Starting phenix.real_space_refine on Sun Oct 25 20:55:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q5a_72224/10_2026/9q5a_72224.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q5a_72224/10_2026/9q5a_72224.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9q5a_72224/10_2026/9q5a_72224.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q5a_72224/10_2026/9q5a_72224.map" model { file = "/net/cci-nas-00/data/ceres_data/9q5a_72224/10_2026/9q5a_72224.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q5a_72224/10_2026/9q5a_72224.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.049 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: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 92 5.16 5 C 11202 2.51 5 N 3172 2.21 5 O 3296 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17764 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 5965 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 54, 'TRANS': 721} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 5965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 5965 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 54, 'TRANS': 721} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2911 Classifications: {'peptide': 372} Link IDs: {'PTRANS': 24, 'TRANS': 347} Chain breaks: 1 Chain: "D" Number of atoms: 2911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2911 Classifications: {'peptide': 372} Link IDs: {'PTRANS': 24, 'TRANS': 347} Chain breaks: 1 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' ZN': 1, 'TMO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' ZN': 1, 'TMO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2028 SG CYS A 285 80.681 80.394 31.921 1.00 55.58 S ATOM 2153 SG CYS A 301 81.963 77.220 31.036 1.00 57.83 S ATOM 2652 SG CYS A 365 82.676 78.443 34.737 1.00 58.89 S ATOM 7993 SG CYS B 285 50.843 64.306 31.915 1.00 55.59 S ATOM 8118 SG CYS B 301 49.565 67.456 31.036 1.00 58.40 S ATOM 8617 SG CYS B 365 48.841 66.230 34.745 1.00 57.32 S Time building chain proxies: 3.55, per 1000 atoms: 0.20 Number of scatterers: 17764 At special positions: 0 Unit cell: (132.342, 145.494, 96.996, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 92 16.00 O 3296 8.00 N 3172 7.00 C 11202 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: 1.45 Conformation dependent library (CDL) restraints added in 599.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 301 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 285 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 365 " pdb=" ZN B 801 " pdb="ZN ZN B 801 " - pdb=" SG CYS B 301 " pdb="ZN ZN B 801 " - pdb=" SG CYS B 285 " pdb="ZN ZN B 801 " - pdb=" SG CYS B 365 " 4568 Ramachandran restraints generated. 2284 Oldfield, 0 Emsley, 2284 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4156 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 28 sheets defined 24.0% alpha, 28.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 85 through 93 Processing helix chain 'A' and resid 96 through 110 Processing helix chain 'A' and resid 226 through 231 Processing helix chain 'A' and resid 238 through 246 Processing helix chain 'A' and resid 286 through 292 removed outlier: 3.827A pdb=" N TYR A 290 " --> pdb=" O SER A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 310 Processing helix chain 'A' and resid 311 through 313 No H-bonds generated for 'chain 'A' and resid 311 through 313' Processing helix chain 'A' and resid 370 through 374 removed outlier: 4.046A pdb=" N ASN A 373 " --> pdb=" O SER A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 419 removed outlier: 3.515A pdb=" N ALA A 419 " --> pdb=" O ASP A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 451 Processing helix chain 'A' and resid 469 through 478 Processing helix chain 'A' and resid 481 through 485 Processing helix chain 'A' and resid 523 through 537 removed outlier: 3.606A pdb=" N GLU A 527 " --> pdb=" O ASP A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 566 Processing helix chain 'A' and resid 615 through 617 No H-bonds generated for 'chain 'A' and resid 615 through 617' Processing helix chain 'A' and resid 618 through 631 removed outlier: 3.508A pdb=" N ALA A 624 " --> pdb=" O ALA A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 651 removed outlier: 3.537A pdb=" N LEU A 645 " --> pdb=" O ALA A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 669 Processing helix chain 'A' and resid 685 through 695 Processing helix chain 'A' and resid 748 through 750 No H-bonds generated for 'chain 'A' and resid 748 through 750' Processing helix chain 'B' and resid 85 through 93 Processing helix chain 'B' and resid 96 through 110 Processing helix chain 'B' and resid 226 through 231 Processing helix chain 'B' and resid 238 through 246 Processing helix chain 'B' and resid 286 through 292 removed outlier: 3.820A pdb=" N TYR B 290 " --> pdb=" O SER B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 310 Processing helix chain 'B' and resid 311 through 313 No H-bonds generated for 'chain 'B' and resid 311 through 313' Processing helix chain 'B' and resid 370 through 374 removed outlier: 4.046A pdb=" N ASN B 373 " --> pdb=" O SER B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 419 removed outlier: 3.513A pdb=" N ALA B 419 " --> pdb=" O ASP B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 451 Processing helix chain 'B' and resid 469 through 478 Processing helix chain 'B' and resid 481 through 485 Processing helix chain 'B' and resid 523 through 537 removed outlier: 3.606A pdb=" N GLU B 527 " --> pdb=" O ASP B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 566 Processing helix chain 'B' and resid 615 through 617 No H-bonds generated for 'chain 'B' and resid 615 through 617' Processing helix chain 'B' and resid 618 through 631 removed outlier: 3.513A pdb=" N ALA B 624 " --> pdb=" O ALA B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 651 removed outlier: 3.537A pdb=" N LEU B 645 " --> pdb=" O ALA B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 669 Processing helix chain 'B' and resid 685 through 695 Processing helix chain 'B' and resid 748 through 750 No H-bonds generated for 'chain 'B' and resid 748 through 750' Processing helix chain 'C' and resid 413 through 418 Processing helix chain 'C' and resid 440 through 451 Processing helix chain 'C' and resid 469 through 478 Processing helix chain 'C' and resid 481 through 485 Processing helix chain 'C' and resid 522 through 537 removed outlier: 4.296A pdb=" N GLY C 526 " --> pdb=" O THR C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 566 Processing helix chain 'C' and resid 615 through 617 No H-bonds generated for 'chain 'C' and resid 615 through 617' Processing helix chain 'C' and resid 618 through 630 Processing helix chain 'C' and resid 639 through 650 Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 685 through 695 Processing helix chain 'D' and resid 413 through 418 Processing helix chain 'D' and resid 440 through 451 Processing helix chain 'D' and resid 469 through 478 Processing helix chain 'D' and resid 481 through 485 Processing helix chain 'D' and resid 522 through 537 removed outlier: 4.297A pdb=" N GLY D 526 " --> pdb=" O THR D 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 558 through 566 Processing helix chain 'D' and resid 615 through 617 No H-bonds generated for 'chain 'D' and resid 615 through 617' Processing helix chain 'D' and resid 618 through 630 Processing helix chain 'D' and resid 639 through 650 Processing helix chain 'D' and resid 670 through 674 Processing helix chain 'D' and resid 685 through 695 Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 22 removed outlier: 4.013A pdb=" N LYS B 766 " --> pdb=" O LYS B 760 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N CYS B 716 " --> pdb=" O GLY B 759 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU B 717 " --> pdb=" O ILE B 724 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N GLY B 725 " --> pdb=" O ASP B 746 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ASP B 746 " --> pdb=" O GLY B 725 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N ILE B 727 " --> pdb=" O ARG B 744 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ARG B 744 " --> pdb=" O ILE B 727 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLN B 739 " --> pdb=" O ILE B 705 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLY B 702 " --> pdb=" O THR B 773 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 37 Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 47 Processing sheet with id=AA4, first strand: chain 'A' and resid 186 through 192 removed outlier: 5.949A pdb=" N SER A 384 " --> pdb=" O ILE A 187 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASP A 189 " --> pdb=" O VAL A 382 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL A 382 " --> pdb=" O ASP A 189 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ARG A 191 " --> pdb=" O ILE A 380 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE A 380 " --> pdb=" O ARG A 191 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N TYR A 349 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ASP A 273 " --> pdb=" O TYR A 349 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU A 351 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL A 268 " --> pdb=" O TYR A 259 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 186 through 192 removed outlier: 5.949A pdb=" N SER A 384 " --> pdb=" O ILE A 187 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASP A 189 " --> pdb=" O VAL A 382 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL A 382 " --> pdb=" O ASP A 189 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ARG A 191 " --> pdb=" O ILE A 380 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE A 380 " --> pdb=" O ARG A 191 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N TYR A 349 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ASP A 273 " --> pdb=" O TYR A 349 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU A 351 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 9.827A pdb=" N ALA A 394 " --> pdb=" O GLU A 269 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL A 271 " --> pdb=" O ALA A 394 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N ALA A 396 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N ASP A 273 " --> pdb=" O ALA A 396 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 197 through 202 Processing sheet with id=AA7, first strand: chain 'A' and resid 329 through 331 Processing sheet with id=AA8, first strand: chain 'A' and resid 409 through 410 removed outlier: 7.200A pdb=" N ARG A 409 " --> pdb=" O TRP A 431 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N ASP A 423 " --> pdb=" O ASN A 434 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 567 through 569 removed outlier: 4.398A pdb=" N ASP A 456 " --> pdb=" O MET A 638 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 490 through 496 removed outlier: 3.611A pdb=" N ASP A 504 " --> pdb=" O MET A 495 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 21 through 22 removed outlier: 4.017A pdb=" N LYS A 766 " --> pdb=" O LYS A 760 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N CYS A 716 " --> pdb=" O GLY A 759 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU A 717 " --> pdb=" O ILE A 724 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N GLY A 725 " --> pdb=" O ASP A 746 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ASP A 746 " --> pdb=" O GLY A 725 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N ILE A 727 " --> pdb=" O ARG A 744 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ARG A 744 " --> pdb=" O ILE A 727 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLN A 739 " --> pdb=" O ILE A 705 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLY A 702 " --> pdb=" O THR A 773 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 32 through 37 Processing sheet with id=AB4, first strand: chain 'B' and resid 42 through 47 Processing sheet with id=AB5, first strand: chain 'B' and resid 186 through 192 removed outlier: 5.950A pdb=" N SER B 384 " --> pdb=" O ILE B 187 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASP B 189 " --> pdb=" O VAL B 382 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL B 382 " --> pdb=" O ASP B 189 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ARG B 191 " --> pdb=" O ILE B 380 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE B 380 " --> pdb=" O ARG B 191 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N TYR B 349 " --> pdb=" O ASP B 273 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ASP B 273 " --> pdb=" O TYR B 349 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU B 351 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL B 268 " --> pdb=" O TYR B 259 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 186 through 192 removed outlier: 5.950A pdb=" N SER B 384 " --> pdb=" O ILE B 187 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASP B 189 " --> pdb=" O VAL B 382 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL B 382 " --> pdb=" O ASP B 189 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ARG B 191 " --> pdb=" O ILE B 380 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE B 380 " --> pdb=" O ARG B 191 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N TYR B 349 " --> pdb=" O ASP B 273 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ASP B 273 " --> pdb=" O TYR B 349 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU B 351 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 9.827A pdb=" N ALA B 394 " --> pdb=" O GLU B 269 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL B 271 " --> pdb=" O ALA B 394 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N ALA B 396 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N ASP B 273 " --> pdb=" O ALA B 396 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 197 through 202 Processing sheet with id=AB8, first strand: chain 'B' and resid 329 through 331 Processing sheet with id=AB9, first strand: chain 'B' and resid 409 through 410 removed outlier: 7.200A pdb=" N ARG B 409 " --> pdb=" O TRP B 431 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ASP B 423 " --> pdb=" O ASN B 434 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 567 through 569 removed outlier: 4.405A pdb=" N ASP B 456 " --> pdb=" O MET B 638 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 490 through 496 removed outlier: 3.611A pdb=" N ASP B 504 " --> pdb=" O MET B 495 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 409 through 410 removed outlier: 6.860A pdb=" N ARG C 409 " --> pdb=" O TRP C 431 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 567 through 569 removed outlier: 4.683A pdb=" N ASP C 456 " --> pdb=" O MET C 638 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 490 through 495 removed outlier: 3.646A pdb=" N ASP C 504 " --> pdb=" O MET C 495 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ARG C 515 " --> pdb=" O MET C 511 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 698 through 705 removed outlier: 4.146A pdb=" N GLN C 739 " --> pdb=" O ILE C 705 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS C 738 " --> pdb=" O SER C 733 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ARG C 744 " --> pdb=" O ILE C 727 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ILE C 727 " --> pdb=" O ARG C 744 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N ASP C 746 " --> pdb=" O GLY C 725 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N GLY C 725 " --> pdb=" O ASP C 746 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU C 717 " --> pdb=" O ILE C 724 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 409 through 410 removed outlier: 6.860A pdb=" N ARG D 409 " --> pdb=" O TRP D 431 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 567 through 569 removed outlier: 4.683A pdb=" N ASP D 456 " --> pdb=" O MET D 638 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 490 through 495 removed outlier: 3.643A pdb=" N ASP D 504 " --> pdb=" O MET D 495 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ARG D 515 " --> pdb=" O MET D 511 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 698 through 705 removed outlier: 4.146A pdb=" N GLN D 739 " --> pdb=" O ILE D 705 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS D 738 " --> pdb=" O SER D 733 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ARG D 744 " --> pdb=" O ILE D 727 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ILE D 727 " --> pdb=" O ARG D 744 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N ASP D 746 " --> pdb=" O GLY D 725 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N GLY D 725 " --> pdb=" O ASP D 746 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU D 717 " --> pdb=" O ILE D 724 " (cutoff:3.500A) 731 hydrogen bonds defined for protein. 2040 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: 4.07 Time building geometry restraints manager: 1.91 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: 6039 1.34 - 1.46: 3505 1.46 - 1.57: 8528 1.57 - 1.69: 0 1.69 - 1.81: 152 Bond restraints: 18224 Sorted by residual: bond pdb=" N GLN D 723 " pdb=" CA GLN D 723 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.22e-02 6.72e+03 6.39e+00 bond pdb=" N HIS B 633 " pdb=" CA HIS B 633 " ideal model delta sigma weight residual 1.456 1.485 -0.030 1.26e-02 6.30e+03 5.55e+00 bond pdb=" CAB TMO B 802 " pdb=" NAC TMO B 802 " ideal model delta sigma weight residual 1.495 1.449 0.046 2.00e-02 2.50e+03 5.37e+00 bond pdb=" CA PRO A 696 " pdb=" CB PRO A 696 " ideal model delta sigma weight residual 1.532 1.501 0.031 1.35e-02 5.49e+03 5.35e+00 bond pdb=" CAA TMO A 802 " pdb=" NAC TMO A 802 " ideal model delta sigma weight residual 1.495 1.449 0.046 2.00e-02 2.50e+03 5.25e+00 ... (remaining 18219 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.07: 23690 1.07 - 2.14: 793 2.14 - 3.21: 233 3.21 - 4.28: 30 4.28 - 5.35: 24 Bond angle restraints: 24770 Sorted by residual: angle pdb=" N GLN D 723 " pdb=" CA GLN D 723 " pdb=" CB GLN D 723 " ideal model delta sigma weight residual 109.97 115.08 -5.11 1.47e+00 4.63e-01 1.21e+01 angle pdb=" N GLN D 548 " pdb=" CA GLN D 548 " pdb=" C GLN D 548 " ideal model delta sigma weight residual 112.94 108.08 