Starting phenix.real_space_refine on Sat Aug 23 18:32:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uyb_42798/08_2025/8uyb_42798.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uyb_42798/08_2025/8uyb_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_42798/08_2025/8uyb_42798.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uyb_42798/08_2025/8uyb_42798.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8uyb_42798/08_2025/8uyb_42798.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uyb_42798/08_2025/8uyb_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 3.49, per 1000 atoms: 0.25 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: 1.13 Conformation dependent library (CDL) restraints added in 605.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.70 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: 2.82 Time building geometry restraints manager: 1.48 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=" C LYS B 80 " pdb=" N LEU B 81 " ideal model delta sigma weight residual 1.330 1.299 0.031 1.47e-02 4.63e+03 4.51e+00 bond pdb=" C LYS A 80 " pdb=" N LEU A 81 " ideal model delta sigma weight residual 1.330 1.301 0.029 1.47e-02 4.63e+03 3.81e+00 bond pdb=" N GLY B 810 " pdb=" CA GLY B 810 " ideal model delta sigma weight residual 1.454 1.444 0.010 1.22e-02 6.72e+03 7.39e-01 bond pdb=" CA GLY B 170 " pdb=" C GLY B 170 " ideal model delta sigma weight residual 1.524 1.514 0.010 1.20e-02 6.94e+03 6.83e-01 bond pdb=" CA LYS A 630 " pdb=" C LYS A 630 " ideal model delta sigma weight residual 1.531 1.522 0.009 1.12e-02 7.97e+03 6.77e-01 ... (remaining 14115 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 18919 1.62 - 3.25: 274 3.25 - 4.87: 46 4.87 - 6.49: 8 6.49 - 8.11: 3 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=" N GLY B 810 " pdb=" CA GLY B 810 " pdb=" C GLY B 810 " ideal model delta sigma weight residual 112.64 109.29 3.35 1.21e+00 6.83e-01 7.67e+00 ... (remaining 19245 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 7873 17.77 - 35.54: 526 35.54 - 53.31: 67 53.31 - 71.08: 12 71.08 - 88.85: 12 Dihedral angle restraints: 8490 sinusoidal: 3285 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=" CA SER A 39 " pdb=" C SER A 39 " pdb=" N ALA A 40 " pdb=" CA ALA A 40 " ideal model delta harmonic sigma weight residual 180.00 160.68 19.32 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 8487 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1541 0.033 - 0.065: 482 0.065 - 0.098: 197 0.098 - 0.131: 56 0.131 - 0.164: 5 Chirality restraints: 2281 Sorted by residual: 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 chirality pdb=" CB ILE A 184 " pdb=" CA ILE A 184 " pdb=" CG1 ILE A 184 " pdb=" CG2 ILE A 184 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.15e-01 chirality pdb=" CB ILE B 184 " pdb=" CA ILE B 184 " pdb=" CG1 ILE B 184 " pdb=" CG2 ILE B 184 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.02e-01 ... (remaining 2278 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.420 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 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 : 0.002 0.031 14120 Z= 0.114 Angle : 0.512 8.113 19250 Z= 0.279 Chirality : 0.040 0.164 2281 Planarity : 0.004 0.048 2444 Dihedral : 12.233 88.846 5106 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 aren 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 covalent geometry : bond 0.00221 (14120) covalent geometry : angle 0.51166 (19250) hydrogen bonds : bond 0.14470 ( 734) hydrogen bonds : angle 6.01527 ( 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 : 0.436 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: 0.9260 (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: 0.0957 time to fit residues: 34.6515 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 : 0.552 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 209 GLN A 734 ASN A 753 GLN B 99 ASN B 753 GLN B 819 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.059557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.047761 restraints weight = 64772.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.049283 restraints weight = 34142.