Starting phenix.real_space_refine on Fri Jul 3 11:35:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uyb_42798/07_2026/8uyb_42798.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uyb_42798/07_2026/8uyb_42798.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8uyb_42798/07_2026/8uyb_42798.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uyb_42798/07_2026/8uyb_42798.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8uyb_42798/07_2026/8uyb_42798.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uyb_42798/07_2026/8uyb_42798.map" } resolution = 3.87 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= 0.005 sd= 0.033 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 6 5.21 5 S 78 5.16 5 C 8840 2.51 5 N 2354 2.21 5 O 2552 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13836 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 898, 6873 Classifications: {'peptide': 898} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 43, 'TRANS': 854} Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 4, 'GLN:plan1': 4, 'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 74 Chain: "B" Number of atoms: 6895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 898, 6895 Classifications: {'peptide': 898} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 43, 'TRANS': 854} Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 2, 'HIS:plan': 1, 'GLN:plan1': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 62 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 3, 'AGS': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 3, 'AGS': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 3.24, per 1000 atoms: 0.23 Number of scatterers: 13836 At special positions: 0 Unit cell: (108.73, 130.31, 128.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 78 16.00 P 6 15.00 Mg 6 11.99 O 2552 8.00 N 2354 7.00 C 8840 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: 1.21 Conformation dependent library (CDL) restraints added in 635.5 milliseconds 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3384 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 10 sheets defined 56.7% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 37 through 48 removed outlier: 3.785A pdb=" N HIS A 41 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N LEU A 43 " --> pdb=" O SER A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 57 removed outlier: 4.005A pdb=" N TRP A 54 " --> pdb=" O GLU A 50 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N LYS A 55 " --> pdb=" O GLU A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 77 Processing helix chain 'A' and resid 81 through 85 Processing helix chain 'A' and resid 88 through 96 Processing helix chain 'A' and resid 99 through 113 Processing helix chain 'A' and resid 120 through 153 removed outlier: 3.637A pdb=" N ILE A 124 " --> pdb=" O ALA A 120 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 128 " --> pdb=" O ILE A 124 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 258 through 261 Processing helix chain 'A' and resid 262 through 267 removed outlier: 3.630A pdb=" N GLN A 266 " --> pdb=" O THR A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 312 Proline residue: A 301 - end of helix Processing helix chain 'A' and resid 313 through 326 Processing helix chain 'A' and resid 327 through 330 Proline residue: A 330 - end of helix No H-bonds generated for 'chain 'A' and resid 327 through 330' Processing helix chain 'A' and resid 331 through 351 removed outlier: 4.446A pdb=" N MET A 335 " --> pdb=" O GLU A 331 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LEU A 341 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA A 342 " --> pdb=" O THR A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 removed outlier: 3.843A pdb=" N ASN A 363 " --> pdb=" O ASP A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 378 removed outlier: 4.147A pdb=" N THR A 377 " --> pdb=" O ASP A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 409 removed outlier: 3.722A pdb=" N LEU A 400 " --> pdb=" O SER A 396 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR A 409 " --> pdb=" O LEU A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 425 Processing helix chain 'A' and resid 426 through 437 Processing helix chain 'A' and resid 471 through 476 Processing helix chain 'A' and resid 483 through 486 Processing helix chain 'A' and resid 491 through 508 Processing helix chain 'A' and resid 528 through 532 Processing helix chain 'A' and resid 550 through 562 Processing helix chain 'A' and resid 572 through 583 Processing helix chain 'A' and resid 593 through 597 Processing helix chain 'A' and resid 600 through 610 Processing helix chain 'A' and resid 618 through 630 removed outlier: 3.633A pdb=" N LYS A 630 " --> pdb=" O VAL A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 652 removed outlier: 4.581A pdb=" N ALA A 648 " --> pdb=" O ASN A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 669 Processing helix chain 'A' and resid 677 through 715 removed outlier: 3.522A pdb=" N LEU A 681 " --> pdb=" O SER A 677 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASN A 706 " --> pdb=" O THR A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 742 Processing helix chain 'A' and resid 743 through 747 Processing helix chain 'A' and resid 762 through 773 removed outlier: 4.205A pdb=" N GLY A 766 " --> pdb=" O PRO A 762 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG A 767 " --> pdb=" O ALA A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 790 removed outlier: 3.590A pdb=" N PHE A 779 " --> pdb=" O ILE A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 797 No H-bonds generated for 'chain 'A' and resid 795 through 797' Processing helix chain 'A' and resid 798 through 817 removed outlier: 4.072A pdb=" N PHE A 802 " --> pdb=" O THR A 798 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 821 Processing helix chain 'A' and resid 834 through 851 Processing helix chain 'A' and resid 855 through 860 removed outlier: 4.419A pdb=" N TYR A 859 " --> pdb=" O PRO A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 895 removed outlier: 4.080A pdb=" N TRP A 872 " --> pdb=" O SER A 868 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLY A 889 " --> pdb=" O GLN A 885 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N PHE A 890 " --> pdb=" O LEU A 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 48 removed outlier: 3.783A pdb=" N HIS B 41 " --> pdb=" O SER B 37 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N LEU B 43 " --> pdb=" O SER B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 57 removed outlier: 4.001A pdb=" N TRP B 54 " --> pdb=" O GLU B 50 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N LYS B 55 " --> pdb=" O GLU B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 77 Processing helix chain 'B' and resid 81 through 85 Processing helix chain 'B' and resid 88 through 96 Processing helix chain 'B' and resid 99 through 113 Processing helix chain 'B' and resid 