4.86 1.41e+00 5.03e-01 1.19e+01 angle pdb=" N GLN C 548 " pdb=" CA GLN C 548 " pdb=" C GLN C 548 " ideal model delta sigma weight residual 112.94 108.12 4.82 1.41e+00 5.03e-01 1.17e+01 angle pdb=" CA GLU B 607 " pdb=" C GLU B 607 " pdb=" O GLU B 607 " ideal model delta sigma weight residual 121.78 117.80 3.98 1.28e+00 6.10e-01 9.66e+00 angle pdb=" CA GLU A 607 " pdb=" C GLU A 607 " pdb=" O GLU A 607 " ideal model delta sigma weight residual 121.78 117.82 3.96 1.28e+00 6.10e-01 9.59e+00 ... (remaining 24765 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.09: 9220 17.09 - 34.17: 1097 34.17 - 51.26: 406 51.26 - 68.34: 77 68.34 - 85.43: 20 Dihedral angle restraints: 10820 sinusoidal: 4318 harmonic: 6502 Sorted by residual: dihedral pdb=" CA HIS C 749 " pdb=" C HIS C 749 " pdb=" N ALA C 750 " pdb=" CA ALA C 750 " ideal model delta harmonic sigma weight residual 180.00 158.79 21.21 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA HIS D 749 " pdb=" C HIS D 749 " pdb=" N ALA D 750 " pdb=" CA ALA D 750 " ideal model delta harmonic sigma weight residual 180.00 158.82 21.18 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA MET A 321 " pdb=" C MET A 321 " pdb=" N ALA A 322 " pdb=" CA ALA A 322 " ideal model delta harmonic sigma weight residual -180.00 -159.39 -20.61 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 10817 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1973 0.043 - 0.087: 449 0.087 - 0.130: 199 0.130 - 0.173: 7 0.173 - 0.217: 2 Chirality restraints: 2630 Sorted by residual: chirality pdb=" CA GLU A 607 " pdb=" N GLU A 607 " pdb=" C GLU A 607 " pdb=" CB GLU A 607 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA GLU B 607 " pdb=" N GLU B 607 " pdb=" C GLU B 607 " pdb=" CB GLU B 607 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA HIS C 414 " pdb=" N HIS C 414 " pdb=" C HIS C 414 " pdb=" CB HIS C 414 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.30e-01 ... (remaining 2627 not shown) Planarity restraints: 3296 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE D 775 " 0.036 5.00e-02 4.00e+02 5.52e-02 4.88e+00 pdb=" N PRO D 776 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO D 776 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 776 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 775 " -0.036 5.00e-02 4.00e+02 5.51e-02 4.85e+00 pdb=" N PRO C 776 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO C 776 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 776 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 547 " 0.010 2.00e-02 2.50e+03 1.99e-02 3.97e+00 pdb=" C ASP C 547 " -0.034 2.00e-02 2.50e+03 pdb=" O ASP C 547 " 0.013 2.00e-02 2.50e+03 pdb=" N GLN C 548 " 0.012 2.00e-02 2.50e+03 ... (remaining 3293 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 197 2.64 - 3.21: 14929 3.21 - 3.77: 28630 3.77 - 4.34: 42238 4.34 - 4.90: 69394 Nonbonded interactions: 155388 Sorted by model distance: nonbonded pdb="ZN ZN B 801 " pdb=" OAE TMO B 802 " model vdw 2.080 2.230 nonbonded pdb="ZN ZN A 801 " pdb=" OAE TMO A 802 " model vdw 2.101 2.230 nonbonded pdb=" OG1 THR D 728 " pdb=" O LEU D 742 " model vdw 2.203 3.040 nonbonded pdb=" OG1 THR C 728 " pdb=" O LEU C 742 " model vdw 2.204 3.040 nonbonded pdb=" OH TYR D 492 " pdb=" OD2 ASP D 505 " model vdw 2.215 3.040 ... (remaining 155383 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.070 Find NCS groups from input model: 0.180 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:7.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18230 Z= 0.139 Angle : 0.523 5.354 24770 Z= 0.285 Chirality : 0.044 0.217 2630 Planarity : 0.005 0.055 3296 Dihedral : 17.246 85.426 6664 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.46 % Allowed : 25.38 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.73 (0.17), residues: 2284 helix: -0.04 (0.24), residues: 498 sheet: -0.15 (0.20), residues: 604 loop : -0.79 (0.17), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 203 TYR 0.014 0.001 TYR A 778 PHE 0.012 0.001 PHE B 659 TRP 0.010 0.001 TRP D 568 HIS 0.003 0.001 HIS C 615 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.14 (18224) covalent geometry : angle 0.52297 / 0.28 (24770) hydrogen bonds : bond 0.13681 / 9.62 ( 703) hydrogen bonds : angle 6.32587 / 4.46 ( 2040) metal coordination : bond 0.00254 / 0.15 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4568 Ramachandran restraints generated. 2284 Oldfield, 0 Emsley, 2284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4568 Ramachandran restraints generated. 2284 Oldfield, 0 Emsley, 2284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 183 time to evaluate : 0.637 Fit side-chains REVERT: A 442 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7098 (mp0) REVERT: A 469 ASP cc_start: 0.8166 (p0) cc_final: 0.7762 (p0) REVERT: A 484 LYS cc_start: 0.8183 (mtpt) cc_final: 0.7584 (mtpt) REVERT: A 527 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.8018 (tp30) REVERT: A 548 GLN cc_start: 0.8926 (OUTLIER) cc_final: 0.8233 (mt0) REVERT: A 687 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7257 (mm-30) REVERT: B 442 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7092 (mp0) REVERT: B 469 ASP cc_start: 0.8160 (p0) cc_final: 0.7763 (p0) REVERT: B 484 LYS cc_start: 0.8192 (mtpt) cc_final: 0.7473 (mmtt) REVERT: B 527 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.8012 (tp30) REVERT: B 548 GLN cc_start: 0.8909 (OUTLIER) cc_final: 0.8212 (mt0) REVERT: B 687 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7256 (mm-30) REVERT: C 636 LYS cc_start: 0.7509 (mtpt) cc_final: 0.7061 (mtpp) REVERT: D 636 LYS cc_start: 0.7501 (mtpt) cc_final: 0.7051 (mtpp) REVERT: D 723 GLN cc_start: 0.5121 (OUTLIER) cc_final: 0.4837 (tt0) outliers start: 45 outliers final: 32 residues processed: 220 average time/residue: 0.5940 time to fit residues: 146.5396 Evaluate side-chains 220 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 183 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 756 ILE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 527 GLU Chi-restraints excluded: chain B residue 548 GLN Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 756 ILE Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 593 ASN Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 699 LYS Chi-restraints excluded: chain C residue 729 SER Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 593 ASN Chi-restraints excluded: chain D residue 654 PHE Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 699 LYS Chi-restraints excluded: chain D residue 723 GLN Chi-restraints excluded: chain D residue 729 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: [216, 98, 194, 227, 107, 10, 66, 130, 124, 103, 200] chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.2980 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 1.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 590 ASN B 590 ASN C 410 GLN D 410 GLN D 723 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.141050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.099813 restraints weight = 19360.390| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 1.50 r_work: 0.2884 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8950 moved from start: 0.0554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 18230 Z= 0.170 Angle : 0.546 6.231 24770 Z= 0.287 Chirality : 0.045 0.147 2630 Planarity : 0.005 0.048 3296 Dihedral : 6.256 51.152 2577 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.98 % Allowed : 21.94 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.17), residues: 2284 helix: 0.94 (0.24), residues: 494 sheet: -0.02 (0.20), residues: 600 loop : -0.69 (0.17), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 203 TYR 0.016 0.001 TYR A 778 PHE 0.015 0.001 PHE B 509 TRP 0.013 0.001 TRP C 528 HIS 0.004 0.001 HIS B 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 (18224) covalent geometry : angle 0.54591 / 0.29 (24770) hydrogen bonds : bond 0.03770 / 2.67 ( 703) hydrogen bonds : angle 4.82180 / 3.39 ( 2040) metal coordination : bond 0.00477 / 0.29 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4568 Ramachandran restraints generated. 2284 Oldfield, 0 Emsley, 2284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4568 Ramachandran restraints generated. 