Starting phenix.real_space_refine on Sun Jan 19 15:38:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uyb_42798/01_2025/8uyb_42798.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uyb_42798/01_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8uyb_42798/01_2025/8uyb_42798.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uyb_42798/01_2025/8uyb_42798.map" model { file = "/net/cci-nas-00/data/ceres_data/8uyb_42798/01_2025/8uyb_42798.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uyb_42798/01_2025/8uyb_42798.cif" } resolution = 3.87 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 4} 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: {'GLN:plan1': 4, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 2} 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: 9.22, per 1000 atoms: 0.67 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: 3.93 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 2.09 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: 5.56 Time building geometry restraints manager: 4.21 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 898 or resid 1001 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 898 or resid 1001 t \ hrough 1004)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.610 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 35.320 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.060 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.120 ------------------------------------------------------------------------------- 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= 0.148 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.006 0.001 TRP B 90 HIS 0.002 0.000 HIS A 819 PHE 0.014 0.001 PHE A 364 TYR 0.009 0.001 TYR A 698 ARG 0.002 0.000 ARG A 482 *********************** 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 : 1.529 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: 0.2048 time to fit residues: 73.1554 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 : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 150 optimal weight: 0.0060 chunk 134 optimal weight: 6.9990 chunk 74 optimal weight: 0.9980 chunk 46 optimal weight: 10.0000 chunk 91 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 139 optimal weight: 0.9990 chunk 53 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 161 optimal weight: 0.0670 overall best weight: 0.6136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3225 r_free = 0.3225 target = 0.059664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.047882 restraints weight = 64291.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.049404 restraints weight = 33975.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.050460 restraints weight = 22361.531| |-----------------------------------------------------------------------------| r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1461 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= 0.174 Angle : 0.579 9.429 19250 Z= 0.296 Chirality : 0.041 0.146 2281 Planarity : 0.005 0.053 2444 Dihedral : 5.524 70.197 1941 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.37 % Allowed : 7.92 % Favored : 90.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (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 TRP 0.010 0.001 TRP B 806 HIS 0.003 0.001 HIS A 230 PHE 0.018 0.001 PHE B 802 TYR 0.014 0.002 TYR B 880 ARG 0.004 0.000 ARG A 20 *********************** 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 164 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 144 time to evaluate : 1.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ASN cc_start: 0.7887 (t0) cc_final: 0.7137 (t0) REVERT: A 104 LEU cc_start: 0.9310 (mm) cc_final: 0.9109 (mp) REVERT: A 127 MET cc_start: 0.8859 (mmp) cc_final: 0.8513 (mmm) REVERT: A 326 VAL cc_start: 0.9406 (t) cc_final: 0.9199 (t) REVERT: A 737 TYR cc_start: 0.8528 (t80) cc_final: 0.8122 (t80) REVERT: A 741 GLN cc_start: 0.9151 (mm110) cc_final: 0.8925 (mm110) REVERT: A 747 ASP cc_start: 0.8856 (t0) cc_final: 0.8614 (t0) REVERT: A 787 MET cc_start: 0.8856 (mmm) cc_final: 0.8504 (mmp) REVERT: A 840 MET cc_start: 0.8646 (mmt) cc_final: 0.7928 (mmm) REVERT: B 79 ASN cc_start: 0.7798 (t0) cc_final: 0.6871 (t0) REVERT: B 99 ASN cc_start: 0.8797 (OUTLIER) cc_final: 0.8582 (p0) REVERT: B 299 MET cc_start: 0.9281 (mtp) cc_final: 0.8704 (mmm) REVERT: B 737 TYR cc_start: 0.8470 (t80) cc_final: 0.8146 (t80) REVERT: B 747 ASP cc_start: 0.8824 (t0) cc_final: 0.8614 (t0) REVERT: B 838 MET cc_start: 0.9106 (OUTLIER) cc_final: 0.8873 (mtm) outliers start: 20 outliers final: 11 residues processed: 157 average time/residue: 