121 through 153 removed outlier: 3.534A pdb=" N VAL B 128 " --> pdb=" O ILE B 124 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N VAL B 153 " --> pdb=" O LEU B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'B' and resid 258 through 261 Processing helix chain 'B' and resid 262 through 267 removed outlier: 3.645A pdb=" N GLN B 266 " --> pdb=" O THR B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 312 Proline residue: B 301 - end of helix Processing helix chain 'B' and resid 313 through 326 Processing helix chain 'B' and resid 327 through 330 Proline residue: B 330 - end of helix No H-bonds generated for 'chain 'B' and resid 327 through 330' Processing helix chain 'B' and resid 331 through 351 removed outlier: 4.478A pdb=" N MET B 335 " --> pdb=" O GLU B 331 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LEU B 341 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA B 342 " --> pdb=" O THR B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 removed outlier: 3.850A pdb=" N ASN B 363 " --> pdb=" O ASP B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 378 removed outlier: 4.175A pdb=" N THR B 377 " --> pdb=" O ASP B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 409 removed outlier: 3.712A pdb=" N LEU B 400 " --> pdb=" O SER B 396 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR B 409 " --> pdb=" O LEU B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 425 Processing helix chain 'B' and resid 426 through 437 Processing helix chain 'B' and resid 470 through 476 Processing helix chain 'B' and resid 483 through 486 Processing helix chain 'B' and resid 491 through 508 Processing helix chain 'B' and resid 528 through 532 Processing helix chain 'B' and resid 550 through 562 Processing helix chain 'B' and resid 572 through 584 Processing helix chain 'B' and resid 593 through 597 Processing helix chain 'B' and resid 600 through 610 Processing helix chain 'B' and resid 618 through 630 removed outlier: 3.624A pdb=" N LYS B 630 " --> pdb=" O VAL B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 652 Processing helix chain 'B' and resid 662 through 669 Processing helix chain 'B' and resid 677 through 715 removed outlier: 3.509A pdb=" N LEU B 681 " --> pdb=" O SER B 677 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASN B 706 " --> pdb=" O THR B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 726 through 742 Processing helix chain 'B' and resid 743 through 747 Processing helix chain 'B' and resid 762 through 773 removed outlier: 4.201A pdb=" N GLY B 766 " --> pdb=" O PRO B 762 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG B 767 " --> pdb=" O ALA B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 773 through 790 removed outlier: 3.699A pdb=" N PHE B 779 " --> pdb=" O ILE B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 795 through 797 No H-bonds generated for 'chain 'B' and resid 795 through 797' Processing helix chain 'B' and resid 798 through 817 removed outlier: 4.089A pdb=" N PHE B 802 " --> pdb=" O THR B 798 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 821 Processing helix chain 'B' and resid 834 through 854 Proline residue: B 852 - end of helix Processing helix chain 'B' and resid 855 through 860 removed outlier: 4.394A pdb=" N TYR B 859 " --> pdb=" O PRO B 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 868 through 895 removed outlier: 4.202A pdb=" N TRP B 872 " --> pdb=" O SER B 868 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLY B 889 " --> pdb=" O GLN B 885 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N PHE B 890 " --> pdb=" O LEU B 886 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR B 891 " --> pdb=" O VAL B 887 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 172 through 175 removed outlier: 3.598A pdb=" N VAL A 159 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A 174 " --> pdb=" O ALA A 157 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N THR A 158 " --> pdb=" O LYS A 186 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N VAL A 246 " --> pdb=" O PHE A 206 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N PHE A 206 " --> pdb=" O VAL A 246 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N SER A 248 " --> pdb=" O ASP A 204 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ASP A 204 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR A 250 " --> pdb=" O ALA A 202 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ALA A 202 " --> pdb=" O THR A 250 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLN A 252 " --> pdb=" O LEU A 200 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEU A 205 " --> pdb=" O LYS A 221 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 172 through 175 removed outlier: 3.598A pdb=" N VAL A 159 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A 174 " --> pdb=" O ALA A 157 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N THR A 158 " --> pdb=" O LYS A 186 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N VAL A 246 " --> pdb=" O PHE A 206 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N PHE A 206 " --> pdb=" O VAL A 246 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N SER A 248 " --> pdb=" O ASP A 204 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ASP A 204 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR A 250 " --> pdb=" O ALA A 202 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ALA A 202 " --> pdb=" O THR A 250 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLN A 252 " --> pdb=" O LEU A 200 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 353 through 355 removed outlier: 6.884A pdb=" N VAL A 636 " --> pdb=" O ILE A 654 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N ILE A 656 " --> pdb=" O VAL A 636 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N PHE A 638 " --> pdb=" O ILE A 656 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N VAL A 658 " --> pdb=" O PHE A 638 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE A 369 " --> pdb=" O GLY A 637 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N MET A 639 " --> pdb=" O ILE A 369 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N CYS A 371 " --> pdb=" O MET A 639 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N LEU A 370 " --> pdb=" O LYS A 566 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N LEU A 568 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR A 372 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N PHE A 614 " --> pdb=" O VAL A 565 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE A 567 " --> pdb=" O PHE A 614 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N VAL A 591 " --> pdb=" O ALA A 615 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 385 through 389 removed outlier: 4.132A pdb=" N LEU A 385 " --> pdb=" O LEU A 544 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR A 389 " --> pdb=" O TYR A 540 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR A 540 " --> pdb=" O THR A 389 " (cutoff:3.500A) removed