0T A1002 " pdb=" C05 P0T A1002 " pdb=" C10 P0T A1002 " both_signs ideal model delta sigma weight residual False -2.55 -2.77 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" C03 P0T C1001 " pdb=" C04 P0T C1001 " pdb=" C05 P0T C1001 " pdb=" C10 P0T C1001 " both_signs ideal model delta sigma weight residual False -2.55 -2.77 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" C03 P0T A1001 " pdb=" C04 P0T A1001 " pdb=" C05 P0T A1001 " pdb=" C10 P0T A1001 " both_signs ideal model delta sigma weight residual False -2.55 -2.77 0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 3145 not shown) Planarity restraints: 3420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 137 " -0.045 5.00e-02 4.00e+02 6.67e-02 7.12e+00 pdb=" N PRO B 138 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO B 138 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 138 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 137 " -0.045 5.00e-02 4.00e+02 6.66e-02 7.11e+00 pdb=" N PRO A 138 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 138 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 138 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET D 137 " -0.045 5.00e-02 4.00e+02 6.66e-02 7.10e+00 pdb=" N PRO D 138 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO D 138 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 138 " -0.037 5.00e-02 4.00e+02 ... (remaining 3417 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 6104 2.82 - 3.34: 17959 3.34 - 3.86: 33559 3.86 - 4.38: 37894 4.38 - 4.90: 66133 Nonbonded interactions: 161649 Sorted by model distance: nonbonded pdb=" O GLU C 90 " pdb=" OG1 THR C 93 " model vdw 2.296 3.040 nonbonded pdb=" O GLU D 90 " pdb=" OG1 THR D 93 " model vdw 2.296 3.040 nonbonded pdb=" O GLU A 90 " pdb=" OG1 THR A 93 " model vdw 2.297 3.040 nonbonded pdb=" O GLU B 90 " pdb=" OG1 THR B 93 " model vdw 2.297 3.040 nonbonded pdb=" O ILE A 529 " pdb=" ND2 ASN B 639 " model vdw 2.302 3.120 ... (remaining 161644 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 32 through 719) selection = chain 'B' selection = (chain 'C' and resid 32 through 719) selection = (chain 'D' and resid 32 through 719) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.120 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: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.540 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 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 0.065 20544 Z= 0.343 Angle : 0.966 11.681 27876 Z= 0.497 Chirality : 0.054 0.225 3148 Planarity : 0.007 0.067 3420 Dihedral : 15.595 96.335 7364 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.37 % Allowed : 8.94 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -3.94 (0.12), residues: 2428 helix: -2.38 (0.09), residues: 1460 sheet: -2.79 (0.43), residues: 92 loop : -2.72 (0.16), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 392 TYR 0.013 0.002 TYR D 111 PHE 0.019 0.003 PHE B 161 TRP 0.019 0.002 TRP D 333 HIS 0.006 0.002 HIS D 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00806 / 0.34 (20544) covalent geometry : angle 0.96569 / 0.50 (27876) hydrogen bonds : bond 0.14053 / 9.21 ( 1072) hydrogen bonds : angle 6.14329 / 4.32 ( 3108) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 405 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.7254 (mm) cc_final: 0.6675 (pp) REVERT: A 113 GLU cc_start: 0.7290 (mt-10) cc_final: 0.6692 (mt-10) REVERT: A 173 GLU cc_start: 0.8400 (tp30) cc_final: 0.8199 (tp30) REVERT: A 541 LEU cc_start: 0.9104 (tp) cc_final: 0.8896 (tp) REVERT: B 255 MET cc_start: 0.8120 (mmm) cc_final: 0.7901 (mmm) REVERT: B 372 MET cc_start: 0.9125 (mtt) cc_final: 0.8904 (mtt) REVERT: B 383 GLN cc_start: 0.7898 (tp40) cc_final: 0.7601 (tt0) REVERT: B 404 MET cc_start: 0.8670 (mmp) cc_final: 0.8460 (mmt) REVERT: B 541 LEU cc_start: 0.9052 (tp) cc_final: 0.8787 (tp) REVERT: B 640 MET cc_start: 0.8412 (ttp) cc_final: 0.8069 (ttp) REVERT: C 113 GLU cc_start: 0.7273 (mt-10) cc_final: 0.7060 (mt-10) REVERT: C 235 GLN cc_start: 0.7661 (mt0) cc_final: 0.7436 (mt0) REVERT: C 255 MET cc_start: 0.8176 (mmm) cc_final: 0.7930 (mmt) REVERT: C 464 TRP cc_start: 0.6065 (m100) cc_final: 0.5830 (m100) REVERT: D 113 GLU cc_start: 0.7296 (mt-10) cc_final: 0.7087 (mt-10) REVERT: D 255 MET cc_start: 0.8169 (mmm) cc_final: 0.7959 (mmt) REVERT: D 305 GLU cc_start: 0.7603 (tt0) cc_final: 0.7064 (mt-10) REVERT: D 464 TRP cc_start: 0.6079 (m100) cc_final: 0.5859 (m100) REVERT: D 473 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7528 (mp0) REVERT: D 528 MET cc_start: 0.8073 (ttt) cc_final: 0.7568 (ttt) REVERT: D 536 ASP cc_start: 0.7392 (t70) cc_final: 0.7189 (t0) outliers start: 8 outliers final: 0 residues processed: 405 average time/residue: 0.1316 time to fit residues: 83.9294 Evaluate side-chains 271 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 