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.050153 restraints weight = 22464.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.050952 restraints weight = 17528.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.051325 restraints weight = 14271.988| |-----------------------------------------------------------------------------| r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14120 Z= 0.128 Angle : 0.581 9.606 19250 Z= 0.297 Chirality : 0.041 0.140 2281 Planarity : 0.005 0.053 2444 Dihedral : 5.524 70.484 1941 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.37 % Allowed : 8.05 % Favored : 90.58 % 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 aren not related in a simple way. whole: 1.14 (0.21), residues: 1792 helix: 1.76 (0.18), residues: 954 sheet: 0.22 (0.39), residues: 174 loop : -0.52 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 20 TYR 0.013 0.001 TYR B 698 PHE 0.017 0.001 PHE B 802 TRP 0.010 0.001 TRP B 806 HIS 0.003 0.001 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00277 (14120) covalent geometry : angle 0.58108 (19250) hydrogen bonds : bond 0.04442 ( 734) hydrogen bonds : angle 4.42708 ( 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 163 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ASN cc_start: 0.7851 (t0) cc_final: 0.7100 (t0) REVERT: A 104 LEU cc_start: 0.9314 (mm) cc_final: 0.9111 (mp) REVERT: A 127 MET cc_start: 0.8813 (mmp) cc_final: 0.8465 (mmm) REVERT: A 326 VAL cc_start: 0.9407 (t) cc_final: 0.9203 (t) REVERT: A 737 TYR cc_start: 0.8510 (t80) cc_final: 0.8114 (t80) REVERT: A 741 GLN cc_start: 0.9153 (mm110) cc_final: 0.8932 (mm110) REVERT: A 747 ASP cc_start: 0.8850 (t0) cc_final: 0.8608 (t0) REVERT: A 787 MET cc_start: 0.8843 (mmm) cc_final: 0.8482 (mmp) REVERT: A 840 MET cc_start: 0.8644 (mmt) cc_final: 0.7925 (mmm) REVERT: B 79 ASN cc_start: 0.7782 (t0) cc_final: 0.6865 (t0) REVERT: B 99 ASN cc_start: 0.8787 (OUTLIER) cc_final: 0.8581 (p0) REVERT: B 299 MET cc_start: 0.9249 (mtp) cc_final: 0.8712 (mmm) REVERT: B 737 TYR cc_start: 0.8457 (t80) cc_final: 0.8130 (t80) REVERT: B 747 ASP cc_start: 0.8815 (t0) cc_final: 0.8608 (t0) REVERT: B 787 MET cc_start: 0.8792 (mmm) cc_final: 0.8527 (mmm) REVERT: B 820 MET cc_start: 0.8577 (mtp) cc_final: 0.8083 (mtm) REVERT: B 838 MET cc_start: 0.9099 (OUTLIER) cc_final: 0.8799 (mtm) REVERT: B 881 MET cc_start: 0.8906 (mtm) cc_final: 0.8606 (mmm) outliers start: 20 outliers final: 11 residues processed: 156 average time/residue: 0.0918 time to fit residues: 23.7983 Evaluate side-chains 127 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 304 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 851 LEU 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: 0.8980 chunk 155 optimal weight: 4.9990 chunk 161 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 24 optimal weight: 0.5980 chunk 120 optimal weight: 1.9990 chunk 44 optimal weight: 8.9990 chunk 144 optimal weight: 3.9990 chunk 147 optimal weight: 10.0000 chunk 177 optimal weight: 0.9980 chunk 118 optimal weight: 8.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN B 819 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.058564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.046946 restraints weight = 65348.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.048408 restraints weight = 34306.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.049255 restraints weight = 22619.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.050011 restraints weight = 17685.