outlier: 8.674A pdb=" N LEU A 535 " --> pdb=" O TYR A 519 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N TYR A 519 " --> pdb=" O LEU A 535 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N LEU A 537 " --> pdb=" O THR A 517 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N THR A 517 " --> pdb=" O LEU A 537 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY A 539 " --> pdb=" O VAL A 515 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N HIS A 462 " --> pdb=" O GLU A 458 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLU A 458 " --> pdb=" O HIS A 462 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N SER A 453 " --> pdb=" O GLU A 442 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N GLU A 442 " --> pdb=" O SER A 453 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N VAL A 455 " --> pdb=" O ILE A 440 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 385 through 389 removed outlier: 4.132A pdb=" N LEU A 385 " --> pdb=" O LEU A 544 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR A 389 " --> pdb=" O TYR A 540 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR A 540 " --> pdb=" O THR A 389 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N CYS A 478 " --> pdb=" O LEU A 535 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N LEU A 537 " --> pdb=" O CYS A 478 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLN A 480 " --> pdb=" O LEU A 537 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N GLY A 539 " --> pdb=" O GLN A 480 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 174 through 175 removed outlier: 3.517A pdb=" N ILE B 174 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N THR B 158 " --> pdb=" O LYS B 186 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N VAL B 246 " --> pdb=" O PHE B 206 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N PHE B 206 " --> pdb=" O VAL B 246 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N SER B 248 " --> pdb=" O ASP B 204 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ASP B 204 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N THR B 250 " --> pdb=" O ALA B 202 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ALA B 202 " --> pdb=" O THR B 250 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLN B 252 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU B 205 " --> pdb=" O LYS B 221 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 174 through 175 removed outlier: 3.517A pdb=" N ILE B 174 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N THR B 158 " --> pdb=" O LYS B 186 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N VAL B 246 " --> pdb=" O PHE B 206 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N PHE B 206 " --> pdb=" O VAL B 246 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N SER B 248 " --> pdb=" O ASP B 204 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ASP B 204 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N THR B 250 " --> pdb=" O ALA B 202 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ALA B 202 " --> pdb=" O THR B 250 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLN B 252 " --> pdb=" O LEU B 200 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 353 through 355 removed outlier: 6.889A pdb=" N VAL B 636 " --> pdb=" O ILE B 654 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N ILE B 656 " --> pdb=" O VAL B 636 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N PHE B 638 " --> pdb=" O ILE B 656 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N VAL B 658 " --> pdb=" O PHE B 638 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE B 369 " --> pdb=" O GLY B 637 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N MET B 639 " --> pdb=" O ILE B 369 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N CYS B 371 " --> pdb=" O MET B 639 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N LEU B 370 " --> pdb=" O LYS B 566 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LEU B 568 " --> pdb=" O LEU B 370 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N THR B 372 " --> pdb=" O LEU B 568 " (cutoff:3.500A) removed outlier: 8.827A pdb=" N PHE B 614 " --> pdb=" O VAL B 565 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE B 567 " --> pdb=" O PHE B 614 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N VAL B 591 " --> pdb=" O ALA B 615 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 385 through 389 removed outlier: 4.190A pdb=" N LEU B 385 " --> pdb=" O LEU B 544 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR B 389 " --> pdb=" O TYR B 540 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR B 540 " --> pdb=" O THR B 389 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N LEU B 535 " --> pdb=" O TYR B 519 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N TYR B 519 " --> pdb=" O LEU B 535 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N LEU B 537 " --> pdb=" O THR B 517 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N THR B 517 " --> pdb=" O LEU B 537 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY B 539 " --> pdb=" O VAL B 515 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N HIS B 462 " --> pdb=" O GLU B 458 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N GLU B 458 " --> pdb=" O HIS B 462 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N SER B 453 " --> pdb=" O GLU B 442 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N GLU B 442 " --> pdb=" O SER B 453 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL B 455 " --> pdb=" O ILE B 440 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 385 through 389 removed outlier: 4.190A pdb=" N LEU B 385 " --> pdb=" O LEU B 544 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR B 389 " --> pdb=" O TYR B 540 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR B 540 " --> pdb=" O THR B 389 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N CYS B 478 " --> pdb=" O LEU B 535 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N LEU B 537 " --> pdb=" O CYS B 478 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLN B 480 " --> pdb=" O LEU B 537 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N GLY B 539 " --> pdb=" O GLN B 480 " (cutoff:3.500A) 759 hydrogen bonds defined for protein. 2181 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.66 Time building geometry restraints manager: 1.