0.3980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.0770 chunk 130 optimal weight: 0.0270 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.5980 chunk 235 optimal weight: 0.9980 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 GLN A 186 ASN ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 263 ASN A 316 GLN B 163 GLN B 186 ASN ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 ASN B 316 GLN C 186 ASN ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN C 316 GLN D 186 ASN ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 ASN D 316 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.156485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.128834 restraints weight = 27069.001| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.78 r_work: 0.3315 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 20544 Z= 0.100 Angle : 0.518 7.973 27876 Z= 0.263 Chirality : 0.036 0.185 3148 Planarity : 0.005 0.064 3420 Dihedral : 5.153 52.445 2708 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.86 % Allowed : 13.64 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.17 (0.16), residues: 2428 helix: 0.02 (0.13), residues: 1452 sheet: -2.14 (0.47), residues: 92 loop : -1.88 (0.19), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 706 TYR 0.014 0.001 TYR C 455 PHE 0.016 0.001 PHE C 467 TRP 0.012 0.001 TRP A 715 HIS 0.004 0.001 HIS B 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.10 (20544) covalent geometry : angle 0.51795 / 0.26 (27876) hydrogen bonds : bond 0.03424 / 2.26 ( 1072) hydrogen bonds : angle 4.12015 / 2.92 ( 3108) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 371 time to evaluate : 0.741 Fit side-chains REVERT: A 92 LEU cc_start: 0.7328 (mm) cc_final: 0.6437 (pp) REVERT: A 178 GLN cc_start: 0.7864 (mt0) cc_final: 0.7458 (mp10) REVERT: A 454 TRP cc_start: 0.8134 (t-100) cc_final: 0.7841 (t60) REVERT: A 519 PHE cc_start: 0.8430 (m-80) cc_final: 0.8176 (m-80) REVERT: B 277 MET cc_start: 0.7487 (mmp) cc_final: 0.7232 (mmp) REVERT: B 305 GLU cc_start: 0.8175 (tt0) cc_final: 0.7873 (mt-10) REVERT: B 318 GLU cc_start: 0.7297 (tt0) cc_final: 0.7021 (tt0) REVERT: B 372 MET cc_start: 0.9127 (mtt) cc_final: 0.8897 (mtt) REVERT: B 383 GLN cc_start: 0.8388 (tp40) cc_final: 0.8162 (tp40) REVERT: B 455 TYR cc_start: 0.9139 (t80) cc_final: 0.8912 (t80) REVERT: B 645 MET cc_start: 0.8325 (tmm) cc_final: 0.7816 (tmm) REVERT: C 111 TYR cc_start: 0.6144 (m-80) cc_final: 0.5699 (m-80) REVERT: C 113 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7332 (mt-10) REVERT: C 118 LYS cc_start: 0.8448 (ttpt) cc_final: 0.8141 (tttt) REVERT: C 235 GLN cc_start: 0.7684 (mt0) cc_final: 0.7446 (mt0) REVERT: C 305 GLU cc_start: 0.8238 (tt0) cc_final: 0.7911 (mt-10) REVERT: C 454 TRP cc_start: 0.8205 (t-100) cc_final: 0.7940 (t60) REVERT: C 455 TYR cc_start: 0.9217 (t80) cc_final: 0.9005 (t80) REVERT: C 457 TRP cc_start: 0.8261 (t-100) cc_final: 0.8033 (t-100) REVERT: C 473 GLU cc_start: 0.8308 (mm-30) cc_final: 0.8103 (mp0) REVERT: D 111 TYR cc_start: 0.6103 (m-80) cc_final: 0.5773 (m-80) REVERT: D 113 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7239 (mt-10) REVERT: D 118 LYS cc_start: 0.8419 (ttpt) cc_final: 0.8065 (tttt) REVERT: D 235 GLN cc_start: 0.7755 (mt0) cc_final: 0.7512 (mt0) REVERT: D 255 MET cc_start: 0.8809 (mmm) cc_final: 0.8421 (mmt) REVERT: D 305 GLU cc_start: 0.8032 (tt0) cc_final: 0.7537 (mt-10) REVERT: D 358 GLU cc_start: 0.8172 (tt0) cc_final: 0.7767 (tt0) REVERT: D 454 TRP cc_start: 0.8110 (t-100) cc_final: 0.7898 (t60) REVERT: D 457 TRP cc_start: 0.8210 (t-100) cc_final: 0.7961 (t-100) outliers start: 40 outliers final: 19 residues processed: 398 average time/residue: 0.1218 time to fit residues: 78.2455 Evaluate side-chains 316 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 297 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 316 GLN Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 316 GLN Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain D residue 316 GLN Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 672 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 83 optimal weight: 0.0050 chunk 87 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 chunk 158 optimal weight: 6.9990 chunk 226 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 234 optimal weight: 0.6980 chunk 38 optimal weight: 0.3980 chunk 176 optimal weight: 0.6980 chunk 71 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 GLN A 487 GLN ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 GLN B 487 GLN C 163 GLN ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN C 487 GLN ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 414 GLN D 487 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.155138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.125674 restraints weight = 