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.050379 restraints weight = 14454.187| |-----------------------------------------------------------------------------| r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14120 Z= 0.149 Angle : 0.581 13.422 19250 Z= 0.290 Chirality : 0.041 0.146 2281 Planarity : 0.005 0.052 2444 Dihedral : 5.426 71.154 1941 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.91 % Allowed : 9.83 % Favored : 88.26 % 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 aren not related in a simple way. whole: 1.24 (0.21), residues: 1792 helix: 1.78 (0.18), residues: 954 sheet: 0.47 (0.40), residues: 172 loop : -0.46 (0.25), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 20 TYR 0.019 0.001 TYR B 698 PHE 0.016 0.001 PHE A 802 TRP 0.011 0.001 TRP A 806 HIS 0.003 0.001 HIS B 230 Details of bonding type rmsd covalent geometry : bond 0.00332 (14120) covalent geometry : angle 0.58065 (19250) hydrogen bonds : bond 0.04052 ( 734) hydrogen bonds : angle 4.33798 ( 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 149 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 0.538 Fit side-chains revert: symmetry clash REVERT: A 79 ASN cc_start: 0.7919 (t0) cc_final: 0.7058 (t0) REVERT: A 104 LEU cc_start: 0.9380 (mm) cc_final: 0.9149 (mp) REVERT: A 725 MET cc_start: 0.9016 (tpp) cc_final: 0.8775 (tpp) REVERT: A 747 ASP cc_start: 0.8893 (t0) cc_final: 0.8636 (t0) REVERT: A 840 MET cc_start: 0.8633 (mmt) cc_final: 0.7933 (mmm) REVERT: B 45 MET cc_start: 0.8973 (mmm) cc_final: 0.8723 (mpp) REVERT: B 48 MET cc_start: 0.8501 (tmm) cc_final: 0.8290 (tmm) REVERT: B 79 ASN cc_start: 0.7819 (t0) cc_final: 0.6942 (t0) REVERT: B 299 MET cc_start: 0.9157 (mtp) cc_final: 0.8845 (mmm) REVERT: B 730 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8305 (mp) REVERT: B 747 ASP cc_start: 0.8847 (t0) cc_final: 0.8589 (t0) REVERT: B 775 ILE cc_start: 0.9426 (pt) cc_final: 0.8953 (mm) REVERT: B 787 MET cc_start: 0.8790 (mmm) cc_final: 0.8504 (mmm) REVERT: B 838 MET cc_start: 0.9130 (OUTLIER) cc_final: 0.8869 (mtm) outliers start: 28 outliers final: 13 residues processed: 141 average time/residue: 0.0820 time to fit residues: 19.4560 Evaluate side-chains 118 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 285 ILE 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 657 SER Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 657 SER 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: 8.9990 chunk 25 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 167 optimal weight: 9.9990 chunk 44 optimal weight: 0.0470 chunk 30 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 chunk 120 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 169 optimal weight: 0.7980 chunk 175 optimal weight: 8.9990 overall best weight: 1.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 734 ASN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 734 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.057887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.046009 restraints weight = 66069.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.047480 restraints weight = 35193.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.048481 restraints weight = 23320.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.049055 restraints weight = 17782.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.049499 restraints weight = 14978.348| |-----------------------------------------------------------------------------| r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14120 Z= 0.158 Angle : 0.582 13.511 19250 Z= 0.289 Chirality : 0.041 0.146 2281 Planarity : 0.005 0.057 2444 Dihedral : 5.417 70.106 1941 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.12 % Allowed : 11.26 % Favored : 86.62 % 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 aren not related in a simple way. whole: 1.25 (0.21), residues: 1792 helix: 1.87 (0.18), residues: 942 sheet: 0.45 (0.40), residues: 172 loop : -0.52 (0.25), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 20 TYR 0.033 0.002 TYR A 737 PHE 0.017 0.001 PHE A 802 TRP 0.010 0.001 TRP A 806 HIS 0.003 0.001 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00353 (14120) covalent geometry : angle 0.58156 (19250) hydrogen bonds : bond 0.03837 ( 734) hydrogen bonds : angle 4.31649 ( 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 137 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 106 time to evaluate : 0.495 Fit side-chains REVERT: A 45 MET cc_start: 0.8967 (mmm) cc_final: 0.8739 (mpp) REVERT: A 79 ASN cc_start: 0.8015 (t0) cc_final: 0.7161 (t0) REVERT: A 299 MET cc_start: 0.8898 (mtp) cc_final: 0.8517 (ttm) REVERT: A 725 MET cc_start: 0.9013 (tpp) cc_final: 0.8722 (tpp) REVERT: A 840 MET