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.37: 4691 1.37 - 1.51: 3929 1.51 - 1.66: 5366 1.66 - 1.80: 102 1.80 - 1.95: 32 Bond restraints: 14120 Sorted by residual: bond pdb=" O3B AGS B1004 " pdb=" PB AGS B1004 " ideal model delta sigma weight residual 1.673 1.583 0.090 2.00e-02 2.50e+03 2.03e+01 bond pdb=" O3B AGS A1004 " pdb=" PB AGS A1004 " ideal model delta sigma weight residual 1.673 1.583 0.090 2.00e-02 2.50e+03 2.01e+01 bond pdb=" O3A AGS B1004 " pdb=" PA AGS B1004 " ideal model delta sigma weight residual 1.664 1.587 0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" O3A AGS A1004 " pdb=" PA AGS A1004 " ideal model delta sigma weight residual 1.664 1.587 0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" O3B AGS B1004 " pdb=" PG AGS B1004 " ideal model delta sigma weight residual 1.614 1.557 0.057 2.00e-02 2.50e+03 8.00e+00 ... (remaining 14115 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 18991 2.00 - 4.00: 209 4.00 - 6.00: 30 6.00 - 7.99: 11 7.99 - 9.99: 9 Bond angle restraints: 19250 Sorted by residual: angle pdb=" N ALA B 40 " pdb=" CA ALA B 40 " pdb=" C ALA B 40 " ideal model delta sigma weight residual 113.18 106.82 6.36 1.33e+00 5.65e-01 2.29e+01 angle pdb=" N ALA A 40 " pdb=" CA ALA A 40 " pdb=" C ALA A 40 " ideal model delta sigma weight residual 113.18 106.86 6.32 1.33e+00 5.65e-01 2.26e+01 angle pdb=" C ASP A 446 " pdb=" N PHE A 447 " pdb=" CA PHE A 447 " ideal model delta sigma weight residual 121.54 128.18 -6.64 1.91e+00 2.74e-01 1.21e+01 angle pdb=" C ASP B 446 " pdb=" N PHE B 447 " pdb=" CA PHE B 447 " ideal model delta sigma weight residual 121.54 128.06 -6.52 1.91e+00 2.74e-01 1.17e+01 angle pdb=" O3A AGS A1004 " pdb=" PB AGS A1004 " pdb=" O3B AGS A1004 " ideal model delta sigma weight residual 100.38 110.37 -9.99 3.00e+00 1.11e-01 1.11e+01 ... (remaining 19245 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.46: 8346 29.46 - 58.91: 154 58.91 - 88.37: 19 88.37 - 117.82: 1 117.82 - 147.28: 6 Dihedral angle restraints: 8526 sinusoidal: 3321 harmonic: 5205 Sorted by residual: dihedral pdb=" CA THR B 823 " pdb=" C THR B 823 " pdb=" N ARG B 824 " pdb=" CA ARG B 824 " ideal model delta harmonic sigma weight residual 180.00 151.91 28.09 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA THR A 823 " pdb=" C THR A 823 " pdb=" N ARG A 824 " pdb=" CA ARG A 824 " ideal model delta harmonic sigma weight residual 180.00 151.92 28.08 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" O1A AGS B1004 " pdb=" O3A AGS B1004 " pdb=" PA AGS B1004 " pdb=" PB AGS B1004 " ideal model delta sinusoidal sigma weight residual 82.37 -64.91 147.28 1 3.00e+01 1.11e-03 1.96e+01 ... (remaining 8523 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1843 0.052 - 0.104: 388 0.104 - 0.155: 42 0.155 - 0.207: 2 0.207 - 0.259: 2 Chirality restraints: 2277 Sorted by residual: chirality pdb=" C3' AGS B1004 " pdb=" C2' AGS B1004 " pdb=" C4' AGS B1004 " pdb=" O3' AGS B1004 " both_signs ideal model delta sigma weight residual False -2.37 -2.63 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" C3' AGS A1004 " pdb=" C2' AGS A1004 " pdb=" C4' AGS A1004 " pdb=" O3' AGS A1004 " both_signs ideal model delta sigma weight residual False -2.37 -2.63 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CG LEU B 133 " pdb=" CB LEU B 133 " pdb=" CD1 LEU B 133 " pdb=" CD2 LEU B 133 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.70e-01 ... (remaining 2274 not shown) Planarity restraints: 2444 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 744 " -0.031 5.00e-02 4.00e+02 4.78e-02 3.65e+00 pdb=" N PRO A 745 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 745 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 745 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 807 " -0.009 2.00e-02 2.50e+03 1.90e-02 3.61e+00 pdb=" C PHE A 807 " 0.033 2.00e-02 2.50e+03 pdb=" O PHE A 807 " -0.012 2.00e-02 2.50e+03 pdb=" N VAL A 808 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 744 " 0.030 5.00e-02 4.00e+02 4.57e-02 3.34e+00 pdb=" N PRO B 745 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 745 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 745 " 0.026 5.00e-02 4.00e+02 ... (remaining 2441 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 147 2.62 - 3.19: 12829 3.19 - 3.76: 22138 3.76 - 4.33: 29058 4.33 - 4.90: 48496 Nonbonded interactions: 112668 Sorted by model distance: nonbonded pdb=" OD1 ASP B 441 " pdb="MG MG B1003 " model vdw 2.054 2.170 nonbonded pdb=" OD1 ASP A 441 " pdb="MG MG A1003 " model vdw 2.057 2.170 nonbonded pdb=" OD1 ASP A 191 " pdb="MG MG A1002 " model vdw 2.073 2.170 nonbonded pdb=" OD1 ASP B 191 " pdb="MG MG B1002 " model vdw 2.078 2.170 nonbonded pdb=" O ASP B 373 " pdb=" OG1 THR B 377 " model vdw 2.199 3.040 ... (remaining 112663 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 11 or (resid 12 and (name N or name CA or name C \ or name O or name CB )) or resid 13 through 1004)) selection = (chain 'B' and ((resid 1 through 10 and (name N or name CA or name C or name O o \ r name CB )) or resid 11 through 892 or (resid 893 through 895 and (name N or na \ me CA or name C or name O or name CB )) or resid 896 through 1004)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.880 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 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 0.090 14120 Z= 0.151 Angle : 0.575 9.993 19250 Z= 0.292 Chirality : 0.041 0.259 2277 Planarity : 0.004 0.048 2444 Dihedral : 13.158 147.281 5142 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.21), residues: 1792 helix: 1.78 (0.18), residues: 936 sheet: -0.25 (0.38), residues: 182 loop : -0.33 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 482 TYR 0.009 0.001 TYR A 698 PHE 0.014 0.001 PHE A 364 TRP 0.006 0.001 TRP B 90 HIS 0.002 0.000 HIS A 819 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.15 (14120) covalent geometry : angle 0.57534 / 0.29 (19250) hydrogen bonds : bond 0.14470 / 10.34 ( 734) hydrogen bonds : angle 6.01527 / 4.20 ( 2181) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ASN cc_start: 0.7553 (t0) cc_final: 0.6882 (t0) REVERT: A 104 LEU cc_start: 0.9285 (mm) cc_final: 0.8900 (tt) REVERT: A 322 LEU cc_start: 0.9594 (tp) cc_final: 0.9256 (tp) REVERT: A 714 LEU cc_start: 0.9663 (tt) cc_final: 0.9191 (tp) REVERT: A 737 TYR cc_start: 0.8651 (t80) cc_final: 0.8268 (t80) REVERT: A 780 ASP cc_start: 0.9223 (m-30) cc_final: 0.8986 (m-30) REVERT: A 821 ILE cc_start: 0.9238 (pt) cc_final: 0.9036 (mm) REVERT: B 79 ASN cc_start: 0.7513 (t0) cc_final: 0.6837 (t0) REVERT: B 104 LEU cc_start: 0.9358 (mt) cc_final: 0.8907 (tt) REVERT: B 322 LEU cc_start: 0.9565 (tp) cc_final: 0.9259 (tp) REVERT: B 737 TYR cc_start: 0.8615 (t80) cc_final: 0.8293 (t80) REVERT: B 780 ASP cc_start: 0.9209 (m-30) cc_final: 0.8957 (m-30) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.0948 time to fit residues: 34.3799 Evaluate side-chains 131 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.0270 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 7.9990 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN A 209 GLN A 734 ASN B 99 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.059608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.047890 restraints weight = 64912.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.049342 restraints weight = 33826.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.050378 restraints weight = 22395.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.050975 restraints weight = 16897.