2284 Oldfield, 0 Emsley, 2284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 199 time to evaluate : 0.532 Fit side-chains REVERT: A 96 GLU cc_start: 0.6613 (OUTLIER) cc_final: 0.6292 (tm-30) REVERT: A 404 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7950 (mp0) REVERT: A 442 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7480 (mp0) REVERT: A 484 LYS cc_start: 0.8274 (mtpt) cc_final: 0.7703 (mmtt) REVERT: A 527 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8292 (tp30) REVERT: A 687 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7660 (mm-30) REVERT: A 693 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8171 (tttm) REVERT: A 786 ARG cc_start: 0.5210 (OUTLIER) cc_final: 0.4982 (mtt-85) REVERT: B 96 GLU cc_start: 0.6620 (OUTLIER) cc_final: 0.6303 (tm-30) REVERT: B 404 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7950 (mp0) REVERT: B 442 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7478 (mp0) REVERT: B 484 LYS cc_start: 0.8269 (mtpt) cc_final: 0.7706 (mmtt) REVERT: B 527 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8290 (tp30) REVERT: B 687 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7651 (mm-30) REVERT: B 693 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8171 (tttm) REVERT: B 786 ARG cc_start: 0.5211 (OUTLIER) cc_final: 0.4972 (mtt-85) REVERT: C 408 THR cc_start: 0.7252 (OUTLIER) cc_final: 0.7047 (t) REVERT: C 426 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6849 (tp30) REVERT: C 445 TYR cc_start: 0.7479 (OUTLIER) cc_final: 0.7148 (t80) REVERT: C 636 LYS cc_start: 0.7857 (mtpt) cc_final: 0.7466 (mtpp) REVERT: C 746 ASP cc_start: 0.6648 (OUTLIER) cc_final: 0.6119 (m-30) REVERT: C 751 ASP cc_start: 0.5905 (OUTLIER) cc_final: 0.5657 (m-30) REVERT: C 781 LYS cc_start: 0.7119 (OUTLIER) cc_final: 0.5935 (mttt) REVERT: D 408 THR cc_start: 0.7258 (OUTLIER) cc_final: 0.7050 (t) REVERT: D 426 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6846 (tp30) REVERT: D 445 TYR cc_start: 0.7459 (OUTLIER) cc_final: 0.7135 (t80) REVERT: D 636 LYS cc_start: 0.7819 (mtpt) cc_final: 0.7449 (mtpp) REVERT: D 746 ASP cc_start: 0.6626 (OUTLIER) cc_final: 0.6089 (m-30) REVERT: D 751 ASP cc_start: 0.5898 (OUTLIER) cc_final: 0.5647 (m-30) REVERT: D 781 LYS cc_start: 0.7143 (OUTLIER) cc_final: 0.5937 (mttt) outliers start: 91 outliers final: 41 residues processed: 274 average time/residue: 0.5709 time to fit residues: 176.0551 Evaluate side-chains 251 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 188 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 445 TYR Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain A residue 638 MET Chi-restraints excluded: chain A residue 693 LYS Chi-restraints excluded: chain A residue 786 ARG Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain B residue 445 TYR Chi-restraints excluded: chain B residue 527 GLU Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain B residue 638 MET Chi-restraints excluded: chain B residue 693 LYS Chi-restraints excluded: chain B residue 786 ARG Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain C residue 445 TYR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 645 LEU Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 746 ASP Chi-restraints excluded: chain C residue 751 ASP Chi-restraints excluded: chain C residue 781 LYS Chi-restraints excluded: chain D residue 408 THR Chi-restraints excluded: chain D residue 426 GLU Chi-restraints excluded: chain D residue 445 TYR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 612 ILE Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 746 ASP Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain D residue 781 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: [15, 24, 4, 126, 54, 155, 217, 84, 104, 61, 5] chunk 15 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 126 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 155 optimal weight: 0.9980 chunk 217 optimal weight: 1.9990 chunk 84 optimal weight: 8.9990 chunk 104 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 590 ASN B 590 ASN C 410 GLN D 410 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.139121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.096887 restraints weight = 19563.406| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 1.46 r_work: 0.2856 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8981 moved from start: 0.0745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 18230 Z= 0.247 Angle : 0.599 7.918 24770 Z= 0.315 Chirality : 0.048 0.228 2630 Planarity : 0.005 0.050 3296 Dihedral : 5.713 52.444 2534 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 5.85 % Allowed : 21.28 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.17), residues: 2284 helix: 0.94 (0.24), residues: 494 sheet: 0.05 (0.20), residues: 582 loop : -0.73 (0.17), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 203 TYR 0.017 0.002 TYR B 778 PHE 0.018 0.002 PHE B 509 TRP 0.012 0.002 TRP C 528 HIS 0.005 0.001 HIS B 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00598 / 0.25 (18224) covalent geometry : angle 0.59865 / 0.32 (24770) hydrogen bonds : bond 0.03960 / 2.82 ( 703) hydrogen bonds : angle 4.78707 / 3.36 ( 2040) metal coordination : bond 0.00686 / 0.41 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4568 Ramachandran restraints generated. 2284 Oldfield, 0 Emsley, 2284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4568 Ramachandran restraints generated. 2284 Oldfield, 0 Emsley, 2284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 188 time to evaluate : 0.713 Fit side-chains REVERT: A 96 GLU cc_start: 0.6723 (OUTLIER) cc_final: 0.6437 (tm-30) REVERT: A 404 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7909 (mp0) REVERT: A 442 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7504 (mp0) REVERT: A 484 LYS cc_start: 0.8304 (mtpt) cc_final: 0.7836 (mtpt) REVERT: A 527 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8350 (tp30) REVERT: A 558 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8324 (mttt) REVERT: A 687 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7688 (mm-30) REVERT: B 96 GLU cc_start: 0.6715 (OUTLIER) cc_final: 0.6433 (tm-30) REVERT: B 404 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7905 (mp0) REVERT: B 442 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7491 (mp0) REVERT: B 484 LYS cc_start: 0.8301 (mtpt) cc_final: 0.7733 (mmtt) REVERT: B 527 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8353 (tp30) REVERT: B 558 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8346 (mttt) REVERT: B 687 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7687 (mm-30) REVERT: B 786 ARG cc_start: 0.5152 (OUTLIER) cc_final: 0.4950 (mtt-85) REVERT: C 426 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6846 (tp30) REVERT: C 636 LYS cc_start: 0.7749 (mtpt) cc_final: 0.7399 (mtpp) REVERT: C 751 ASP cc_start: 0.5849 (OUTLIER) cc_final: 0.5599 (m-30) REVERT: D 426 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6843 (tp30) REVERT: D 636 LYS cc_start: 0.7747 (mtpt) cc_final: 0.7400 (mtpp) REVERT: D 746 ASP cc_start: 0.6621 (OUTLIER) cc_final: 0.6086 (m-30) REVERT: D 751 ASP cc_start: 0.5873 (OUTLIER) cc_final: 0.5619 (m-30) outliers start: 107 outliers final: 63 residues processed: 279 average time/residue: 0.5619 time to fit residues: 177.0655 Evaluate side-chains 261 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 184 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 445 TYR Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain A residue 638 MET Chi-restraints excluded: chain A residue 716 CYS Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain B residue 445 TYR Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 509 PHE Chi-restraints excluded: chain B residue 527 GLU Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain B residue 638 MET Chi-restraints excluded: chain B residue 716 CYS Chi-restraints excluded: chain B residue 786 ARG Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 645 LEU Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 703 ILE Chi-restraints excluded: chain C residue 751 ASP Chi-restraints excluded: chain D residue 415 ASP Chi-restraints excluded: chain D residue 426 GLU Chi-restraints excluded: chain D residue 447 SER Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 612 ILE Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 654 PHE Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 703 ILE Chi-restraints excluded: chain D residue 746 ASP Chi-restraints excluded: chain D residue 751 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: [164, 188, 227, 200, 33, 186, 43, 160, 99, 18, 158] chunk 164 optimal weight: 2.9990 chunk 188 optimal weight: 1.9990 chunk 227 optimal weight: 0.0050 chunk 200 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 186 optimal weight: 10.0000 chunk 43 optimal weight: 0.7980 chunk 160 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 18 optimal weight: 0.4980 chunk 158 optimal weight: 6.9990 overall best weight: 1.0598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 590 ASN B 590 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.141567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.100338 restraints weight = 19418.693| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 1.39 r_work: 0.2893 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 moved from start: 0.0741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18230 Z= 0.135 Angle : 0.514 5.363 24770 Z= 0.269 Chirality : 0.044 0.144 2630 Planarity : 0.005 0.049 3296 Dihedral : 5.324 51.759 2534 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.43 % Allowed : 23.03 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.17), residues: 2284 helix: 1.24 (0.24), residues: 494 sheet: 0.06 (0.20), residues: 586 loop : -0.62 (0.17), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 203 TYR 0.013 0.001 TYR A 445 PHE 0.013 0.001 PHE A 509 TRP 0.012 0.001 TRP C 528 HIS 0.003 0.001 HIS B 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (18224) covalent geometry : angle 0.51369 / 0.27 (24770) hydrogen bonds : bond 0.03209 / 2.28 ( 703) hydrogen bonds : angle 4.52936 / 3.18 ( 2040) metal coordination : bond 0.00338 / 0.21 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4568 Ramachandran restraints generated. 