cc_start: 0.8671 (mmt) cc_final: 0.7965 (mmm) REVERT: B 45 MET cc_start: 0.8943 (mmm) cc_final: 0.8736 (mpp) REVERT: B 79 ASN cc_start: 0.7866 (t0) cc_final: 0.7045 (t0) REVERT: B 299 MET cc_start: 0.9131 (mtp) cc_final: 0.8830 (mmm) REVERT: B 326 VAL cc_start: 0.9373 (t) cc_final: 0.9148 (m) REVERT: B 714 LEU cc_start: 0.9738 (tt) cc_final: 0.9501 (tp) REVERT: B 725 MET cc_start: 0.9040 (ttm) cc_final: 0.8724 (tpp) REVERT: B 787 MET cc_start: 0.8824 (mmm) cc_final: 0.8384 (mmm) outliers start: 31 outliers final: 15 residues processed: 131 average time/residue: 0.0813 time to fit residues: 17.9449 Evaluate side-chains 117 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ILE 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 372 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 873 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 54 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 138 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 chunk 161 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 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 = 0.3204 r_free = 0.3204 target = 0.058787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.046996 restraints weight = 65525.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.048470 restraints weight = 35036.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.049474 restraints weight = 23169.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.050148 restraints weight = 17563.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.050416 restraints weight = 14694.056| |-----------------------------------------------------------------------------| r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2231 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= 0.111 Angle : 0.562 12.649 19250 Z= 0.276 Chirality : 0.040 0.153 2281 Planarity : 0.004 0.059 2444 Dihedral : 5.240 66.264 1941 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.98 % Allowed : 12.22 % Favored : 85.80 % 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 aren not related in a simple way. whole: 1.26 (0.21), residues: 1792 helix: 1.77 (0.18), residues: 956 sheet: 0.47 (0.44), residues: 136 loop : -0.35 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 20 TYR 0.021 0.002 TYR B 698 PHE 0.015 0.001 PHE A 802 TRP 0.007 0.001 TRP A 806 HIS 0.003 0.001 HIS A 19 Details of bonding type rmsd covalent geometry : bond 0.00243 (14120) covalent geometry : angle 0.56176 (19250) hydrogen bonds : bond 0.03561 ( 734) hydrogen bonds : angle 4.13800 ( 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 147 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 118 time to evaluate : 0.489 Fit side-chains REVERT: A 79 ASN cc_start: 0.7898 (t0) cc_final: 0.7096 (t0) REVERT: A 106 THR cc_start: 0.9264 (m) cc_final: 0.9047 (p) REVERT: A 299 MET cc_start: 0.8853 (mtp) cc_final: 0.8476 (ttm) REVERT: A 725 MET cc_start: 0.8973 (tpp) cc_final: 0.8745 (tpp) REVERT: A 840 MET cc_start: 0.8669 (mmt) cc_final: 0.7994 (mmm) REVERT: B 45 MET cc_start: 0.9011 (mmm) cc_final: 0.8682 (mpp) REVERT: B 48 MET cc_start: 0.8714 (ppp) cc_final: 0.8390 (tmm) REVERT: B 79 ASN cc_start: 0.7793 (t0) cc_final: 0.7016 (t0) REVERT: B 106 THR cc_start: 0.9222 (m) cc_final: 0.8989 (p) REVERT: B 747 ASP cc_start: 0.8901 (t0) cc_final: 0.8577 (t0) REVERT: B 840 MET cc_start: 0.9123 (mmm) cc_final: 0.8400 (mmm) outliers start: 29 outliers final: 16 residues processed: 140 average time/residue: 0.0818 time to fit residues: 19.4084 Evaluate side-chains 126 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 304 LEU 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 821 ILE 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 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 849 ILE 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: 7.9990 chunk 48 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 155 optimal weight: 6.9990 chunk 92 optimal weight: 0.3980 chunk 26 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 60 optimal weight: 7.9990 chunk 64 optimal weight: 0.4980 chunk 50 optimal weight: 7.