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.051438 restraints weight = 14131.553| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14120 Z= 0.121 Angle : 0.561 10.407 19250 Z= 0.284 Chirality : 0.041 0.137 2277 Planarity : 0.004 0.053 2444 Dihedral : 8.284 122.538 1977 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.37 % Allowed : 7.78 % Favored : 90.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.21), residues: 1792 helix: 1.89 (0.18), residues: 954 sheet: 0.22 (0.39), residues: 174 loop : -0.49 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 20 TYR 0.015 0.001 TYR B 698 PHE 0.014 0.001 PHE B 364 TRP 0.012 0.001 TRP A 806 HIS 0.002 0.001 HIS A 581 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (14120) covalent geometry : angle 0.56081 / 0.28 (19250) hydrogen bonds : bond 0.04094 / 2.93 ( 734) hydrogen bonds : angle 4.33625 / 3.09 ( 2181) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ASN cc_start: 0.7891 (t0) cc_final: 0.7077 (t0) REVERT: A 127 MET cc_start: 0.8821 (mmp) cc_final: 0.8481 (mmm) REVERT: A 326 VAL cc_start: 0.9378 (t) cc_final: 0.9169 (t) REVERT: A 737 TYR cc_start: 0.8524 (t80) cc_final: 0.8147 (t80) REVERT: A 741 GLN cc_start: 0.9144 (mm110) cc_final: 0.8942 (mm110) REVERT: A 747 ASP cc_start: 0.8843 (t0) cc_final: 0.8617 (t0) REVERT: A 838 MET cc_start: 0.9170 (OUTLIER) cc_final: 0.8965 (mtm) REVERT: A 840 MET cc_start: 0.8638 (mmt) cc_final: 0.7931 (mmm) REVERT: B 79 ASN cc_start: 0.7792 (t0) cc_final: 0.6883 (t0) REVERT: B 104 LEU cc_start: 0.9348 (mt) cc_final: 0.9125 (mp) REVERT: B 299 MET cc_start: 0.9248 (mtp) cc_final: 0.8664 (mmm) REVERT: B 737 TYR cc_start: 0.8466 (t80) cc_final: 0.8152 (t80) REVERT: B 747 ASP cc_start: 0.8787 (t0) cc_final: 0.8583 (t0) REVERT: B 838 MET cc_start: 0.9135 (OUTLIER) cc_final: 0.8855 (mtm) outliers start: 20 outliers final: 10 residues processed: 153 average time/residue: 0.0805 time to fit residues: 20.6547 Evaluate side-chains 127 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 838 MET Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 657 SER Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain B residue 838 MET Chi-restraints excluded: chain B residue 849 ILE Chi-restraints excluded: chain B residue 873 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 14 optimal weight: 0.9990 chunk 155 optimal weight: 5.9990 chunk 161 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 chunk 24 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 144 optimal weight: 0.9990 chunk 147 optimal weight: 6.9990 chunk 177 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.059388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.047614 restraints weight = 65342.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.049117 restraints weight = 34354.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.050159 restraints weight = 22558.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.050774 restraints weight = 17054.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.051153 restraints weight = 14242.169| |-----------------------------------------------------------------------------| r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14120 Z= 0.115 Angle : 0.557 13.766 19250 Z= 0.276 Chirality : 0.040 0.144 2277 Planarity : 0.004 0.055 2444 Dihedral : 6.470 83.974 1977 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.50 % Allowed : 10.03 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.21), residues: 1792 helix: 1.93 (0.18), residues: 950 sheet: 0.47 (0.39), residues: 172 loop : -0.39 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 20 TYR 0.016 0.001 TYR A 698 PHE 0.016 0.001 PHE A 802 TRP 0.006 0.001 TRP B 806 HIS 0.007 0.001 HIS A 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (14120) covalent geometry : angle 0.55707 / 0.28 (19250) hydrogen bonds : bond 0.03617 / 2.59 ( 734) hydrogen bonds : angle 4.17849 / 2.99 ( 2181) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 ASN cc_start: 0.7937 (t0) cc_final: 0.7101 (t0) REVERT: A 127 MET cc_start: 0.8761 (mmp) cc_final: 0.8463 (mmm) REVERT: A 299 MET cc_start: 0.8868 (mtp) cc_final: 0.8487 (ttm) REVERT: A 725 MET cc_start: 0.9015 (tpp) cc_final: 0.8799 (tpp) REVERT: A 737 TYR cc_start: 0.8531 (t80) cc_final: 0.8130 (t80) REVERT: A 741 GLN cc_start: 0.9164 (mm110) cc_final: 0.8939 (mm110) REVERT: A 747 ASP cc_start: 0.8872 (t0) cc_final: 0.8560 (t0) REVERT: A 838 MET cc_start: 0.9140 (OUTLIER) cc_final: 0.8917 (mtm) REVERT: A 840 MET cc_start: 0.8653 (mmt) cc_final: 0.7946 (mmm) REVERT: B 45 MET cc_start: 0.8938 (mmm) cc_final: 0.8721 (mpp) REVERT: B 79 ASN cc_start: 0.7818 (t0) cc_final: 0.6943 (t0) REVERT: B 299 MET cc_start: 0.9142 (mtp) cc_final: 0.8679 (mmm) REVERT: B 714 LEU cc_start: 0.9710 (tt) cc_final: 0.9452 (tp) REVERT: B 730 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8340 (mp) REVERT: B 747 ASP cc_start: 0.8864 (t0) cc_final: 0.8555 (t0) REVERT: B 838 MET cc_start: 0.9126 (OUTLIER) cc_final: 0.8850 (mtm) outliers start: 22 outliers final: 8 residues processed: 142 average time/residue: 0.0853 time to fit residues: 20.4093 Evaluate side-chains 117 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 838 MET Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain B residue 838 MET Chi-restraints excluded: chain B residue 849 ILE Chi-restraints excluded: chain B residue 873 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 93 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 167 optimal weight: 9.9990 chunk 44 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 59 optimal weight: 8.9990 chunk 120 optimal weight: 0.2980 chunk 107 optimal weight: 0.0980 chunk 169 optimal weight: 0.9990 chunk 175 optimal weight: 8.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 734 ASN B 734 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.059197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.047388 restraints weight = 65707.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.048874 restraints weight = 35109.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.049879 restraints weight = 23234.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.050416 restraints weight = 17702.