0.2015 time to fit residues: 52.1164 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 : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain B residue 99 ASN 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 70 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 133 optimal weight: 0.0770 chunk 166 optimal weight: 0.9980 chunk 130 optimal weight: 0.6980 chunk 57 optimal weight: 7.9990 chunk 84 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 19 optimal weight: 7.9990 overall best weight: 0.9540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 819 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.059369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.047709 restraints weight = 64481.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.049197 restraints weight = 34063.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.050231 restraints weight = 22376.867| |-----------------------------------------------------------------------------| r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14120 Z= 0.176 Angle : 0.575 12.697 19250 Z= 0.285 Chirality : 0.041 0.148 2281 Planarity : 0.005 0.052 2444 Dihedral : 5.423 70.142 1941 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.91 % Allowed : 10.03 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.21), residues: 1792 helix: 1.78 (0.18), residues: 954 sheet: 0.54 (0.40), residues: 172 loop : -0.46 (0.25), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 806 HIS 0.003 0.001 HIS B 819 PHE 0.016 0.001 PHE A 802 TYR 0.018 0.001 TYR A 880 ARG 0.003 0.000 ARG B 20 *********************** 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 152 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 124 time to evaluate : 1.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ASN cc_start: 0.7932 (t0) cc_final: 0.7165 (t0) REVERT: A 127 MET cc_start: 0.8827 (mmp) cc_final: 0.8523 (mmm) REVERT: A 725 MET cc_start: 0.8992 (tpp) cc_final: 0.8758 (tpp) REVERT: A 747 ASP cc_start: 0.8885 (t0) cc_final: 0.8619 (t0) REVERT: A 840 MET cc_start: 0.8652 (mmt) cc_final: 0.7946 (mmm) REVERT: B 45 MET cc_start: 0.8970 (mmm) cc_final: 0.8731 (mpp) REVERT: B 48 MET cc_start: 0.8514 (tmm) cc_final: 0.8304 (tmm) REVERT: B 79 ASN cc_start: 0.7759 (t0) cc_final: 0.6862 (t0) REVERT: B 299 MET cc_start: 0.9208 (mtp) cc_final: 0.8899 (mmm) REVERT: B 730 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8416 (mp) REVERT: B 747 ASP cc_start: 0.8843 (t0) cc_final: 0.8561 (t0) REVERT: B 775 ILE cc_start: 0.9393 (pt) cc_final: 0.8902 (mm) REVERT: B 838 MET cc_start: 0.9137 (OUTLIER) cc_final: 0.8866 (mtm) outliers start: 28 outliers final: 13 residues processed: 142 average time/residue: 0.1954 time to fit residues: 45.9982 Evaluate side-chains 124 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 1.605 ------------------------------------------------------------------------------- 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 742 VAL Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain B residue 285 ILE 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 851 LEU 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 58 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 155 optimal weight: 0.8980 chunk 77 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 174 optimal weight: 10.0000 chunk 160 optimal weight: 0.0970 chunk 112 optimal weight: 8.9990 chunk 124 optimal weight: 2.9990 chunk 120 optimal weight: 0.7980 overall best weight: 1.3582 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.058679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.046973 restraints weight = 65157.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.048455 restraints weight = 34682.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.049455 restraints weight = 22847.099| |-----------------------------------------------------------------------------| r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14120 Z= 0.189 Angle : 0.559 12.418 19250 Z= 0.276 Chirality : 0.041 0.134 2281 Planarity : 0.004 0.054 2444 Dihedral : 5.301 69.442 1941 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.39 % Allowed : 10.03 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.21), residues: 1792 helix: 1.80 (0.18), residues: 956 sheet: 0.54 (0.40), residues: 172 loop : -0.36 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 806 HIS 0.002 0.001 HIS A 230 PHE 0.017 0.001 PHE A 802 TYR 0.018 0.002 TYR B 698 ARG 0.003 0.000 ARG B 20 *********************** 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 150 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 115 time