27006.324| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.81 r_work: 0.3291 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 20544 Z= 0.104 Angle : 0.518 9.631 27876 Z= 0.252 Chirality : 0.036 0.196 3148 Planarity : 0.004 0.059 3420 Dihedral : 4.497 41.552 2708 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.58 % Allowed : 16.25 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.17), residues: 2428 helix: 1.04 (0.13), residues: 1464 sheet: -1.71 (0.49), residues: 92 loop : -1.64 (0.20), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 317 TYR 0.012 0.001 TYR D 455 PHE 0.017 0.001 PHE D 467 TRP 0.008 0.001 TRP A 715 HIS 0.005 0.001 HIS D 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.10 (20544) covalent geometry : angle 0.51761 / 0.25 (27876) hydrogen bonds : bond 0.03138 / 2.07 ( 1072) hydrogen bonds : angle 3.79230 / 2.69 ( 3108) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 329 time to evaluate : 0.610 Fit side-chains revert: symmetry clash REVERT: A 92 LEU cc_start: 0.7334 (mm) cc_final: 0.6367 (pp) REVERT: A 178 GLN cc_start: 0.7937 (mt0) cc_final: 0.7574 (mp10) REVERT: A 269 HIS cc_start: 0.7918 (t70) cc_final: 0.7571 (t70) REVERT: A 454 TRP cc_start: 0.8199 (t-100) cc_final: 0.7868 (t60) REVERT: A 670 GLU cc_start: 0.7923 (tm-30) cc_final: 0.7576 (tp30) REVERT: B 305 GLU cc_start: 0.8150 (tt0) cc_final: 0.7754 (mt-10) REVERT: B 324 GLN cc_start: 0.8384 (tm-30) cc_final: 0.8142 (tm-30) REVERT: B 383 GLN cc_start: 0.8388 (tp40) cc_final: 0.8170 (tp40) REVERT: B 455 TYR cc_start: 0.9189 (t80) cc_final: 0.8907 (t80) REVERT: B 645 MET cc_start: 0.8294 (tmm) cc_final: 0.7617 (tmm) REVERT: B 687 ARG cc_start: 0.7926 (ttm110) cc_final: 0.7718 (mtm110) REVERT: C 111 TYR cc_start: 0.5937 (m-80) cc_final: 0.5520 (m-80) REVERT: C 113 GLU cc_start: 0.7642 (mt-10) cc_final: 0.7113 (mt-10) REVERT: C 178 GLN cc_start: 0.7917 (mt0) cc_final: 0.7519 (mp10) REVERT: C 235 GLN cc_start: 0.7798 (mt0) cc_final: 0.7541 (mt0) REVERT: C 305 GLU cc_start: 0.8202 (tt0) cc_final: 0.7801 (mt-10) REVERT: C 454 TRP cc_start: 0.8237 (t-100) cc_final: 0.7935 (t60) REVERT: C 455 TYR cc_start: 0.9210 (t80) cc_final: 0.8920 (t80) REVERT: C 457 TRP cc_start: 0.8304 (t-100) cc_final: 0.8078 (t-100) REVERT: D 111 TYR cc_start: 0.6023 (m-80) cc_final: 0.5663 (m-80) REVERT: D 113 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7201 (mt-10) REVERT: D 118 LYS cc_start: 0.8319 (ttpt) cc_final: 0.8003 (tttt) REVERT: D 178 GLN cc_start: 0.7921 (mt0) cc_final: 0.7526 (mp10) REVERT: D 235 GLN cc_start: 0.7789 (mt0) cc_final: 0.7548 (mt0) REVERT: D 269 HIS cc_start: 0.7864 (t70) cc_final: 0.7581 (t70) REVERT: D 454 TRP cc_start: 0.8141 (t-100) cc_final: 0.7898 (t60) outliers start: 34 outliers final: 18 residues processed: 349 average time/residue: 0.1216 time to fit residues: 67.9756 Evaluate side-chains 308 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 290 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain B residue 111 TYR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 672 GLU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain D residue 375 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 192 optimal weight: 7.9990 chunk 75 optimal weight: 6.9990 chunk 194 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 chunk 12 optimal weight: 9.9990 chunk 159 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 125 optimal weight: 10.0000 chunk 223 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 GLN C 127 ASN ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.152087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.122006 restraints weight = 27151.348| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.83 r_work: 0.3234 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20544 Z= 0.158 Angle : 0.558 8.578 27876 Z= 0.274 Chirality : 0.038 0.182 3148 Planarity : 0.004 0.054 3420 Dihedral : 4.936 49.448 2708 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.75 % Allowed : 16.95 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.17), residues: 2428 helix: 1.34 (0.14), residues: 1472 sheet: -1.60 (0.50), residues: 92 loop : -1.49 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 706 TYR 0.012 0.001 TYR D 455 PHE 0.019 0.002 PHE A 405 TRP 0.010 0.001 TRP D 715 HIS 0.006 0.001 HIS A 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 (20544) covalent geometry : angle 0.55768 / 0.27 (27876) hydrogen bonds : bond 0.03423 / 2.26 ( 1072) hydrogen bonds : angle 3.82111 / 2.70 ( 3108) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 287 time to evaluate : 0.783 Fit side-chains REVERT: A 39 PHE cc_start: 0.7145 (OUTLIER) cc_final: 0.5877 (p90) REVERT: A 92 LEU cc_start: 0.7352 (mm) cc_final: 0.6409 (pp) REVERT: A 178 GLN cc_start: 0.7997 (mt0) cc_final: 0.7601 (mp10) REVERT: A 269 HIS cc_start: 0.7935 (t70) cc_final: 