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.050958 restraints weight = 14974.805| |-----------------------------------------------------------------------------| r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14120 Z= 0.114 Angle : 0.544 12.490 19250 Z= 0.267 Chirality : 0.040 0.130 2277 Planarity : 0.004 0.060 2444 Dihedral : 6.395 70.908 1977 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.46 % Allowed : 10.38 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.21), residues: 1792 helix: 1.91 (0.18), residues: 954 sheet: 0.37 (0.39), residues: 176 loop : -0.30 (0.25), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 20 TYR 0.016 0.001 TYR B 698 PHE 0.014 0.001 PHE A 802 TRP 0.006 0.001 TRP B 90 HIS 0.005 0.001 HIS A 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (14120) covalent geometry : angle 0.54372 / 0.27 (19250) hydrogen bonds : bond 0.03396 / 2.44 ( 734) hydrogen bonds : angle 4.09665 / 2.93 ( 2181) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 119 time to evaluate : 0.499 Fit side-chains revert: symmetry clash REVERT: A 45 MET cc_start: 0.8814 (mmt) cc_final: 0.8540 (mmt) REVERT: A 48 MET cc_start: 0.8478 (tmm) cc_final: 0.8081 (tmm) REVERT: A 79 ASN cc_start: 0.7961 (t0) cc_final: 0.7193 (t0) REVERT: A 127 MET cc_start: 0.8712 (mmp) cc_final: 0.8410 (mmm) REVERT: A 299 MET cc_start: 0.8900 (mtp) cc_final: 0.8542 (ttm) REVERT: A 747 ASP cc_start: 0.8926 (t0) cc_final: 0.8639 (t0) REVERT: A 775 ILE cc_start: 0.9378 (pt) cc_final: 0.9150 (mp) REVERT: A 838 MET cc_start: 0.9137 (OUTLIER) cc_final: 0.8915 (mtm) REVERT: A 840 MET cc_start: 0.8662 (mmt) cc_final: 0.7999 (mmm) REVERT: B 79 ASN cc_start: 0.7772 (t0) cc_final: 0.6958 (t0) REVERT: B 326 VAL cc_start: 0.9350 (t) cc_final: 0.9126 (m) REVERT: B 714 LEU cc_start: 0.9715 (tt) cc_final: 0.9477 (tp) REVERT: B 747 ASP cc_start: 0.8887 (t0) cc_final: 0.8539 (t0) REVERT: B 840 MET cc_start: 0.9091 (mmm) cc_final: 0.8377 (mmm) outliers start: 36 outliers final: 17 residues processed: 145 average time/residue: 0.0868 time to fit residues: 21.0539 Evaluate side-chains 127 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 838 MET Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 657 SER Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain B residue 849 ILE Chi-restraints excluded: chain B residue 873 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 54 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 138 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 chunk 109 optimal weight: 0.7980 chunk 65 optimal weight: 0.4980 chunk 95 optimal weight: 0.7980 chunk 161 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.059630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.047835 restraints weight = 65342.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.049327 restraints weight = 34808.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.050194 restraints weight = 22993.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.050958 restraints weight = 18011.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.051178 restraints weight = 14789.081| |-----------------------------------------------------------------------------| r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 14120 Z= 0.104 Angle : 0.545 13.743 19250 Z= 0.267 Chirality : 0.040 0.145 2277 Planarity : 0.004 0.062 2444 Dihedral : 6.279 69.317 1977 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.12 % Allowed : 11.33 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.21), residues: 1792 helix: 1.98 (0.18), residues: 942 sheet: 0.33 (0.40), residues: 166 loop : -0.20 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 20 TYR 0.018 0.001 TYR B 737 PHE 0.014 0.001 PHE A 802 TRP 0.006 0.001 TRP B 806 HIS 0.013 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 (14120) covalent geometry : angle 0.54526 / 0.27 (19250) hydrogen bonds : bond 0.03246 / 2.31 ( 734) hydrogen bonds : angle 4.01106 / 2.88 ( 2181) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 117 time to evaluate : 0.615 Fit side-chains revert: symmetry clash REVERT: A 45 MET cc_start: 0.8710 (mmt) cc_final: 0.8474 (mmt) REVERT: A 48 MET cc_start: 0.8366 (tmm) cc_final: 0.8007 (tmm) REVERT: A 79 ASN cc_start: 0.7886 (t0) cc_final: 0.7125 (t0) REVERT: A 106 THR cc_start: 0.9258 (m) cc_final: 0.9016 (p) REVERT: A 299 MET cc_start: 0.8975 (mtp) cc_final: 0.8580 (ttm) REVERT: A 725 MET cc_start: 0.8902 (tpp) cc_final: 0.8701 (tpp) REVERT: A 747 ASP cc_start: 0.8971 (t0) cc_final: 0.8652 (t0) REVERT: A 775 ILE cc_start: 0.9340 (pt) cc_final: 0.9083 (mp) REVERT: A 838 MET cc_start: 0.9150 (OUTLIER) cc_final: 0.8940 (mtm) REVERT: A 840 MET cc_start: 0.8668 (mmt) cc_final: 0.7808 (mmm) REVERT: B 79 ASN cc_start: 0.7780 (t0) cc_final: 0.6971 (t0) REVERT: B 106 THR cc_start: 0.9222 (m) cc_final: 0.8990 (p) REVERT: B 239 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8785 (mm) REVERT: B 747 ASP cc_start: 0.8951 (t0) cc_final: 0.8574 (t0) REVERT: B 840 MET cc_start: 0.9072 (mmm) cc_final: 0.8352 (mmm) outliers start: 31 outliers final: 15 residues processed: 139 average time/residue: 0.0872 time to fit residues: 20.5824 Evaluate side-chains 123 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 838 MET Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain B residue 873 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 139 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 155 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 107 optimal weight: 0.0770 chunk 47 optimal weight: 0.6980 chunk 60 optimal weight: 8.9990 chunk 64 optimal weight: 0.7980 chunk 50 optimal weight: 7.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.059993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.048154 restraints weight = 65572.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.049591 restraints weight = 35790.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.050597 restraints weight = 24189.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.051278 restraints weight = 18477.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.051619 restraints weight = 15486.062| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14120 Z= 0.100 Angle : 0.547 12.522 19250 Z= 0.266 Chirality : 0.040 0.197 2277 Planarity : 0.004 0.062 2444 Dihedral : 6.168 67.543 1977 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.25 % Allowed : 11.88 % Favored : 85.87 % 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: 1.46 (0.21), residues: 1792 helix: 1.93 (0.18), residues: 952 sheet: 0.43 (0.42), residues: 146 loop : -0.22 (0.25), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 451 TYR 0.020 0.002 TYR A 737 PHE 0.021 0.001 PHE A 784 TRP 0.009 0.001 TRP B 315 HIS 0.007 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (14120) covalent geometry : angle 0.54736 / 0.27 (19250) hydrogen bonds : bond 0.03138 / 2.26 ( 734) hydrogen bonds : angle 3.92965 / 2.81 ( 2181) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 121 time to evaluate : 0.544 Fit side-chains REVERT: A 79 ASN cc_start: 0.7933 (t0) cc_final: 0.7139 (t0) REVERT: A 106 THR cc_start: 0.9255 (m) cc_final: 0.8999 (p) REVERT: A 127 MET cc_start: 0.8586 (mmp) cc_final: 0.8257 (mmm) REVERT: A 299 MET cc_start: 0.9065 (mtp) cc_final: 0.8605 (ttm) REVERT: A 725 MET cc_start: 0.8912 (tpp) cc_final: 0.8671 (tpp) REVERT: A 747 ASP cc_start: 0.9032 (t0) cc_final: 0.8628 (t0) REVERT: A 838 MET cc_start: 0.9191 (OUTLIER) cc_final: 0.8952 (mtm) REVERT: A 840 MET cc_start: 0.8520 (mmt) cc_final: 0.7924 (mmm) REVERT: B 79 ASN cc_start: 0.7826 (t0) cc_final: 0.7015 (t0) REVERT: B 106 THR cc_start: 0.9241 (m) cc_final: 0.9001 (p) REVERT: B 299 MET cc_start: 0.8893 (mtp) cc_final: 0.8658 (ttm) REVERT: B 636 VAL cc_start: 0.9606 (t) cc_final: 0.9399 (p) REVERT: B 747 ASP cc_start: 0.8994 (t0) cc_final: 0.8571 (t0) REVERT: B 840 MET cc_start: 0.9053 (mmm) cc_final: 0.8427 (mmm) outliers start: 33 outliers final: 19 residues processed: 144 average time/residue: 0.0845 time to fit residues: 20.8002 Evaluate side-chains 133 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 838 MET Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain B residue 849 ILE Chi-restraints excluded: chain B residue 873 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 67 optimal weight: 2.9990 chunk 94 optimal weight: 0.3980 chunk 146 optimal weight: 0.5980 chunk 152 optimal weight: 6.9990 chunk 108 optimal weight: 8.9990 chunk 3 optimal weight: 0.1980 chunk 96 optimal weight: 4.9990 chunk 168 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 99 optimal weight: 0.9980 chunk 61 optimal weight: 7.