2284 Oldfield, 0 Emsley, 2284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4568 Ramachandran restraints generated. 2284 Oldfield, 0 Emsley, 2284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 187 time to evaluate : 0.732 Fit side-chains REVERT: A 96 GLU cc_start: 0.6753 (OUTLIER) cc_final: 0.6469 (tm-30) REVERT: A 404 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.7932 (mp0) REVERT: A 442 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7455 (mp0) REVERT: A 484 LYS cc_start: 0.8290 (mtpt) cc_final: 0.7820 (mtpt) REVERT: A 527 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8288 (tp30) REVERT: A 558 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8359 (mttt) REVERT: A 687 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7672 (mm-30) REVERT: B 96 GLU cc_start: 0.6725 (OUTLIER) cc_final: 0.6443 (tm-30) REVERT: B 404 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7930 (mp0) REVERT: B 442 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7448 (mp0) REVERT: B 484 LYS cc_start: 0.8293 (mtpt) cc_final: 0.7830 (mtpt) REVERT: B 527 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8308 (tp30) REVERT: B 558 LYS cc_start: 0.8883 (OUTLIER) cc_final: 0.8360 (mttt) REVERT: B 687 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7663 (mm-30) REVERT: B 786 ARG cc_start: 0.5241 (OUTLIER) cc_final: 0.4988 (mtt-85) REVERT: C 422 ARG cc_start: 0.7129 (mpp-170) cc_final: 0.6811 (mmt-90) REVERT: C 426 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6797 (tp30) REVERT: C 636 LYS cc_start: 0.7720 (mtpt) cc_final: 0.7390 (mtpp) REVERT: C 746 ASP cc_start: 0.6634 (OUTLIER) cc_final: 0.6111 (m-30) REVERT: C 751 ASP cc_start: 0.5765 (OUTLIER) cc_final: 0.5495 (m-30) REVERT: D 422 ARG cc_start: 0.7120 (mpp-170) cc_final: 0.6807 (mmt-90) REVERT: D 426 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.6783 (tp30) REVERT: D 636 LYS cc_start: 0.7708 (mtpt) cc_final: 0.7377 (mtpp) REVERT: D 746 ASP cc_start: 0.6615 (OUTLIER) cc_final: 0.6129 (m-30) REVERT: D 751 ASP cc_start: 0.5780 (OUTLIER) cc_final: 0.5509 (m-30) outliers start: 81 outliers final: 45 residues processed: 255 average time/residue: 0.5751 time to fit residues: 164.8911 Evaluate side-chains 241 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 181 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 445 TYR Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 638 MET Chi-restraints excluded: chain A residue 716 CYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain B residue 445 TYR Chi-restraints excluded: chain B residue 527 GLU Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 638 MET Chi-restraints excluded: chain B residue 716 CYS Chi-restraints excluded: chain B residue 786 ARG Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 699 LYS Chi-restraints excluded: chain C residue 703 ILE Chi-restraints excluded: chain C residue 746 ASP Chi-restraints excluded: chain C residue 751 ASP Chi-restraints excluded: chain D residue 426 GLU Chi-restraints excluded: chain D residue 447 SER Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 612 ILE Chi-restraints excluded: chain D residue 654 PHE Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 699 LYS Chi-restraints excluded: chain D residue 703 ILE Chi-restraints excluded: chain D residue 746 ASP Chi-restraints excluded: chain D residue 751 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: [75, 101, 98, 14, 150, 166, 156, 74, 78, 115, 132] chunk 75 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 chunk 166 optimal weight: 5.9990 chunk 156 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 78 optimal weight: 8.9990 chunk 115 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 590 ASN B 590 ASN C 410 GLN D 410 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.137746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.092290 restraints weight = 19413.924| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 1.46 r_work: 0.2813 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9014 moved from start: 0.0797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 18230 Z= 0.212 Angle : 0.569 7.054 24770 Z= 0.299 Chirality : 0.047 0.204 2630 Planarity : 0.005 0.050 3296 Dihedral : 5.487 52.351 2530 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.98 % Allowed : 22.37 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.17), residues: 2284 helix: 1.13 (0.24), residues: 494 sheet: 0.06 (0.20), residues: 598 loop : -0.65 (0.17), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 203 TYR 0.016 0.002 TYR B 778 PHE 0.018 0.002 PHE B 509 TRP 0.009 0.001 TRP D 528 HIS 0.005 0.001 HIS A 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.21 (18224) covalent geometry : angle 0.56861 / 0.30 (24770) hydrogen bonds : bond 0.03588 / 2.55 ( 703) hydrogen bonds : angle 4.58746 / 3.21 ( 2040) metal coordination : bond 0.00614 / 0.37 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4568 Ramachandran restraints generated. 2284 Oldfield, 0 Emsley, 2284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4568 Ramachandran restraints generated. 2284 Oldfield, 0 Emsley, 2284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 186 time to evaluate : 0.651 Fit side-chains REVERT: A 96 GLU cc_start: 0.6762 (OUTLIER) cc_final: 0.6459 (tm-30) REVERT: A 283 MET cc_start: 0.9121 (ptt) cc_final: 0.8747 (ptt) REVERT: A 404 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7950 (mp0) REVERT: A 442 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7613 (mp0) REVERT: A 484 LYS cc_start: 0.8332 (mtpt) cc_final: 0.7907 (mtpt) REVERT: A 558 LYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8385 (mttt) REVERT: A 687 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7747 (mm-30) REVERT: B 96 GLU cc_start: 0.6740 (OUTLIER) cc_final: 0.6435 (tm-30) REVERT: B 404 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7941 (mp0) REVERT: B 442 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7589 (mp0) REVERT: B 484 LYS cc_start: 0.8336 (mtpt) cc_final: 0.7909 (mtpt) REVERT: B 558 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8397 (mttt) REVERT: B 687 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7747 (mm-30) REVERT: B 786 ARG cc_start: 0.5269 (OUTLIER) cc_final: 0.4978 (mtt-85) REVERT: C 426 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.6794 (tp30) REVERT: C 636 LYS cc_start: 0.7826 (mtpt) cc_final: 0.7485 (mtpp) REVERT: C 751 ASP cc_start: 0.5935 (OUTLIER) cc_final: 0.5658 (m-30) REVERT: D 426 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6779 (tp30) REVERT: D 636 LYS cc_start: 0.7814 (mtpt) cc_final: 0.7428 (mtpp) REVERT: D 751 ASP cc_start: 0.5921 (OUTLIER) cc_final: 0.5645 (m-30) outliers start: 91 outliers final: 55 residues processed: 262 average time/residue: 0.5629 time to fit residues: 166.1758 Evaluate side-chains 248 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 182 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 445 TYR Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 638 MET Chi-restraints excluded: chain A residue 716 CYS Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain B residue 445 TYR Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 638 MET Chi-restraints excluded: chain B residue 716 CYS Chi-restraints excluded: chain B residue 786 ARG Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 645 LEU Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 699 LYS Chi-restraints excluded: chain C residue 703 ILE Chi-restraints excluded: chain C residue 751 ASP Chi-restraints excluded: chain D residue 408 THR Chi-restraints excluded: chain D residue 415 ASP Chi-restraints excluded: chain D residue 426 GLU Chi-restraints excluded: chain D residue 447 SER Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 612 ILE Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 654 PHE Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 699 LYS Chi-restraints excluded: chain D residue 703 ILE Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain D residue 751 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: [164, 20, 136, 196, 64, 183, 131, 16, 180, 139, 219] chunk 164 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 chunk 196 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 183 optimal weight: 10.0000 chunk 131 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 180 optimal weight: 0.9980 chunk 139 optimal weight: 0.7980 chunk 219 optimal weight: 0.0770 overall best weight: 1.1140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 590 ASN B 590 ASN C 410 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.139419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.094327 restraints weight = 19311.384| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 1.46 r_work: 0.2835 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8985 moved from start: 0.0795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18230 Z= 0.140 Angle : 0.518 5.370 24770 Z= 0.271 Chirality : 0.044 0.142 2630 Planarity : 0.005 0.049 3296 Dihedral : 4.850 41.258 2524 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.98 % Allowed : 22.37 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.17), residues: 2284 helix: 1.33 (0.24), residues: 494 sheet: 0.11 (0.20), residues: 586 loop : -0.62 (0.17), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 203 TYR 0.014 0.001 TYR A 445 PHE 0.014 0.001 PHE B 509 TRP 0.011 0.001 TRP D 528 HIS 0.003 0.001 HIS A 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (18224) covalent geometry : angle 0.51834 / 0.27 (24770) hydrogen bonds : bond 0.03197 / 2.27 ( 703) hydrogen bonds : angle 4.45334 / 3.12 ( 2040) metal coordination : bond 0.00365 / 0.22 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4568 Ramachandran restraints generated. 