0.7654 (t70) REVERT: B 39 PHE cc_start: 0.7162 (OUTLIER) cc_final: 0.5954 (p90) REVERT: B 277 MET cc_start: 0.7784 (OUTLIER) cc_final: 0.7524 (mmp) REVERT: B 383 GLN cc_start: 0.8406 (tp40) cc_final: 0.8001 (tt0) REVERT: B 634 TYR cc_start: 0.8310 (OUTLIER) cc_final: 0.7381 (m-80) REVERT: B 645 MET cc_start: 0.8537 (tmm) cc_final: 0.7829 (tmm) REVERT: C 39 PHE cc_start: 0.7198 (OUTLIER) cc_final: 0.5749 (p90) REVERT: C 235 GLN cc_start: 0.7919 (mt0) cc_final: 0.7672 (mt0) REVERT: C 670 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7819 (tt0) REVERT: D 39 PHE cc_start: 0.7108 (OUTLIER) cc_final: 0.5661 (p90) REVERT: D 111 TYR cc_start: 0.6028 (m-80) cc_final: 0.5506 (m-80) REVERT: D 178 GLN cc_start: 0.8094 (mt0) cc_final: 0.7651 (mp10) REVERT: D 670 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7640 (tp30) outliers start: 59 outliers final: 28 residues processed: 333 average time/residue: 0.1209 time to fit residues: 65.1743 Evaluate side-chains 290 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 255 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 672 GLU Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain C residue 39 PHE Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 670 GLU Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 39 PHE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 672 GLU Chi-restraints excluded: chain D residue 707 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 195 optimal weight: 10.0000 chunk 216 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 201 optimal weight: 7.9990 chunk 29 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 215 optimal weight: 0.9980 chunk 225 optimal weight: 3.9990 chunk 232 optimal weight: 0.5980 chunk 7 optimal weight: 9.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 127 ASN ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 127 ASN ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 ASN ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.151717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.123425 restraints weight = 26975.039| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.81 r_work: 0.3236 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20544 Z= 0.152 Angle : 0.540 8.343 27876 Z= 0.266 Chirality : 0.038 0.171 3148 Planarity : 0.004 0.053 3420 Dihedral : 4.828 52.223 2708 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.98 % Allowed : 17.13 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.17), residues: 2428 helix: 1.51 (0.13), residues: 1480 sheet: -1.60 (0.50), residues: 92 loop : -1.39 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 706 TYR 0.013 0.001 TYR C 455 PHE 0.019 0.001 PHE C 405 TRP 0.016 0.001 TRP D 715 HIS 0.006 0.001 HIS D 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 (20544) covalent geometry : angle 0.54029 / 0.27 (27876) hydrogen bonds : bond 0.03331 / 2.20 ( 1072) hydrogen bonds : angle 3.78853 / 2.68 ( 3108) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 291 time to evaluate : 0.745 Fit side-chains revert: symmetry clash REVERT: A 39 PHE cc_start: 0.7093 (OUTLIER) cc_final: 0.5633 (p90) REVERT: A 92 LEU cc_start: 0.7463 (mm) cc_final: 0.6501 (pp) REVERT: A 670 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7582 (tp30) REVERT: B 39 PHE cc_start: 0.7237 (OUTLIER) cc_final: 0.5955 (p90) REVERT: B 277 MET cc_start: 0.7780 (OUTLIER) cc_final: 0.7514 (mmp) REVERT: B 383 GLN cc_start: 0.8392 (tp40) cc_final: 0.8059 (tt0) REVERT: B 473 GLU cc_start: 0.8536 (mp0) cc_final: 0.8308 (mm-30) REVERT: B 634 TYR cc_start: 0.8347 (OUTLIER) cc_final: 0.7435 (m-80) REVERT: B 645 MET cc_start: 0.8513 (tmm) cc_final: 0.7763 (tmm) REVERT: C 39 PHE cc_start: 0.7199 (OUTLIER) cc_final: 0.5751 (p90) REVERT: C 634 TYR cc_start: 0.8308 (OUTLIER) cc_final: 0.7368 (m-80) REVERT: C 670 GLU cc_start: 0.8032 (tm-30) cc_final: 0.7626 (tp30) REVERT: D 255 MET cc_start: 0.8703 (mmt) cc_final: 0.8417 (mmm) REVERT: D 305 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7854 (mt-10) REVERT: D 670 GLU cc_start: 0.8053 (tm-30) cc_final: 0.7628 (tp30) outliers start: 64 outliers final: 30 residues processed: 336 average time/residue: 0.1269 time to fit residues: 69.2201 Evaluate side-chains 303 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 266 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 670 GLU Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 520 GLN Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 672 GLU Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain C residue 39 PHE Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 672 GLU Chi-restraints excluded: chain D residue 707 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 223 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 chunk 104 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 chunk 152 optimal weight: 