to evaluate : 1.597 Fit side-chains REVERT: A 79 ASN cc_start: 0.8001 (t0) cc_final: 0.7178 (t0) REVERT: A 127 MET cc_start: 0.8834 (mmp) cc_final: 0.8514 (mmm) REVERT: A 299 MET cc_start: 0.8922 (mtp) cc_final: 0.8569 (ttm) REVERT: A 725 MET cc_start: 0.9002 (tpp) cc_final: 0.8728 (tpp) REVERT: A 840 MET cc_start: 0.8664 (mmt) cc_final: 0.7951 (mmm) REVERT: B 79 ASN cc_start: 0.7803 (t0) cc_final: 0.6965 (t0) REVERT: B 299 MET cc_start: 0.9207 (mtp) cc_final: 0.8710 (mmm) REVERT: B 730 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8348 (mp) REVERT: B 747 ASP cc_start: 0.8911 (t0) cc_final: 0.8575 (t0) REVERT: B 838 MET cc_start: 0.9167 (OUTLIER) cc_final: 0.8902 (mtm) outliers start: 35 outliers final: 17 residues processed: 140 average time/residue: 0.1987 time to fit residues: 45.9735 Evaluate side-chains 128 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 1.610 ------------------------------------------------------------------------------- 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 304 LEU Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 372 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 38 optimal weight: 5.9990 chunk 96 optimal weight: 9.9990 chunk 115 optimal weight: 0.0170 chunk 88 optimal weight: 0.9980 chunk 129 optimal weight: 7.9990 chunk 140 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 75 optimal weight: 0.1980 overall best weight: 0.8422 ------------------------------------------------------------------------------- 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 = 0.3216 r_free = 0.3216 target = 0.059188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.047437 restraints weight = 64950.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.048925 restraints weight = 34110.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.049948 restraints weight = 22451.120| |-----------------------------------------------------------------------------| r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2187 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= 0.162 Angle : 0.561 12.635 19250 Z= 0.276 Chirality : 0.040 0.143 2281 Planarity : 0.004 0.059 2444 Dihedral : 5.196 66.540 1941 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.25 % Allowed : 11.40 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.21), residues: 1792 helix: 1.92 (0.18), residues: 940 sheet: 0.46 (0.39), residues: 172 loop : -0.39 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 806 HIS 0.010 0.001 HIS B 41 PHE 0.015 0.001 PHE A 802 TYR 0.020 0.002 TYR B 698 ARG 0.001 0.000 ARG B 20 *********************** 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 149 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 116 time to evaluate : 1.588 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.8479 (tmm) cc_final: 0.8166 (tmm) REVERT: A 79 ASN cc_start: 0.7941 (t0) cc_final: 0.7183 (t0) REVERT: A 106 THR cc_start: 0.9271 (m) cc_final: 0.9035 (p) REVERT: A 127 MET cc_start: 0.8848 (mmp) cc_final: 0.8522 (mmm) REVERT: A 299 MET cc_start: 0.8921 (mtp) cc_final: 0.8547 (ttm) REVERT: A 725 MET cc_start: 0.9001 (tpp) cc_final: 0.8777 (tpp) REVERT: A 840 MET cc_start: 0.8656 (mmt) cc_final: 0.7983 (mmm) REVERT: B 79 ASN cc_start: 0.7806 (t0) cc_final: 0.6992 (t0) REVERT: B 299 MET cc_start: 0.9121 (mtp) cc_final: 0.8868 (mmm) REVERT: B 747 ASP cc_start: 0.8924 (t0) cc_final: 0.8575 (t0) REVERT: B 840 MET cc_start: 0.9118 (mmm) cc_final: 0.8825 (mmt) outliers start: 33 outliers final: 18 residues processed: 140 average time/residue: 0.1938 time to fit residues: 45.3009 Evaluate side-chains 125 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 1.758 ------------------------------------------------------------------------------- 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 239 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 787 MET 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 285 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 45 optimal weight: 10.0000 chunk 113 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 67 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 155 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.3198 r_free = 0.3198 target = 0.058457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.046720 restraints weight = 65624.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.048163 restraints weight = 35196.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.049152 restraints weight = 23428.656| |-----------------------------------------------------------------------------| r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14120 Z= 0.222 Angle : 0.584 12.236 19250 Z= 0.287 Chirality : 0.041 0.163 2281 Planarity : 0.004 0.059 2444 Dihedral : 5.166 67.200 1941 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.46 % Allowed : 12.