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 734 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.059415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.047685 restraints weight = 65455.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.049113 restraints weight = 35987.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.050076 restraints weight = 24263.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.050663 restraints weight = 18640.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.051151 restraints weight = 15721.997| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14120 Z= 0.113 Angle : 0.571 15.179 19250 Z= 0.275 Chirality : 0.040 0.166 2277 Planarity : 0.004 0.061 2444 Dihedral : 6.176 65.741 1977 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.77 % Allowed : 13.52 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.21), residues: 1792 helix: 2.01 (0.18), residues: 940 sheet: 0.42 (0.42), residues: 146 loop : -0.26 (0.25), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 20 TYR 0.020 0.002 TYR B 698 PHE 0.020 0.001 PHE B 807 TRP 0.010 0.001 TRP B 806 HIS 0.008 0.001 HIS A 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (14120) covalent geometry : angle 0.57140 / 0.28 (19250) hydrogen bonds : bond 0.03284 / 2.37 ( 734) hydrogen bonds : angle 3.98812 / 2.85 ( 2181) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 115 time to evaluate : 0.524 Fit side-chains REVERT: A 48 MET cc_start: 0.8334 (ppp) cc_final: 0.8050 (ppp) REVERT: A 79 ASN cc_start: 0.7958 (t0) cc_final: 0.7130 (t0) REVERT: A 106 THR cc_start: 0.9301 (m) cc_final: 0.9068 (p) REVERT: A 127 MET cc_start: 0.8590 (mmp) cc_final: 0.8254 (mmm) REVERT: A 299 MET cc_start: 0.9052 (mtp) cc_final: 0.8573 (ttm) REVERT: A 747 ASP cc_start: 0.9047 (t0) cc_final: 0.8673 (t0) REVERT: A 838 MET cc_start: 0.9196 (OUTLIER) cc_final: 0.8938 (mtm) REVERT: A 840 MET cc_start: 0.8566 (mmt) cc_final: 0.7995 (mmm) REVERT: B 79 ASN cc_start: 0.7850 (t0) cc_final: 0.7007 (t0) REVERT: B 106 THR cc_start: 0.9263 (m) cc_final: 0.9027 (p) REVERT: B 299 MET cc_start: 0.8992 (mtp) cc_final: 0.8776 (ttm) REVERT: B 636 VAL cc_start: 0.9599 (t) cc_final: 0.9393 (p) REVERT: B 725 MET cc_start: 0.9098 (tpp) cc_final: 0.8844 (tpp) REVERT: B 747 ASP cc_start: 0.8960 (t0) cc_final: 0.8494 (t0) REVERT: B 787 MET cc_start: 0.8669 (mmm) cc_final: 0.8461 (mmp) REVERT: B 840 MET cc_start: 0.9074 (mmm) cc_final: 0.8385 (mmm) outliers start: 26 outliers final: 20 residues processed: 131 average time/residue: 0.0834 time to fit residues: 18.5884 Evaluate side-chains 129 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 838 MET Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain B residue 849 ILE Chi-restraints excluded: chain B residue 873 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 114 optimal weight: 7.9990 chunk 153 optimal weight: 0.4980 chunk 112 optimal weight: 8.9990 chunk 92 optimal weight: 0.9980 chunk 169 optimal weight: 0.6980 chunk 176 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 30 optimal weight: 6.9990 chunk 126 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.059746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.048063 restraints weight = 65223.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.049452 restraints weight = 35814.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.050426 restraints weight = 24367.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.051025 restraints weight = 18733.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.051436 restraints weight = 15778.442| |-----------------------------------------------------------------------------| r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14120 Z= 0.105 Angle : 0.578 13.779 19250 Z= 0.279 Chirality : 0.040 0.195 2277 Planarity : 0.004 0.060 2444 Dihedral : 6.089 64.165 1977 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.91 % Allowed : 13.38 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.21), residues: 1792 helix: 1.96 (0.18), residues: 938 sheet: 0.45 (0.41), residues: 146 loop : -0.26 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 451 TYR 0.020 0.002 TYR B 880 PHE 0.018 0.001 PHE B 807 TRP 0.006 0.001 TRP B 90 HIS 0.011 0.001 HIS B 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 (14120) covalent geometry : angle 0.57848 / 0.28 (19250) hydrogen bonds : bond 0.03227 / 2.31 ( 734) hydrogen bonds : angle 3.96539 / 2.84 ( 2181) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 0.564 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.8312 (ppp) cc_final: 0.7978 (ppp) REVERT: A 79 ASN cc_start: 0.7895 (t0) cc_final: 0.7073 (t0) REVERT: A 106 THR cc_start: 0.9309 (m) cc_final: 0.9064 (p) REVERT: A 127 MET cc_start: 0.8562 (mmp) cc_final: 0.8231 (mmm) REVERT: A 747 ASP cc_start: 0.9072 (t0) cc_final: 0.8715 (t0) REVERT: A 838 MET cc_start: 0.9211 (OUTLIER) cc_final: 0.8966 (mtm) REVERT: A 840 MET cc_start: 0.8579 (mmt) cc_final: 0.8012 (mmm) REVERT: B 79 ASN cc_start: 0.7871 (t0) cc_final: 0.7009 (t0) REVERT: B 106 THR cc_start: 0.9222 (m) cc_final: 0.8967 (p) REVERT: B 299 MET cc_start: 0.9032 (mtp) cc_final: 0.8741 (ttm) REVERT: B 725 MET cc_start: 0.9023 (tpp) cc_final: 0.8755 (tpp) REVERT: B 747 ASP cc_start: 0.8967 (t0) cc_final: 0.8540 (t0) REVERT: B 787 MET cc_start: 0.8679 (mmm) cc_final: 0.8475 (mmp) REVERT: B 840 MET cc_start: 0.9010 (mmm) cc_final: 0.8312 (mmm) outliers start: 28 outliers final: 18 residues processed: 129 average time/residue: 0.0885 time to fit residues: 19.3477 Evaluate side-chains 128 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 838 MET Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain B residue 873 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 61 optimal weight: 0.0870 chunk 10 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 46 optimal weight: 10.0000 chunk 35 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 162 optimal weight: 5.9990 chunk 71 optimal weight: 0.1980 chunk 105 optimal weight: 10.0000 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.060156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.048364 restraints weight = 66033.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.049827 restraints weight = 36067.