0.5980 chunk 185 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 chunk 101 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 GLN ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 269 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.154353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.126041 restraints weight = 26920.811| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.98 r_work: 0.3264 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 20544 Z= 0.103 Angle : 0.502 7.795 27876 Z= 0.247 Chirality : 0.036 0.160 3148 Planarity : 0.003 0.051 3420 Dihedral : 4.193 44.090 2708 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.47 % Allowed : 17.97 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.17), residues: 2428 helix: 1.91 (0.14), residues: 1456 sheet: -1.57 (0.49), residues: 92 loop : -1.32 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 197 TYR 0.012 0.001 TYR C 455 PHE 0.021 0.001 PHE A 467 TRP 0.018 0.001 TRP D 715 HIS 0.006 0.001 HIS B 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 (20544) covalent geometry : angle 0.50194 / 0.25 (27876) hydrogen bonds : bond 0.03025 / 2.00 ( 1072) hydrogen bonds : angle 3.63002 / 2.57 ( 3108) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 313 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.7197 (mm) cc_final: 0.6347 (pp) REVERT: A 269 HIS cc_start: 0.8004 (t70) cc_final: 0.7725 (t70) REVERT: A 634 TYR cc_start: 0.8298 (OUTLIER) cc_final: 0.7397 (m-80) REVERT: B 277 MET cc_start: 0.7676 (OUTLIER) cc_final: 0.7368 (mmp) REVERT: B 383 GLN cc_start: 0.8351 (tp40) cc_final: 0.7997 (tt0) REVERT: B 634 TYR cc_start: 0.8366 (OUTLIER) cc_final: 0.7460 (m-80) REVERT: B 645 MET cc_start: 0.8378 (tmm) cc_final: 0.8151 (ttm) REVERT: C 235 GLN cc_start: 0.7898 (mt0) cc_final: 0.7596 (mt0) REVERT: C 634 TYR cc_start: 0.8260 (OUTLIER) cc_final: 0.7324 (m-80) REVERT: C 670 GLU cc_start: 0.8042 (tm-30) cc_final: 0.7632 (tp30) REVERT: D 39 PHE cc_start: 0.7075 (OUTLIER) cc_final: 0.5534 (p90) REVERT: D 92 LEU cc_start: 0.7711 (mt) cc_final: 0.6276 (pp) REVERT: D 235 GLN cc_start: 0.7883 (mt0) cc_final: 0.7583 (mt0) REVERT: D 255 MET cc_start: 0.8612 (mmt) cc_final: 0.8327 (mmm) REVERT: D 305 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7714 (mt-10) REVERT: D 519 PHE cc_start: 0.8303 (m-80) cc_final: 0.8094 (m-10) REVERT: D 634 TYR cc_start: 0.8293 (OUTLIER) cc_final: 0.7384 (m-80) REVERT: D 670 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7651 (tp30) outliers start: 53 outliers final: 29 residues processed: 344 average time/residue: 0.1339 time to fit residues: 74.2355 Evaluate side-chains 308 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 272 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 520 GLN Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain B residue 672 GLU Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 520 GLN Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain D residue 39 PHE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 634 TYR Chi-restraints excluded: chain D residue 670 GLU Chi-restraints excluded: chain D residue 672 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 157 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 144 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 240 optimal weight: 0.7980 chunk 132 optimal weight: 5.9990 chunk 236 optimal weight: 2.9990 chunk 130 optimal weight: 0.0870 overall best weight: 1.4962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 GLN C 163 GLN ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 GLN ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 269 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.152420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.124248 restraints weight = 27188.044| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.85 r_work: 0.3231 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 20544 Z= 0.141 Angle : 0.552 12.041 27876 Z= 0.266 Chirality : 0.038 0.164 3148 Planarity : 0.003 0.047 3420 Dihedral : 4.476 50.061 2708 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.75 % Allowed : 18.53 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.17), residues: 2428 helix: 1.90 (0.14), residues: 1456 sheet: -1.58 (0.49), residues: 92 loop : -1.29 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 197 TYR 0.012 0.001 TYR C 455 PHE 0.021 0.001 PHE B 467 TRP 0.021 0.001 TRP D 715 HIS 0.006 0.001 HIS A 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (20544) covalent geometry : angle 0.55249 / 0.27 (27876) hydrogen bonds : bond 0.03244 / 2.14 ( 1072) hydrogen bonds : angle 3.68582 / 2.60 ( 3108) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 293 time to evaluate : 0.739 Fit side-chains revert: symmetry clash REVERT: A 39 PHE cc_start: 0.7157 (OUTLIER) cc_final: 0.5556 (p90) REVERT: A 92 LEU