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.21), residues: 1792 helix: 1.83 (0.18), residues: 952 sheet: 0.49 (0.44), residues: 136 loop : -0.33 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 806 HIS 0.006 0.001 HIS B 41 PHE 0.014 0.001 PHE B 802 TYR 0.031 0.002 TYR B 698 ARG 0.002 0.000 ARG A 496 *********************** 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 146 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 110 time to evaluate : 1.614 Fit side-chains REVERT: A 48 MET cc_start: 0.8462 (tmm) cc_final: 0.8246 (tmm) REVERT: A 79 ASN cc_start: 0.7976 (t0) cc_final: 0.7148 (t0) REVERT: A 106 THR cc_start: 0.9264 (m) cc_final: 0.9039 (p) REVERT: A 127 MET cc_start: 0.8789 (mmp) cc_final: 0.8485 (mmm) REVERT: A 725 MET cc_start: 0.8984 (tpp) cc_final: 0.8740 (tpp) REVERT: A 840 MET cc_start: 0.8669 (mmt) cc_final: 0.8018 (mmm) REVERT: B 48 MET cc_start: 0.8531 (tmm) cc_final: 0.8221 (tmm) REVERT: B 79 ASN cc_start: 0.7812 (t0) cc_final: 0.6924 (t0) REVERT: B 299 MET cc_start: 0.9120 (mtp) cc_final: 0.8757 (mmm) REVERT: B 747 ASP cc_start: 0.8942 (t0) cc_final: 0.8506 (t0) REVERT: B 840 MET cc_start: 0.9092 (mmm) cc_final: 0.8397 (mmm) outliers start: 36 outliers final: 23 residues processed: 138 average time/residue: 0.1930 time to fit residues: 44.7169 Evaluate side-chains 129 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 1.481 ------------------------------------------------------------------------------- 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 372 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 787 MET 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 285 ILE Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 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 120 optimal weight: 7.9990 chunk 82 optimal weight: 0.8980 chunk 113 optimal weight: 0.2980 chunk 88 optimal weight: 1.9990 chunk 64 optimal weight: 0.0060 chunk 13 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 147 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 overall best weight: 0.8398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.059147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.047346 restraints weight = 65141.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.048814 restraints weight = 34771.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.049806 restraints weight = 23118.362| |-----------------------------------------------------------------------------| r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2466 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= 0.159 Angle : 0.571 12.281 19250 Z= 0.279 Chirality : 0.040 0.134 2281 Planarity : 0.004 0.057 2444 Dihedral : 5.062 64.057 1941 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.84 % Allowed : 12.83 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.21), residues: 1792 helix: 1.87 (0.18), residues: 942 sheet: 0.21 (0.42), residues: 146 loop : -0.25 (0.25), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 806 HIS 0.005 0.001 HIS A 41 PHE 0.013 0.001 PHE B 802 TYR 0.024 0.002 TYR B 698 ARG 0.002 0.000 ARG A 20 *********************** 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 146 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 119 time to evaluate : 1.713 Fit side-chains revert: symmetry clash REVERT: A 79 ASN cc_start: 0.7935 (t0) cc_final: 0.7134 (t0) REVERT: A 106 THR cc_start: 0.9247 (m) cc_final: 0.9011 (p) REVERT: A 725 MET cc_start: 0.8975 (tpp) cc_final: 0.8766 (tpp) REVERT: A 840 MET cc_start: 0.8673 (mmt) cc_final: 0.7851 (mmm) REVERT: B 79 ASN cc_start: 0.7778 (t0) cc_final: 0.6921 (t0) REVERT: B 299 MET cc_start: 0.9060 (mtp) cc_final: 0.8806 (mmm) REVERT: B 747 ASP cc_start: 0.8929 (t0) cc_final: 0.8590 (t0) REVERT: B 840 MET cc_start: 0.9083 (mmm) cc_final: 0.8367 (mmm) outliers start: 27 outliers final: 19 residues processed: 138 average time/residue: 0.2049 time to fit residues: 47.2144 Evaluate side-chains 131 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 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 285 ILE Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 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 72 optimal weight: 0.3980 chunk 133 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 100 optimal weight: 6.9990 chunk 153 optimal weight: 0.8980 chunk 21 optimal weight: 10.0000 chunk 112 optimal weight: 1.9990 chunk 174 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 734 ASN ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.058969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.047204 restraints weight = 65095.