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 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 = 0.3180 r_free = 0.3180 target = 0.057869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.046074 restraints weight = 66007.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.047496 restraints weight = 35610.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.048323 restraints weight = 23838.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.049041 restraints weight = 18876.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.049407 restraints weight = 15639.178| |-----------------------------------------------------------------------------| r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14120 Z= 0.161 Angle : 0.593 12.557 19250 Z= 0.292 Chirality : 0.041 0.143 2281 Planarity : 0.004 0.059 2444 Dihedral : 5.245 67.779 1941 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.98 % Allowed : 13.04 % Favored : 84.98 % 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 aren not related in a simple way. whole: 1.24 (0.21), residues: 1792 helix: 1.78 (0.18), residues: 956 sheet: 0.35 (0.44), residues: 136 loop : -0.37 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 822 TYR 0.022 0.002 TYR B 698 PHE 0.015 0.001 PHE A 802 TRP 0.007 0.001 TRP B 806 HIS 0.019 0.001 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00364 (14120) covalent geometry : angle 0.59261 (19250) hydrogen bonds : bond 0.03608 ( 734) hydrogen bonds : angle 4.22037 ( 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 137 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 0.609 Fit side-chains REVERT: A 48 MET cc_start: 0.8474 (tmm) cc_final: 0.8187 (tmm) REVERT: A 79 ASN cc_start: 0.7927 (t0) cc_final: 0.7104 (t0) REVERT: A 106 THR cc_start: 0.9283 (m) cc_final: 0.9061 (p) REVERT: A 840 MET cc_start: 0.8671 (mmt) cc_final: 0.8032 (mmm) REVERT: B 45 MET cc_start: 0.9064 (mmm) cc_final: 0.8748 (mpp) REVERT: B 79 ASN cc_start: 0.7857 (t0) cc_final: 0.6995 (t0) REVERT: B 242 MET cc_start: 0.8601 (mmm) cc_final: 0.8267 (mmm) REVERT: B 840 MET cc_start: 0.9111 (mmm) cc_final: 0.8345 (mmm) outliers start: 29 outliers final: 22 residues processed: 131 average time/residue: 0.0858 time to fit residues: 19.1324 Evaluate side-chains 124 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU 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 488 VAL Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 821 ILE 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 290 MET Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 488 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 67 optimal weight: 0.6980 chunk 94 optimal weight: 0.0570 chunk 146 optimal weight: 3.9990 chunk 152 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 3 optimal weight: 0.0020 chunk 96 optimal weight: 7.9990 chunk 168 optimal weight: 0.8980 chunk 32 optimal weight: 7.9990 chunk 99 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 overall best weight: 0.4706 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 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 = 0.3211 r_free = 0.3211 target = 0.059024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.047211 restraints weight = 65078.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.048717 restraints weight = 34393.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.049758 restraints weight = 22679.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.050386 restraints weight = 17049.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.050888 restraints weight = 14239.676| |-----------------------------------------------------------------------------| r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14120 Z= 0.102 Angle : 0.579 13.057 19250 Z= 0.280 Chirality : 0.040 0.139 2281 Planarity : 0.004 0.058 2444 Dihedral : 5.091 63.272 1941 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.77 % Allowed : 12.97 % Favored : 85.26 % 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 aren not related in a simple way. whole: 1.34 (0.21), residues: 1792 helix: 1.95 (0.18), residues: 930 sheet: 0.06 (0.42), residues: 146 loop : -0.31 (0.25), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 