cc_start: 0.7354 (mm) cc_final: 0.6449 (pp) REVERT: A 473 GLU cc_start: 0.8487 (mp0) cc_final: 0.8263 (mm-30) REVERT: A 528 MET cc_start: 0.8518 (ptm) cc_final: 0.8248 (ttp) REVERT: A 670 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7627 (tp30) REVERT: B 39 PHE cc_start: 0.7256 (OUTLIER) cc_final: 0.5940 (p90) REVERT: B 277 MET cc_start: 0.7781 (OUTLIER) cc_final: 0.7497 (mmp) REVERT: B 383 GLN cc_start: 0.8398 (tp40) cc_final: 0.8080 (tt0) REVERT: B 473 GLU cc_start: 0.8499 (mp0) cc_final: 0.8283 (mm-30) REVERT: B 634 TYR cc_start: 0.8286 (OUTLIER) cc_final: 0.7322 (m-80) REVERT: B 645 MET cc_start: 0.8494 (tmm) cc_final: 0.7740 (tmm) REVERT: C 39 PHE cc_start: 0.7160 (OUTLIER) cc_final: 0.5704 (p90) REVERT: C 92 LEU cc_start: 0.7672 (mt) cc_final: 0.6299 (pp) REVERT: C 528 MET cc_start: 0.8513 (ptm) cc_final: 0.8219 (ttp) REVERT: C 634 TYR cc_start: 0.8340 (OUTLIER) cc_final: 0.7402 (m-80) REVERT: C 670 GLU cc_start: 0.8033 (tm-30) cc_final: 0.7647 (tp30) REVERT: D 39 PHE cc_start: 0.7122 (OUTLIER) cc_final: 0.5403 (p90) REVERT: D 92 LEU cc_start: 0.7731 (mt) cc_final: 0.6287 (pp) REVERT: D 269 HIS cc_start: 0.7956 (t70) cc_final: 0.7751 (t70) REVERT: D 473 GLU cc_start: 0.8486 (mp0) cc_final: 0.8204 (mm-30) REVERT: D 634 TYR cc_start: 0.8303 (OUTLIER) cc_final: 0.7380 (m-80) REVERT: D 670 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7695 (tp30) outliers start: 59 outliers final: 36 residues processed: 331 average time/residue: 0.1310 time to fit residues: 69.9381 Evaluate side-chains 316 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 270 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain A residue 670 GLU Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 520 GLN Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain B residue 672 GLU Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain C residue 39 PHE Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 520 GLN Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 39 PHE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 520 GLN Chi-restraints excluded: chain D residue 634 TYR Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 670 GLU Chi-restraints excluded: chain D residue 672 GLU Chi-restraints excluded: chain D residue 707 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 115 optimal weight: 0.7980 chunk 137 optimal weight: 0.0970 chunk 25 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 70 optimal weight: 0.0770 chunk 6 optimal weight: 0.0970 chunk 183 optimal weight: 0.7980 chunk 106 optimal weight: 0.0570 chunk 230 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 overall best weight: 0.2052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 GLN ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 GLN D 269 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.156757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.129074 restraints weight = 26994.400| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.83 r_work: 0.3304 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 20544 Z= 0.090 Angle : 0.503 9.296 27876 Z= 0.244 Chirality : 0.036 0.169 3148 Planarity : 0.003 0.048 3420 Dihedral : 3.783 37.163 2708 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.96 % Allowed : 19.65 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.29 (0.18), residues: 2428 helix: 2.19 (0.14), residues: 1452 sheet: -2.37 (0.44), residues: 112 loop : -1.06 (0.22), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 197 TYR 0.014 0.001 TYR C 455 PHE 0.023 0.001 PHE A 467 TRP 0.029 0.001 TRP D 715 HIS 0.004 0.000 HIS D 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00192 / 0.09 (20544) covalent geometry : angle 0.50319 / 0.24 (27876) hydrogen bonds : bond 0.02809 / 1.84 ( 1072) hydrogen bonds : angle 3.49962 / 2.48 ( 3108) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 307 time to evaluate : 0.790 Fit side-chains revert: symmetry clash REVERT: A 163 GLN cc_start: 0.8186 (tt0) cc_final: 0.7339 (tp40) REVERT: A 178 GLN cc_start: 0.8188 (mt0) cc_final: 0.7824 (mp10) REVERT: A 235 GLN cc_start: 0.7691 (mt0) cc_final: 0.7467 (mt0) REVERT: A 528 MET cc_start: 0.8405 (ptm) cc_final: 0.8183 (ttp) REVERT: A 591 ARG cc_start: 0.7971 (mmt-90) cc_final: 0.7764 (tpp-160) REVERT: A 634 TYR cc_start: 0.8225 (OUTLIER) cc_final: 0.7345 (m-80) REVERT: B 39 PHE cc_start: 0.7118 (OUTLIER) cc_final: 0.5677 (p90) REVERT: B 235 GLN cc_start: 0.7692 (mt0) cc_final: 0.7482 (mt0) REVERT: B 383 GLN cc_start: 0.8288 (tp40) cc_final: 0.7963 (tt0) REVERT: B 634 TYR cc_start: 0.8255 (OUTLIER) cc_final: 0.7318 (m-80) REVERT: C 92 LEU cc_start: 0.7538 (mt) cc_final: 0.6265 (pp) REVERT: C 163 GLN cc_start: 0.8193 (tt0) cc_final: 0.7373 (tp40) REVERT: C 178 GLN cc_start: 0.8124 (mt0) cc_final: 0.7746 (mp10) REVERT: C 235 GLN cc_start: 0.7745 (mt0) cc_final: 0.7524 (mt0) REVERT: C 528 MET cc_start: 0.8436 (ptm) cc_final: 0.8164 (ttp) REVERT: C 634 TYR cc_start: 0.8254 (OUTLIER) cc_final: 0.7316 (m-80) REVERT: D 92 LEU cc_start: 0.7656 (mt) cc_final: 0.6232 (pp) REVERT: D 163 GLN cc_start: 0.8218 (tt0) cc_final: 0.7365 (tp40) REVERT: D 235 GLN cc_start: 0.7743 (mt0) cc_final: 0.7522 (mt0) REVERT: D 269 HIS cc_start: 0.7899 (t-90) cc_final: 0.7646 (t70) REVERT: D 457 TRP cc_start: 0.8457 (t-100) cc_final: 0.7606 (t-100) REVERT: D 473 GLU cc_start: 0.8345 (mp0) cc_final: 0.8012 (mm-30) REVERT: D 634 TYR cc_start: 0.8191 (OUTLIER) cc_final: 0.7307 (m-80) REVERT: D 670 GLU cc_start: 0.8025 (tm-30) cc_final: 0.7658 (tp30) outliers start: 42 outliers final: 22 residues processed: 330 average time/residue: 0.1375 time to fit residues: 72.9482 Evaluate side-chains 303 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 276 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 634 TYR Chi-restraints excluded: chain D residue 672 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 196 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 210 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 215 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 154 optimal weight: 4.9990 chunk 219 optimal weight: 3.9990 chunk 121 optimal weight: 0.6980 chunk 46 optimal weight: 8.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 163 GLN ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 269 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.150426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.121576 restraints weight = 27138.528| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.90 r_work: 0.3204 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 20544 Z= 0.210 Angle : 0.635 11.427 27876 Z= 0.303 Chirality : 0.040 0.190 3148 Planarity : 0.004 0.044 3420 Dihedral : 4.915 58.244 2708 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.28 % Allowed : 19.93 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.17), residues: 2428 helix: 1.78 (0.13), residues: 1476 sheet: -1.60 (0.50), residues: 92 loop : -1.34 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 197 TYR 0.012 0.002 TYR D 455 PHE 0.022 0.002 PHE A 467 TRP 0.035 0.001 TRP D 715 HIS 0.005 0.001 HIS A 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.21 (20544) covalent geometry : angle 0.63486 / 0.30 (27876) hydrogen bonds : bond 0.03620 / 2.39 ( 1072) hydrogen bonds : angle 3.81920 / 2.69 ( 3108) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 281 time to evaluate : 0.778 Fit side-chains REVERT: A 39 PHE cc_start: 0.7134 (OUTLIER) cc_final: 0.5516 (p90) REVERT: A 92 LEU cc_start: 0.7405 (mm) cc_final: 0.6519 (pp) REVERT: A 537 LEU cc_start: 0.7983 (mt) cc_final: 0.7390 (mt) REVERT: A 634 TYR cc_start: 0.8419 (OUTLIER) cc_final: 0.7430 (m-80) REVERT: A 670 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7705 (tp30) REVERT: B 39 PHE cc_start: 0.7285 (OUTLIER) cc_final: 0.6163 (p90) REVERT: B 383 GLN cc_start: 0.8370 (tp40) cc_final: 0.8082 (tt0) REVERT: B 473 GLU cc_start: 0.8481 (mp0) cc_final: 0.8270 (mm-30) REVERT: B 634 TYR cc_start: 0.8308 (OUTLIER) cc_final: 0.7358 (m-80) REVERT: C 39 PHE cc_start: 0.7213 (OUTLIER) cc_final: 0.5667 (p90) REVERT: C 634 TYR cc_start: 0.8331 (OUTLIER) cc_final: 0.7374 (m-80) REVERT: C 670 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7740 (tp30) REVERT: D 39 PHE cc_start: 0.7170 (OUTLIER) cc_final: 0.5349 (p90) REVERT: D 92 LEU cc_start: 0.7634 (mt) cc_final: 0.6218 (pp) REVERT: D 269 HIS cc_start: 0.8013 (t70) cc_final: 0.7766 (t70) REVERT: D 519 PHE cc_start: 0.8314 (m-10) cc_final: 0.8091 (m-10) REVERT: D 670 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7788 (tp30) outliers start: 49 outliers final: 30 residues processed: 314 average time/residue: 0.1277 time to fit residues: 65.5006 Evaluate side-chains 300 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 261 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain A residue 670 GLU Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 520 GLN Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain C residue 39 PHE Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 349 ASP Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain C residue 670 GLU Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 39 PHE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 672 GLU Chi-restraints excluded: chain D residue 707 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 224 optimal weight: 0.7980 chunk 218 optimal weight: 3.9990 chunk 242 optimal weight: 0.2980 chunk 125 optimal weight: 9.9990 chunk 147 optimal weight: 0.7980 chunk 73 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 105 optimal weight: 0.0980 chunk 225 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 chunk 83 optimal weight: 5.