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.048682 restraints weight = 34839.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.049674 restraints weight = 23115.962| |-----------------------------------------------------------------------------| r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14120 Z= 0.173 Angle : 0.585 11.895 19250 Z= 0.286 Chirality : 0.041 0.138 2281 Planarity : 0.004 0.056 2444 Dihedral : 4.996 63.488 1941 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.77 % Allowed : 13.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.21), residues: 1792 helix: 1.80 (0.18), residues: 946 sheet: 0.20 (0.41), residues: 146 loop : -0.27 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 806 HIS 0.019 0.001 HIS B 76 PHE 0.013 0.001 PHE A 802 TYR 0.021 0.002 TYR B 698 ARG 0.002 0.000 ARG A 20 *********************** 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 141 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 115 time to evaluate : 1.601 Fit side-chains revert: symmetry clash REVERT: A 79 ASN cc_start: 0.7977 (t0) cc_final: 0.7177 (t0) REVERT: A 106 THR cc_start: 0.9264 (m) cc_final: 0.9024 (p) REVERT: A 725 MET cc_start: 0.8954 (tpp) cc_final: 0.8738 (tpp) REVERT: A 816 LEU cc_start: 0.9605 (mm) cc_final: 0.9325 (mm) REVERT: A 820 MET cc_start: 0.7884 (ptm) cc_final: 0.7614 (ptm) REVERT: A 840 MET cc_start: 0.8523 (mmt) cc_final: 0.7943 (mmm) REVERT: B 79 ASN cc_start: 0.7824 (t0) cc_final: 0.6917 (t0) REVERT: B 242 MET cc_start: 0.8404 (mmm) cc_final: 0.7990 (mmm) REVERT: B 636 VAL cc_start: 0.9597 (t) cc_final: 0.9393 (p) REVERT: B 747 ASP cc_start: 0.8929 (t0) cc_final: 0.8597 (t0) REVERT: B 840 MET cc_start: 0.9097 (mmm) cc_final: 0.8350 (mmm) outliers start: 26 outliers final: 19 residues processed: 133 average time/residue: 0.2011 time to fit residues: 44.7937 Evaluate side-chains 132 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 1.821 ------------------------------------------------------------------------------- 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 225 THR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 372 THR 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 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 72 optimal weight: 0.0970 chunk 64 optimal weight: 0.2980 chunk 61 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 119 optimal weight: 0.0020 chunk 24 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 150 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 chunk 136 optimal weight: 7.9990 chunk 97 optimal weight: 0.9990 overall best weight: 0.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 734 ASN ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.059801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.048167 restraints weight = 64912.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.049619 restraints weight = 35603.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.050583 restraints weight = 23837.050| |-----------------------------------------------------------------------------| r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14120 Z= 0.148 Angle : 0.591 11.433 19250 Z= 0.288 Chirality : 0.041 0.145 2281 Planarity : 0.004 0.057 2444 Dihedral : 4.920 60.062 1941 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.43 % Allowed : 13.79 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.21), residues: 1792 helix: 1.85 (0.18), residues: 930 sheet: 0.23 (0.41), residues: 146 loop : -0.32 (0.25), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 806 HIS 0.015 0.001 HIS B 76 PHE 0.013 0.001 PHE A 802 TYR 0.019 0.002 TYR B 698 ARG 0.001 0.000 ARG A 451 *********************** 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 145 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 1.545 Fit side-chains revert: symmetry clash REVERT: A 79 ASN cc_start: 0.7920 (t0) cc_final: 0.7084 (t0) REVERT: A 106 THR cc_start: 0.9235 (m) cc_final: 0.9000 (p) REVERT: A 127 MET cc_start: 0.8639 (mmp) cc_final: 0.8298 (mmm) REVERT: A 254 MET cc_start: 0.8051 (tpp) cc_final: 0.7777 (tpp) REVERT: A 725 MET cc_start: 0.8903 (tpp) cc_final: 0.8693 (tpp) REVERT: A 820 MET cc_start: 0.7176 (ptm) cc_final: 0.6976 (ptt) REVERT: A 840 MET cc_start: 0.8561 (mmt) cc_final: 0.7978 (mmm) REVERT: B 79 ASN cc_start: 0.7848 (t0) cc_final: 0.7044 (t0) REVERT: B 106 THR cc_start: 0.9224 (m) cc_final: 0.8982 (p) REVERT: B 