20 TYR 0.019 0.002 TYR B 698 PHE 0.014 0.001 PHE A 802 TRP 0.007 0.001 TRP B 788 HIS 0.009 0.001 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00219 (14120) covalent geometry : angle 0.57880 (19250) hydrogen bonds : bond 0.03447 ( 734) hydrogen bonds : angle 4.04644 ( 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 142 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 0.551 Fit side-chains REVERT: A 79 ASN cc_start: 0.7893 (t0) cc_final: 0.7093 (t0) REVERT: A 106 THR cc_start: 0.9248 (m) cc_final: 0.9002 (p) REVERT: A 127 MET cc_start: 0.8622 (mmp) cc_final: 0.8271 (mmm) REVERT: A 725 MET cc_start: 0.8892 (tpp) cc_final: 0.8619 (tpp) REVERT: A 840 MET cc_start: 0.8654 (mmt) cc_final: 0.7825 (mmm) REVERT: B 79 ASN cc_start: 0.7862 (t0) cc_final: 0.7078 (t0) REVERT: B 106 THR cc_start: 0.9253 (m) cc_final: 0.9008 (p) REVERT: B 299 MET cc_start: 0.8851 (mtp) cc_final: 0.8544 (ttm) REVERT: B 840 MET cc_start: 0.9075 (mmm) cc_final: 0.8352 (mmm) outliers start: 26 outliers final: 14 residues processed: 133 average time/residue: 0.0754 time to fit residues: 17.1232 Evaluate side-chains 126 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 304 LEU 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 873 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 488 VAL 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 873 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 114 optimal weight: 8.9990 chunk 153 optimal weight: 0.7980 chunk 112 optimal weight: 0.0020 chunk 92 optimal weight: 0.0870 chunk 169 optimal weight: 0.9980 chunk 176 optimal weight: 0.9980 chunk 46 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 126 optimal weight: 0.7980 overall best weight: 0.5366 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 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 = 0.3220 r_free = 0.3220 target = 0.059375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.047583 restraints weight = 64970.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.049076 restraints weight = 34269.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.049928 restraints weight = 22585.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.050706 restraints weight = 17697.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.051119 restraints weight = 14492.790| |-----------------------------------------------------------------------------| r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 14120 Z= 0.103 Angle : 0.576 12.551 19250 Z= 0.280 Chirality : 0.040 0.154 2281 Planarity : 0.004 0.059 2444 Dihedral : 4.991 61.794 1941 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.43 % Allowed : 13.45 % Favored : 85.12 % 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 aren not related in a simple way. whole: 1.32 (0.21), residues: 1792 helix: 1.94 (0.18), residues: 932 sheet: 0.02 (0.41), residues: 146 loop : -0.34 (0.25), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 20 TYR 0.019 0.002 TYR B 880 PHE 0.014 0.001 PHE A 802 TRP 0.006 0.001 TRP A 90 HIS 0.009 0.001 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00228 (14120) covalent geometry : angle 0.57584 (19250) hydrogen bonds : bond 0.03351 ( 734) hydrogen bonds : angle 4.02431 ( 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 139 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: A 79 ASN cc_start: 0.7895 (t0) cc_final: 0.7136 (t0) REVERT: A 106 THR cc_start: 0.9244 (m) cc_final: 0.9004 (p) REVERT: A 242 MET cc_start: 0.8436 (mmm) cc_final: 0.8005 (mmm) REVERT: A 725 MET cc_start: 0.8898 (tpp) cc_final: 0.8591 (tpp) REVERT: A 820 MET cc_start: 0.7722 (ptm) cc_final: 0.7456 (ptm) REVERT: A 840 MET cc_start: 0.8518 (mmt) cc_final: 0.7919 (mmm) REVERT: B 79 ASN cc_start: 0.7838 (t0) cc_final: 0.7074 (t0) REVERT: B 239 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8812 (mm) REVERT: B 299 MET cc_start: 0.8823 (mtp) cc_final: 0.8545 (ttm) REVERT: B 636 VAL cc_start: 0.9581 (t) cc_final: 0.9375 (p) REVERT: B 725 MET cc_start: 0.8763 (tpp) cc_final: 0.8551 (tpp) REVERT: B 747 ASP cc_start: 0.8906 (t0) cc_final: 0.8502 (t0) REVERT: B 840 MET cc_start: 