2284 Oldfield, 0 Emsley, 2284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4568 Ramachandran restraints generated. 2284 Oldfield, 0 Emsley, 2284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 191 time to evaluate : 0.474 Fit side-chains REVERT: A 96 GLU cc_start: 0.6815 (OUTLIER) cc_final: 0.6524 (tm-30) REVERT: A 404 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7959 (mp0) REVERT: A 442 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7597 (mp0) REVERT: A 484 LYS cc_start: 0.8324 (mtpt) cc_final: 0.7892 (mtpt) REVERT: A 558 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8420 (mttt) REVERT: A 687 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7748 (mm-30) REVERT: B 96 GLU cc_start: 0.6787 (OUTLIER) cc_final: 0.6496 (tm-30) REVERT: B 404 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7952 (mp0) REVERT: B 442 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7554 (mp0) REVERT: B 484 LYS cc_start: 0.8329 (mtpt) cc_final: 0.7892 (mtpt) REVERT: B 558 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8419 (mttt) REVERT: B 687 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7724 (mm-30) REVERT: B 786 ARG cc_start: 0.5312 (OUTLIER) cc_final: 0.5024 (mtt-85) REVERT: C 422 ARG cc_start: 0.7180 (mpp-170) cc_final: 0.6842 (mmt-90) REVERT: C 426 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6792 (tp30) REVERT: C 445 TYR cc_start: 0.7497 (OUTLIER) cc_final: 0.7134 (t80) REVERT: C 455 MET cc_start: 0.8621 (ttm) cc_final: 0.8217 (ttt) REVERT: C 636 LYS cc_start: 0.7784 (mtpt) cc_final: 0.7406 (mtpp) REVERT: C 704 GLU cc_start: 0.6380 (OUTLIER) cc_final: 0.5689 (pt0) REVERT: C 751 ASP cc_start: 0.5804 (OUTLIER) cc_final: 0.5536 (m-30) REVERT: D 422 ARG cc_start: 0.7148 (mpp-170) cc_final: 0.6817 (mmt-90) REVERT: D 426 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6806 (tp30) REVERT: D 445 TYR cc_start: 0.7520 (OUTLIER) cc_final: 0.7151 (t80) REVERT: D 455 MET cc_start: 0.8590 (ttm) cc_final: 0.8182 (ttt) REVERT: D 636 LYS cc_start: 0.7784 (mtpt) cc_final: 0.7385 (mtpp) REVERT: D 704 GLU cc_start: 0.6368 (OUTLIER) cc_final: 0.5677 (pt0) REVERT: D 751 ASP cc_start: 0.5794 (OUTLIER) cc_final: 0.5530 (m-30) outliers start: 91 outliers final: 51 residues processed: 264 average time/residue: 0.5675 time to fit residues: 168.8812 Evaluate side-chains 251 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 185 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 445 TYR Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 638 MET Chi-restraints excluded: chain A residue 716 CYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain B residue 445 TYR Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 638 MET Chi-restraints excluded: chain B residue 716 CYS Chi-restraints excluded: chain B residue 786 ARG Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain C residue 445 TYR Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 699 LYS Chi-restraints excluded: chain C residue 703 ILE Chi-restraints excluded: chain C residue 704 GLU Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 751 ASP Chi-restraints excluded: chain D residue 408 THR Chi-restraints excluded: chain D residue 426 GLU Chi-restraints excluded: chain D residue 445 TYR Chi-restraints excluded: chain D residue 447 SER Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 612 ILE Chi-restraints excluded: chain D residue 654 PHE Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 699 LYS Chi-restraints excluded: chain D residue 703 ILE Chi-restraints excluded: chain D residue 704 GLU Chi-restraints excluded: chain D residue 751 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: [16, 67, 191, 97, 225, 87, 23, 120, 175, 222, 33] chunk 16 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 191 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 225 optimal weight: 0.8980 chunk 87 optimal weight: 20.0000 chunk 23 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 222 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 539 ASN A 590 ASN B 539 ASN B 590 ASN C 410 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.138582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.093260 restraints weight = 19445.859| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 1.47 r_work: 0.2818 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8998 moved from start: 0.0856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18230 Z= 0.175 Angle : 0.546 6.163 24770 Z= 0.286 Chirality : 0.045 0.175 2630 Planarity : 0.005 0.049 3296 Dihedral : 4.933 41.441 2524 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.81 % Allowed : 22.43 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.06 (0.17), residues: 2284 helix: 1.30 (0.24), residues: 494 sheet: 0.12 (0.20), residues: 602 loop : -0.65 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 203 TYR 0.014 0.001 TYR B 778 PHE 0.016 0.002 PHE B 509 TRP 0.010 0.001 TRP C 528 HIS 0.004 0.001 HIS A 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 (18224) covalent geometry : angle 0.54635 / 0.29 (24770) hydrogen bonds : bond 0.03353 / 2.38 ( 703) hydrogen bonds : angle 4.47804 / 3.14 ( 2040) metal coordination : bond 0.00504 / 0.30 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4568 Ramachandran restraints generated. 2284 Oldfield, 0 Emsley, 2284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4568 Ramachandran restraints generated. 2284 Oldfield, 0 Emsley, 2284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 188 time to evaluate : 0.701 Fit side-chains REVERT: A 96 GLU cc_start: 0.6780 (OUTLIER) cc_final: 0.6487 (tm-30) REVERT: A 404 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7961 (mp0) REVERT: A 442 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7616 (mp0) REVERT: A 484 LYS cc_start: 0.8318 (mtpt) cc_final: 0.7845 (mmtt) REVERT: A 558 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8431 (mttt) REVERT: A 687 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7730 (mm-30) REVERT: B 96 GLU cc_start: 0.6750 (OUTLIER) cc_final: 0.6460 (tm-30) REVERT: B 404 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7953 (mp0) REVERT: B 442 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7578 (mp0) REVERT: B 484 LYS cc_start: 0.8332 (mtpt) cc_final: 0.7848 (mmtt) REVERT: B 558 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8430 (mttt) REVERT: B 687 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7738 (mm-30) REVERT: B 786 ARG cc_start: 0.5288 (OUTLIER) cc_final: 0.4991 (mtt-85) REVERT: C 426 GLU cc_start: 0.7042 (OUTLIER) cc_final: 0.6790 (tp30) REVERT: C 445 TYR cc_start: 0.7572 (OUTLIER) cc_final: 0.7218 (t80) REVERT: C 455 MET cc_start: 0.8624 (ttm) cc_final: 0.8225 (ttt) REVERT: C 636 LYS cc_start: 0.7797 (mtpt) cc_final: 0.7401 (mtpp) REVERT: C 751 ASP cc_start: 0.5776 (OUTLIER) cc_final: 0.5496 (m-30) REVERT: C 781 LYS cc_start: 0.7244 (OUTLIER) cc_final: 0.5927 (mttt) REVERT: D 426 GLU cc_start: 0.7036 (OUTLIER) cc_final: 0.6788 (tp30) REVERT: D 445 TYR cc_start: 0.7579 (OUTLIER) cc_final: 0.7224 (t80) REVERT: D 455 MET cc_start: 0.8608 (ttm) cc_final: 0.8212 (ttt) REVERT: D 636 LYS cc_start: 0.7789 (mtpt) cc_final: 0.7386 (mtpp) REVERT: D 751 ASP cc_start: 0.5764 (OUTLIER) cc_final: 0.5489 (m-30) REVERT: D 781 LYS cc_start: 0.7207 (OUTLIER) cc_final: 0.5931 (mttt) outliers start: 88 outliers final: 54 residues processed: 263 average time/residue: 0.5512 time to fit residues: 163.9679 Evaluate side-chains 251 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 182 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 445 TYR Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 638 MET Chi-restraints excluded: chain A residue 716 CYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain B residue 445 TYR Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 638 MET Chi-restraints excluded: chain B residue 716 CYS Chi-restraints excluded: chain B residue 786 ARG Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain C residue 445 TYR Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 569 THR Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 699 LYS Chi-restraints excluded: chain C residue 703 ILE Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 