242 MET cc_start: 0.8340 (mmm) cc_final: 0.7956 (mmm) REVERT: B 747 ASP cc_start: 0.8971 (t0) cc_final: 0.8629 (t0) REVERT: B 840 MET cc_start: 0.9081 (mmm) cc_final: 0.8379 (mmm) outliers start: 21 outliers final: 18 residues processed: 141 average time/residue: 0.1880 time to fit residues: 44.3251 Evaluate side-chains 133 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 1.498 ------------------------------------------------------------------------------- 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 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 304 LEU Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 742 VAL 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 132 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 chunk 176 optimal weight: 0.9980 chunk 144 optimal weight: 0.8980 chunk 49 optimal weight: 6.9990 chunk 165 optimal weight: 3.9990 chunk 136 optimal weight: 0.0870 chunk 153 optimal weight: 0.6980 chunk 105 optimal weight: 0.9980 chunk 9 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- 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 = 0.3230 r_free = 0.3230 target = 0.059758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.048069 restraints weight = 65413.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.049548 restraints weight = 34828.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.050376 restraints weight = 23026.546| |-----------------------------------------------------------------------------| r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14120 Z= 0.160 Angle : 0.603 11.845 19250 Z= 0.295 Chirality : 0.041 0.149 2281 Planarity : 0.004 0.057 2444 Dihedral : 4.807 58.594 1941 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.37 % Allowed : 14.06 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.21), residues: 1792 helix: 1.84 (0.18), residues: 930 sheet: 0.28 (0.41), residues: 146 loop : -0.31 (0.25), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 806 HIS 0.014 0.001 HIS B 76 PHE 0.012 0.001 PHE A 802 TYR 0.021 0.002 TYR B 880 ARG 0.001 0.000 ARG A 20 ********************** 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 137 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 1.661 Fit side-chains revert: symmetry clash REVERT: A 79 ASN cc_start: 0.7949 (t0) cc_final: 0.7136 (t0) REVERT: A 106 THR cc_start: 0.9270 (m) cc_final: 0.9014 (p) REVERT: A 840 MET cc_start: 0.8544 (mmt) cc_final: 0.7938 (mmm) REVERT: B 79 ASN cc_start: 0.7895 (t0) cc_final: 0.7106 (t0) REVERT: B 106 THR cc_start: 0.9244 (m) cc_final: 0.9001 (p) REVERT: B 747 ASP cc_start: 0.8981 (t0) cc_final: 0.8658 (t0) REVERT: B 840 MET cc_start: 0.9057 (mmm) cc_final: 0.8423 (mmm) outliers start: 20 outliers final: 20 residues processed: 131 average time/residue: 0.2073 time to fit residues: 45.4616 Evaluate side-chains 133 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 1.681 ------------------------------------------------------------------------------- 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 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 299 MET 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 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 95 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 153 optimal weight: 0.9990 chunk 7 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 53 optimal weight: 9.9990 chunk 79 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 125 optimal weight: 4.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 = 0.3206 r_free = 0.3206 target = 0.058766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.046807 restraints weight = 66772.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.048291 restraints weight = 35395.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.049310 restraints weight = 23424.435| |-----------------------------------------------------------------------------| r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14120 Z= 0.212 Angle : 0.632 14.366 19250 Z= 0.310 Chirality : 0.041 0.172 2281 Planarity : 0.004 0.057 2444 Dihedral : 4.772 58.224 1941 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.50 % Allowed : 14.33 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.21), residues: 1792 helix: 1.83 (0.18), residues: 932 sheet: 0.16 (0.39), residues: 166 loop : -0.25 (0.25), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 315 HIS 0.014 0.001 HIS B 41 PHE 0.014 0.001 PHE A 802 TYR 0.027 0.002 TYR A 698 ARG 0.002 0.000 ARG B 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3540.91 seconds wall clock time: 65 minutes 30.03 seconds (3930.03 seconds total)