0.9093 (mmm) cc_final: 0.8392 (mmm) outliers start: 21 outliers final: 15 residues processed: 134 average time/residue: 0.0659 time to fit residues: 14.9535 Evaluate side-chains 128 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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 488 VAL Chi-restraints excluded: chain A residue 742 VAL 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 304 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 61 optimal weight: 0.9990 chunk 10 optimal weight: 0.0270 chunk 103 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 82 optimal weight: 0.2980 chunk 17 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 105 optimal weight: 8.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 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 = 0.3227 r_free = 0.3227 target = 0.059576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.047846 restraints weight = 65408.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.049344 restraints weight = 34853.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.050195 restraints weight = 22989.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.050947 restraints weight = 17969.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.051266 restraints weight = 14762.288| |-----------------------------------------------------------------------------| r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14120 Z= 0.105 Angle : 0.587 13.243 19250 Z= 0.285 Chirality : 0.041 0.160 2281 Planarity : 0.004 0.061 2444 Dihedral : 4.873 59.899 1941 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.37 % Allowed : 14.33 % Favored : 84.30 % 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 aren not related in a simple way. whole: 1.32 (0.21), residues: 1792 helix: 1.93 (0.18), residues: 932 sheet: 0.06 (0.41), residues: 146 loop : -0.32 (0.25), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 451 TYR 0.019 0.002 TYR B 698 PHE 0.015 0.001 PHE B 807 TRP 0.007 0.001 TRP B 835 HIS 0.007 0.001 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00231 (14120) covalent geometry : angle 0.58709 (19250) hydrogen bonds : bond 0.03319 ( 734) hydrogen bonds : angle 3.99566 ( 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 139 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.421 Fit side-chains REVERT: A 79 ASN cc_start: 0.7881 (t0) cc_final: 0.7110 (t0) REVERT: A 106 THR cc_start: 0.9231 (m) cc_final: 0.8993 (p) REVERT: A 127 MET cc_start: 0.8528 (mmp) cc_final: 0.8217 (mmm) REVERT: A 254 MET cc_start: 0.8047 (tpp) cc_final: 0.7817 (tpp) REVERT: A 725 MET cc_start: 0.8875 (tpp) cc_final: 0.8616 (tpp) REVERT: A 840 MET cc_start: 0.8564 (mmt) cc_final: 0.8023 (mmm) REVERT: B 79 ASN cc_start: 0.7859 (t0) cc_final: 0.7096 (t0) REVERT: B 106 THR cc_start: 0.9236 (m) cc_final: 0.8986 (p) REVERT: B 299 MET cc_start: 0.8850 (mtp) cc_final: 0.8518 (ttm) REVERT: B 636 VAL cc_start: 0.9596 (t) cc_final: 0.9396 (p) REVERT: B 725 MET cc_start: 0.9044 (tpp) cc_final: 0.8607 (tpp) REVERT: B 747 ASP cc_start: 0.8882 (t0) cc_final: 0.8470 (t0) REVERT: B 840 MET cc_start: 0.9062 (mmm) cc_final: 0.8370 (mmm) outliers start: 20 outliers final: 19 residues processed: 132 average time/residue: 0.0721 time to fit residues: 16.2291 Evaluate side-chains 134 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.422 ------------------------------------------------------------------------------- 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 488 VAL Chi-restraints excluded: chain A residue 742 VAL 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 298 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 149 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 chunk 111 optimal weight: 3.9990 chunk 141 optimal weight: 0.0670 chunk 9 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 173 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 overall best weight: 1.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.058066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.046221 restraints weight = 66093.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.047668 restraints weight = 35861.