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 269 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.154666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.127125 restraints weight = 26994.261| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.82 r_work: 0.3287 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 20544 Z= 0.104 Angle : 0.563 8.912 27876 Z= 0.268 Chirality : 0.037 0.171 3148 Planarity : 0.003 0.047 3420 Dihedral : 4.037 45.544 2708 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.72 % Allowed : 20.95 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.27 (0.18), residues: 2428 helix: 2.11 (0.14), residues: 1452 sheet: -1.58 (0.49), residues: 92 loop : -1.10 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 197 TYR 0.014 0.001 TYR D 455 PHE 0.020 0.001 PHE A 405 TRP 0.039 0.001 TRP D 715 HIS 0.005 0.001 HIS A 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.10 (20544) covalent geometry : angle 0.56280 / 0.27 (27876) hydrogen bonds : bond 0.03039 / 2.00 ( 1072) hydrogen bonds : angle 3.61549 / 2.56 ( 3108) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 287 time to evaluate : 0.838 Fit side-chains revert: symmetry clash REVERT: A 92 LEU cc_start: 0.7227 (mm) cc_final: 0.6446 (pp) REVERT: A 178 GLN cc_start: 0.8170 (mt0) cc_final: 0.7815 (mp10) REVERT: A 235 GLN cc_start: 0.7784 (mt0) cc_final: 0.7513 (mt0) REVERT: A 528 MET cc_start: 0.8408 (ptm) cc_final: 0.8168 (ttp) REVERT: A 634 TYR cc_start: 0.8272 (OUTLIER) cc_final: 0.7372 (m-80) REVERT: A 670 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7620 (tp30) REVERT: B 39 PHE cc_start: 0.7129 (OUTLIER) cc_final: 0.5742 (p90) REVERT: B 383 GLN cc_start: 0.8284 (tp40) cc_final: 0.7965 (tt0) REVERT: B 473 GLU cc_start: 0.8400 (mp0) cc_final: 0.8171 (mm-30) REVERT: B 634 TYR cc_start: 0.8242 (OUTLIER) cc_final: 0.7232 (m-80) REVERT: C 92 LEU cc_start: 0.7651 (mt) cc_final: 0.6314 (pp) REVERT: C 235 GLN cc_start: 0.7853 (mt0) cc_final: 0.7506 (mt0) REVERT: C 634 TYR cc_start: 0.8272 (OUTLIER) cc_final: 0.7326 (m-80) REVERT: C 670 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7607 (tp30) REVERT: D 39 PHE cc_start: 0.7103 (OUTLIER) cc_final: 0.5419 (p90) REVERT: D 92 LEU cc_start: 0.7647 (mt) cc_final: 0.6255 (pp) REVERT: D 235 GLN cc_start: 0.7773 (mt0) cc_final: 0.7512 (mt0) REVERT: D 269 HIS cc_start: 0.7829 (t-90) cc_final: 0.7501 (t70) REVERT: D 519 PHE cc_start: 0.8078 (m-10) cc_final: 0.7865 (m-10) REVERT: D 634 TYR cc_start: 0.8245 (OUTLIER) cc_final: 0.7316 (m-80) REVERT: D 670 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7665 (tp30) outliers start: 37 outliers final: 24 residues processed: 308 average time/residue: 0.1344 time to fit residues: 67.0630 Evaluate side-chains 302 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 270 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 520 GLN Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 349 ASP Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain C residue 670 GLU Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain D residue 39 PHE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 634 TYR Chi-restraints excluded: chain D residue 670 GLU Chi-restraints excluded: chain D residue 672 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 95 optimal weight: 1.9990 chunk 228 optimal weight: 0.8980 chunk 125 optimal weight: 0.5980 chunk 141 optimal weight: 0.4980 chunk 202 optimal weight: 4.9990 chunk 154 optimal weight: 4.9990 chunk 127 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 182 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 222 GLN B 163 GLN C 163 GLN ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 GLN ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 269 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.154374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.126944 restraints weight = 27058.882| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.83 r_work: 0.3288 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20544 Z= 0.108 Angle : 0.557 9.612 27876 Z= 0.265 Chirality : 0.037 0.163 3148 Planarity : 0.003 0.047 3420 Dihedral : 3.904 43.205 2708 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.68 % Allowed : 21.32 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.32 (0.18), residues: 2428 helix: 2.18 (0.14), residues: 1452 sheet: -2.35 (0.45), residues: 112 loop : -0.99 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 687 TYR 0.014 0.001 TYR A 455 PHE 0.019 0.001 PHE A 405 TRP 0.040 0.001 TRP A 715 HIS 0.005 0.001 HIS A 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (20544) covalent geometry : angle 0.55719 / 0.27 (27876) hydrogen bonds : bond 0.03034 / 2.00 ( 1072) hydrogen bonds : angle 3.58150 / 2.53 ( 3108) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4646.47 seconds wall clock time: 80 minutes 33.83 seconds (4833.83 seconds total)