751 ASP Chi-restraints excluded: chain C residue 781 LYS Chi-restraints excluded: chain D residue 408 THR Chi-restraints excluded: chain D residue 426 GLU Chi-restraints excluded: chain D residue 445 TYR Chi-restraints excluded: chain D residue 447 SER Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 612 ILE Chi-restraints excluded: chain D residue 654 PHE Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 699 LYS Chi-restraints excluded: chain D residue 703 ILE Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain D residue 781 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: [143, 81, 163, 134, 14, 10, 59, 135, 58, 218, 221] chunk 143 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 chunk 163 optimal weight: 5.9990 chunk 134 optimal weight: 0.9990 chunk 14 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 135 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 218 optimal weight: 1.9990 chunk 221 optimal weight: 10.0000 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 590 ASN B 590 ASN C 410 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.139504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.094349 restraints weight = 19439.751| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 1.46 r_work: 0.2834 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8995 moved from start: 0.0860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18230 Z= 0.161 Angle : 0.536 5.540 24770 Z= 0.280 Chirality : 0.045 0.164 2630 Planarity : 0.005 0.050 3296 Dihedral : 4.873 41.496 2524 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.81 % Allowed : 22.37 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.17), residues: 2284 helix: 1.37 (0.24), residues: 494 sheet: 0.01 (0.20), residues: 622 loop : -0.60 (0.17), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 203 TYR 0.014 0.001 TYR A 445 PHE 0.015 0.001 PHE B 509 TRP 0.011 0.001 TRP D 528 HIS 0.004 0.001 HIS A 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 (18224) covalent geometry : angle 0.53633 / 0.28 (24770) hydrogen bonds : bond 0.03266 / 2.32 ( 703) hydrogen bonds : angle 4.44577 / 3.12 ( 2040) metal coordination : bond 0.00468 / 0.28 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4568 Ramachandran restraints generated. 2284 Oldfield, 0 Emsley, 2284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4568 Ramachandran restraints generated. 2284 Oldfield, 0 Emsley, 2284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 182 time to evaluate : 0.721 Fit side-chains REVERT: A 96 GLU cc_start: 0.6827 (OUTLIER) cc_final: 0.6536 (tm-30) REVERT: A 404 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.7945 (mp0) REVERT: A 442 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7606 (mp0) REVERT: A 484 LYS cc_start: 0.8348 (mtpt) cc_final: 0.7878 (mmtt) REVERT: A 558 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8435 (mttt) REVERT: A 687 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7745 (mm-30) REVERT: B 96 GLU cc_start: 0.6799 (OUTLIER) cc_final: 0.6508 (tm-30) REVERT: B 404 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7943 (mp0) REVERT: B 442 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7580 (mp0) REVERT: B 484 LYS cc_start: 0.8333 (mtpt) cc_final: 0.7854 (mmtt) REVERT: B 558 LYS cc_start: 0.8942 (OUTLIER) cc_final: 0.8427 (mttt) REVERT: B 687 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7744 (mm-30) REVERT: B 786 ARG cc_start: 0.5334 (OUTLIER) cc_final: 0.5047 (mtt-85) REVERT: C 422 ARG cc_start: 0.7178 (mpp-170) cc_final: 0.6838 (mmt-90) REVERT: C 426 GLU cc_start: 0.7042 (OUTLIER) cc_final: 0.6788 (tp30) REVERT: C 445 TYR cc_start: 0.7553 (OUTLIER) cc_final: 0.7192 (t80) REVERT: C 455 MET cc_start: 0.8626 (ttm) cc_final: 0.8231 (ttt) REVERT: C 636 LYS cc_start: 0.7760 (mtpt) cc_final: 0.7409 (mtpp) REVERT: C 704 GLU cc_start: 0.6387 (OUTLIER) cc_final: 0.5671 (pt0) REVERT: C 751 ASP cc_start: 0.5746 (OUTLIER) cc_final: 0.5488 (m-30) REVERT: C 781 LYS cc_start: 0.7240 (OUTLIER) cc_final: 0.5928 (mttt) REVERT: D 422 ARG cc_start: 0.7152 (mpp-170) cc_final: 0.6819 (mmt-90) REVERT: D 426 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6781 (tp30) REVERT: D 445 TYR cc_start: 0.7575 (OUTLIER) cc_final: 0.7209 (t80) REVERT: D 455 MET cc_start: 0.8608 (ttm) cc_final: 0.8215 (ttt) REVERT: D 636 LYS cc_start: 0.7745 (mtpt) cc_final: 0.7392 (mtpp) REVERT: D 704 GLU cc_start: 0.6380 (OUTLIER) cc_final: 0.5700 (pt0) REVERT: D 751 ASP cc_start: 0.5732 (OUTLIER) cc_final: 0.5478 (m-30) REVERT: D 781 LYS cc_start: 0.7209 (OUTLIER) cc_final: 0.5941 (mttt) outliers start: 88 outliers final: 56 residues processed: 260 average time/residue: 0.5988 time to fit residues: 174.5771 Evaluate side-chains 256 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 183 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 445 TYR Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 638 MET Chi-restraints excluded: chain A residue 716 CYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain B residue 445 TYR Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 638 MET Chi-restraints excluded: chain B residue 716 CYS Chi-restraints excluded: chain B residue 786 ARG Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain C residue 445 TYR Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 569 THR Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain C residue 660 THR Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 699 LYS Chi-restraints excluded: chain C residue 703 ILE Chi-restraints excluded: chain C residue 704 GLU Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 751 ASP Chi-restraints excluded: chain C residue 781 LYS Chi-restraints excluded: chain D residue 408 THR Chi-restraints excluded: chain D residue 426 GLU Chi-restraints excluded: chain D residue 445 TYR Chi-restraints excluded: chain D residue 447 SER Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 612 ILE Chi-restraints excluded: chain D residue 654 PHE Chi-restraints excluded: chain D residue 660 THR Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 699 LYS Chi-restraints excluded: chain D residue 703 ILE Chi-restraints excluded: chain D residue 704 GLU Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain D residue 781 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: [52, 134, 184, 189, 159, 224, 123, 219, 139, 23, 164] chunk 52 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 chunk 184 optimal weight: 9.9990 chunk 189 optimal weight: 9.9990 chunk 159 optimal weight: 5.9990 chunk 224 optimal weight: 20.0000 chunk 123 optimal weight: 1.9990 chunk 219 optimal weight: 8.9990 chunk 139 optimal weight: 0.4980 chunk 23 optimal weight: 0.1980 chunk 164 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 590 ASN B 590 ASN C 410 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.139063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.093860 restraints weight = 19338.415| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 1.46 r_work: 0.2828 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8991 moved from start: 0.0880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18230 Z= 0.158 Angle : 0.532 5.570 24770 Z= 0.278 Chirality : 0.045 0.166 2630 Planarity : 0.005 0.052 3296 Dihedral : 4.856 41.601 2524 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 4.87 % Allowed : 22.32 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.17), residues: 2284 helix: 1.40 (0.24), residues: 494 sheet: 0.02 (0.20), residues: 622 loop : -0.60 (0.17), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 203 TYR 0.014 0.001 TYR A 445 PHE 0.015 0.001 PHE B 509 TRP 0.009 0.001 TRP C 528 HIS 0.004 0.001 HIS B 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (18224) covalent geometry : angle 0.53237 / 0.28 (24770) hydrogen bonds : bond 0.03233 / 2.30 ( 703) hydrogen bonds : angle 4.42466 / 3.11 ( 2040) metal coordination : bond 0.00460 / 0.28 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4568 Ramachandran restraints generated. 2284 Oldfield, 0 Emsley, 2284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4568 Ramachandran restraints generated. 