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.050793 restraints weight = 24170.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.051346 restraints weight = 18608.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.051799 restraints weight = 15734.208| |-----------------------------------------------------------------------------| r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14120 Z= 0.100 Angle : 0.580 13.363 19250 Z= 0.279 Chirality : 0.040 0.190 2277 Planarity : 0.004 0.060 2444 Dihedral : 6.029 63.856 1977 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.50 % Allowed : 14.33 % Favored : 84.16 % 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: 1.45 (0.21), residues: 1792 helix: 2.01 (0.18), residues: 926 sheet: 0.43 (0.39), residues: 166 loop : -0.30 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 825 TYR 0.030 0.002 TYR B 880 PHE 0.017 0.001 PHE B 807 TRP 0.006 0.001 TRP B 90 HIS 0.008 0.001 HIS B 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (14120) covalent geometry : angle 0.58012 / 0.28 (19250) hydrogen bonds : bond 0.03186 / 2.26 ( 734) hydrogen bonds : angle 3.98627 / 2.86 ( 2181) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.555 Fit side-chains REVERT: A 45 MET cc_start: 0.8831 (mmt) cc_final: 0.8414 (tpp) REVERT: A 48 MET cc_start: 0.8291 (ppp) cc_final: 0.7888 (ppp) REVERT: A 79 ASN cc_start: 0.7877 (t0) cc_final: 0.7078 (t0) REVERT: A 106 THR cc_start: 0.9268 (m) cc_final: 0.9037 (p) REVERT: A 725 MET cc_start: 0.8633 (tpp) cc_final: 0.8308 (tpp) REVERT: A 747 ASP cc_start: 0.9090 (t0) cc_final: 0.8734 (t0) REVERT: A 838 MET cc_start: 0.9226 (OUTLIER) cc_final: 0.8958 (mtm) REVERT: A 840 MET cc_start: 0.8576 (mmt) cc_final: 0.8051 (mmm) REVERT: B 79 ASN cc_start: 0.7846 (t0) cc_final: 0.7042 (t0) REVERT: B 106 THR cc_start: 0.9240 (m) cc_final: 0.8984 (p) REVERT: B 299 MET cc_start: 0.9033 (mtp) cc_final: 0.8727 (ttm) REVERT: B 372 THR cc_start: 0.9495 (OUTLIER) cc_final: 0.9291 (t) REVERT: B 725 MET cc_start: 0.8995 (tpp) cc_final: 0.8763 (tpp) REVERT: B 747 ASP cc_start: 0.9000 (t0) cc_final: 0.8581 (t0) REVERT: B 840 MET cc_start: 0.8983 (mmm) cc_final: 0.8409 (mmm) outliers start: 22 outliers final: 17 residues processed: 134 average time/residue: 0.0852 time to fit residues: 19.4172 Evaluate side-chains 132 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 838 MET Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain B residue 873 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 149 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 111 optimal weight: 9.9990 chunk 141 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 69 optimal weight: 0.5980 chunk 88 optimal weight: 4.9990 chunk 22 optimal weight: 8.9990 chunk 0 optimal weight: 30.0000 chunk 173 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 464 GLN ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.058012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.046166 restraints weight = 66382.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.047567 restraints weight = 37028.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.048508 restraints weight = 25236.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.049074 restraints weight = 19599.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.049541 restraints weight = 16663.287| |-----------------------------------------------------------------------------| r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14120 Z= 0.170 Angle : 0.653 14.030 19250 Z= 0.312 Chirality : 0.042 0.188 2277 Planarity : 0.004 0.059 2444 Dihedral : 6.261 62.375 1977 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.43 % Allowed : 14.54 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.21), residues: 1792 helix: 1.89 (0.18), residues: 930 sheet: 0.21 (0.41), residues: 152 loop : -0.20 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 20 TYR 0.029 0.002 TYR B 698 PHE 0.015 0.002 PHE A 779 TRP 0.009 0.001 TRP B 404 HIS 0.004 0.001 HIS A 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 (14120) covalent geometry : angle 0.65324 / 0.31 (19250) hydrogen bonds : bond 0.03636 / 2.58 ( 734) hydrogen bonds : angle 4.23393 / 3.04 ( 2181) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 0.564 Fit side-chains REVERT: A 48 MET cc_start: 0.8338 (ppp) cc_final: 0.7958 (ppp) REVERT: A 79 ASN cc_start: 0.8068 (t0) cc_final: 0.7234 (t0) REVERT: A 106 THR cc_start: 0.9318 (m) cc_final: 0.9085 (p) REVERT: A 816 LEU cc_start: 0.9554 (mm) cc_final: 0.9344 (mm) REVERT: A 840 MET cc_start: 0.8571 (mmt) cc_final: 0.8084 (mmm) REVERT: B 79 ASN cc_start: 0.7895 (t0) cc_final: 0.7026 (t0) REVERT: B 106 THR cc_start: 0.9291 (m) cc_final: 0.9066 (p) REVERT: B 299 MET cc_start: 0.9003 (mtp) cc_final: 0.8712 (ttm) REVERT: B 725 MET cc_start: 0.9111 (tpp) cc_final: 0.8797 (tpp) REVERT: B 747 ASP cc_start: 0.9063 (t0) cc_final: 0.8633 (t0) outliers start: 21 outliers final: 18 residues processed: 127 average time/residue: 0.0869 time to fit residues: 18.7165 Evaluate side-chains 128 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain B residue 873 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 159 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 141 optimal weight: 0.0770 chunk 8 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 123 optimal weight: 0.9990 chunk 163 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 158 optimal weight: 0.6980 chunk 174 optimal weight: 3.9990 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.059094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.047356 restraints weight = 65657.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.048833 restraints weight = 35269.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.049846 restraints weight = 23399.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.050345 restraints weight = 17723.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.050893 restraints weight = 15114.905| |-----------------------------------------------------------------------------| r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14120 Z= 0.113 Angle : 0.622 14.068 19250 Z= 0.296 Chirality : 0.041 0.182 2277 Planarity : 0.004 0.059 2444 Dihedral : 6.071 62.042 1977 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.30 % Allowed : 14.95 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.21), residues: 1792 helix: 1.93 (0.18), residues: 924 sheet: 0.03 (0.39), residues: 166 loop : -0.26 (0.25), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 20 TYR 0.025 0.002 TYR B 698 PHE 0.016 0.001 PHE B 807 TRP 0.007 0.001 TRP A 54 HIS 0.005 0.001 HIS A 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (14120) covalent geometry : angle 0.62170 / 0.30 (19250) hydrogen bonds : bond 0.03389 / 2.42 ( 734) hydrogen bonds : angle 4.14890 / 2.98 ( 2181) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1996.97 seconds wall clock time: 35 minutes 36.13 seconds (2136.13 seconds total)