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.048625 restraints weight = 24011.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.049143 restraints weight = 18461.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.049688 restraints weight = 15711.036| |-----------------------------------------------------------------------------| r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14120 Z= 0.163 Angle : 0.634 13.528 19250 Z= 0.310 Chirality : 0.041 0.165 2281 Planarity : 0.005 0.062 2444 Dihedral : 4.908 62.085 1941 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.50 % Allowed : 14.74 % 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 aren not related in a simple way. whole: 1.23 (0.21), residues: 1792 helix: 1.80 (0.18), residues: 946 sheet: 0.22 (0.44), residues: 134 loop : -0.36 (0.25), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 20 TYR 0.025 0.002 TYR A 880 PHE 0.015 0.001 PHE A 802 TRP 0.009 0.001 TRP B 789 HIS 0.008 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00369 (14120) covalent geometry : angle 0.63443 (19250) hydrogen bonds : bond 0.03610 ( 734) hydrogen bonds : angle 4.22576 ( 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 132 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 79 ASN cc_start: 0.8003 (t0) cc_final: 0.7150 (t0) REVERT: A 106 THR cc_start: 0.9276 (m) cc_final: 0.9049 (p) REVERT: A 840 MET cc_start: 0.8570 (mmt) cc_final: 0.7977 (mmm) REVERT: B 79 ASN cc_start: 0.7928 (t0) cc_final: 0.7124 (t0) REVERT: B 106 THR cc_start: 0.9290 (m) cc_final: 0.9061 (p) REVERT: B 636 VAL cc_start: 0.9588 (t) cc_final: 0.9383 (p) REVERT: B 725 MET cc_start: 0.9086 (tpp) cc_final: 0.8849 (tpp) REVERT: B 840 MET cc_start: 0.9054 (mmm) cc_final: 0.8418 (mmm) outliers start: 22 outliers final: 20 residues processed: 126 average time/residue: 0.0801 time to fit residues: 17.1503 Evaluate side-chains 128 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.358 ------------------------------------------------------------------------------- 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 488 VAL Chi-restraints excluded: chain A residue 742 VAL 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 298 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 159 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 141 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 155 optimal weight: 5.9990 chunk 123 optimal weight: 0.3980 chunk 163 optimal weight: 0.1980 chunk 15 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 158 optimal weight: 0.6980 chunk 174 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3215 r_free = 0.3215 target = 0.059118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.047347 restraints weight = 65458.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.048810 restraints weight = 34962.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.049809 restraints weight = 23258.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.050486 restraints weight = 17704.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.050681 restraints weight = 14744.551| |-----------------------------------------------------------------------------| r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14120 Z= 0.108 Angle : 0.621 13.524 19250 Z= 0.300 Chirality : 0.041 0.212 2281 Planarity : 0.004 0.062 2444 Dihedral : 4.811 57.800 1941 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.50 % Allowed : 14.81 % Favored : 83.69 % 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 aren not related in a simple way. whole: 1.29 (0.21), residues: 1792 helix: 1.88 (0.18), residues: 932 sheet: -0.01 (0.39), residues: 166 loop : -0.28 (0.25), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 451 TYR 0.020 0.002 TYR A 698 PHE 0.013 0.001 PHE A 802 TRP 0.006 0.001 TRP B 835 HIS 0.007 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00239 (14120) covalent geometry : angle 0.62075 (19250) hydrogen bonds : bond 0.03483 ( 734) hydrogen bonds : angle 4.10112 ( 2181) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1930.37 seconds wall clock time: 34 minutes 28.19 seconds (2068.19 seconds total)