2284 Oldfield, 0 Emsley, 2284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 185 time to evaluate : 0.544 Fit side-chains REVERT: A 96 GLU cc_start: 0.6828 (OUTLIER) cc_final: 0.6524 (tm-30) REVERT: A 404 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.7951 (mp0) REVERT: A 442 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7602 (mp0) REVERT: A 484 LYS cc_start: 0.8323 (mtpt) cc_final: 0.7844 (mmtt) REVERT: A 558 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8429 (mttt) REVERT: A 687 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7739 (mm-30) REVERT: B 96 GLU cc_start: 0.6798 (OUTLIER) cc_final: 0.6491 (tm-30) REVERT: B 404 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7950 (mp0) REVERT: B 442 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7570 (mp0) REVERT: B 484 LYS cc_start: 0.8327 (mtpt) cc_final: 0.7844 (mmtt) REVERT: B 558 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8422 (mttt) REVERT: B 687 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7733 (mm-30) REVERT: B 786 ARG cc_start: 0.5329 (OUTLIER) cc_final: 0.5039 (mtt-85) REVERT: C 422 ARG cc_start: 0.7179 (mpp-170) cc_final: 0.6838 (mmt-90) REVERT: C 426 GLU cc_start: 0.7034 (OUTLIER) cc_final: 0.6786 (tp30) REVERT: C 445 TYR cc_start: 0.7508 (OUTLIER) cc_final: 0.7191 (t80) REVERT: C 455 MET cc_start: 0.8618 (ttm) cc_final: 0.8226 (ttt) REVERT: C 636 LYS cc_start: 0.7745 (mtpt) cc_final: 0.7392 (mtpp) REVERT: C 704 GLU cc_start: 0.6360 (OUTLIER) cc_final: 0.5657 (pt0) REVERT: C 751 ASP cc_start: 0.5675 (OUTLIER) cc_final: 0.5423 (m-30) REVERT: C 781 LYS cc_start: 0.7233 (OUTLIER) cc_final: 0.5928 (mttt) REVERT: D 426 GLU cc_start: 0.7024 (OUTLIER) cc_final: 0.6775 (tp30) REVERT: D 445 TYR cc_start: 0.7521 (OUTLIER) cc_final: 0.7204 (t80) REVERT: D 455 MET cc_start: 0.8612 (ttm) cc_final: 0.8221 (ttt) REVERT: D 636 LYS cc_start: 0.7729 (mtpt) cc_final: 0.7374 (mtpp) REVERT: D 704 GLU cc_start: 0.6352 (OUTLIER) cc_final: 0.5649 (pt0) REVERT: D 781 LYS cc_start: 0.7199 (OUTLIER) cc_final: 0.5938 (mttt) outliers start: 89 outliers final: 58 residues processed: 263 average time/residue: 0.5588 time to fit residues: 165.4487 Evaluate side-chains 256 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 182 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 445 TYR Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 638 MET Chi-restraints excluded: chain A residue 716 CYS Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain B residue 445 TYR Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 638 MET Chi-restraints excluded: chain B residue 716 CYS Chi-restraints excluded: chain B residue 786 ARG Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain C residue 445 TYR Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 569 THR Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain C residue 660 THR Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 699 LYS Chi-restraints excluded: chain C residue 703 ILE Chi-restraints excluded: chain C residue 704 GLU Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 751 ASP Chi-restraints excluded: chain C residue 781 LYS Chi-restraints excluded: chain D residue 408 THR Chi-restraints excluded: chain D residue 426 GLU Chi-restraints excluded: chain D residue 445 TYR Chi-restraints excluded: chain D residue 447 SER Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 612 ILE Chi-restraints excluded: chain D residue 654 PHE Chi-restraints excluded: chain D residue 660 THR Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 699 LYS Chi-restraints excluded: chain D residue 703 ILE Chi-restraints excluded: chain D residue 704 GLU Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain D residue 781 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: [28, 72, 77, 33, 34, 58, 225, 67, 115, 104, 100] chunk 28 optimal weight: 0.0970 chunk 72 optimal weight: 0.0060 chunk 77 optimal weight: 0.0570 chunk 33 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 225 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 overall best weight: 0.6114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 590 ASN B 590 ASN C 410 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.143456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.103357 restraints weight = 19193.395| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.37 r_work: 0.2974 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.0969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 18230 Z= 0.106 Angle : 0.489 5.182 24770 Z= 0.254 Chirality : 0.043 0.143 2630 Planarity : 0.005 0.052 3296 Dihedral : 4.563 42.027 2524 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.99 % Allowed : 23.30 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.17), residues: 2284 helix: 1.60 (0.24), residues: 494 sheet: 0.10 (0.20), residues: 606 loop : -0.51 (0.17), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 203 TYR 0.012 0.001 TYR B 445 PHE 0.012 0.001 PHE B 509 TRP 0.012 0.001 TRP C 528 HIS 0.003 0.001 HIS C 615 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (18224) covalent geometry : angle 0.48875 / 0.25 (24770) hydrogen bonds : bond 0.02847 / 2.02 ( 703) hydrogen bonds : angle 4.27128 / 3.00 ( 2040) metal coordination : bond 0.00251 / 0.15 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4568 Ramachandran restraints generated. 2284 Oldfield, 0 Emsley, 2284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4568 Ramachandran restraints generated. 2284 Oldfield, 0 Emsley, 2284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 183 time to evaluate : 0.692 Fit side-chains REVERT: A 96 GLU cc_start: 0.6813 (OUTLIER) cc_final: 0.6532 (tm-30) REVERT: A 404 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7944 (mp0) REVERT: A 442 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7448 (mp0) REVERT: A 484 LYS cc_start: 0.8264 (mtpt) cc_final: 0.7800 (mmtt) REVERT: B 96 GLU cc_start: 0.6789 (OUTLIER) cc_final: 0.6506 (tm-30) REVERT: B 404 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7938 (mp0) REVERT: B 442 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7482 (mp0) REVERT: B 484 LYS cc_start: 0.8241 (mtpt) cc_final: 0.7754 (mmtt) REVERT: B 687 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7656 (mm-30) REVERT: B 786 ARG cc_start: 0.5155 (OUTLIER) cc_final: 0.4930 (mtt-85) REVERT: C 422 ARG cc_start: 0.7083 (mpp-170) cc_final: 0.6760 (mmt-90) REVERT: C 426 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6764 (tp30) REVERT: C 455 MET cc_start: 0.8540 (ttm) cc_final: 0.8143 (ttt) REVERT: C 636 LYS cc_start: 0.7705 (mtpt) cc_final: 0.7371 (mtpp) REVERT: C 704 GLU cc_start: 0.6318 (OUTLIER) cc_final: 0.5633 (pt0) REVERT: C 781 LYS cc_start: 0.7154 (OUTLIER) cc_final: 0.5962 (mttt) REVERT: D 422 ARG cc_start: 0.7078 (mpp-170) cc_final: 0.6758 (mmt-90) REVERT: D 426 GLU cc_start: 0.7011 (OUTLIER) cc_final: 0.6743 (tp30) REVERT: D 455 MET cc_start: 0.8538 (ttm) cc_final: 0.8134 (ttt) REVERT: D 636 LYS cc_start: 0.7694 (mtpt) cc_final: 0.7353 (mtpp) REVERT: D 704 GLU cc_start: 0.6310 (OUTLIER) cc_final: 0.5632 (pt0) REVERT: D 781 LYS cc_start: 0.7134 (OUTLIER) cc_final: 0.5965 (mttt) outliers start: 73 outliers final: 50 residues processed: 248 average time/residue: 0.5727 time to fit residues: 159.7117 Evaluate side-chains 237 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 176 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 716 CYS Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain B residue 445 TYR Chi-restraints excluded: chain B residue 716 CYS Chi-restraints excluded: chain B residue 786 ARG Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 569 THR Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 645 LEU Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain C residue 660 THR Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 699 LYS Chi-restraints excluded: chain C residue 703 ILE Chi-restraints excluded: chain C residue 704 GLU Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 781 LYS Chi-restraints excluded: chain D residue 408 THR Chi-restraints excluded: chain D residue 426 GLU Chi-restraints excluded: chain D residue 447 SER Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 612 ILE Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 654 PHE Chi-restraints excluded: chain D residue 660 THR Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 699 LYS Chi-restraints excluded: chain D residue 703 ILE Chi-restraints excluded: chain D residue 704 GLU Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain D residue 781 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: [168, 29, 49, 79, 97, 122, 174, 84, 204, 132, 83] chunk 168 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 174 optimal weight: 0.5980 chunk 84 optimal weight: 0.7980 chunk 204 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 539 ASN B 539 ASN C 410 GLN D 410 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.137980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.092536 restraints weight = 19376.763| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 1.46 r_work: 0.2809 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9008 moved from start: 0.0949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 18230 Z= 0.217 Angle : 0.575 7.002 24770 Z= 0.301 Chirality : 0.047 0.208 2630 Planarity : 0.005 0.054 3296 Dihedral : 4.854 41.729 2520 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.56 % Allowed : 23.91 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.17), residues: 2284 helix: 1.39 (0.24), residues: 494 sheet: 0.06 (0.20), residues: 616 loop : -0.57 (0.17), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 203 TYR 0.017 0.002 TYR A 445 PHE 0.018 0.002 PHE B 509 TRP 0.009 0.001 TRP C 584 HIS 0.004 0.001 HIS B 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.22 (18224) covalent geometry : angle 0.57528 / 0.30 (24770) hydrogen bonds : bond 0.03532 / 2.52 ( 703) hydrogen bonds : angle 4.47687 / 3.14 ( 2040) metal coordination : bond 0.00624 / 0.37 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5750.57 seconds wall clock time: 98 minutes 35.63 seconds (5915.63 seconds total)