Starting phenix.real_space_refine on Mon Dec 30 20:28:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uyb_42798/12_2024/8uyb_42798.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uyb_42798/12_2024/8uyb_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_42798/12_2024/8uyb_42798.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uyb_42798/12_2024/8uyb_42798.map" model { file = "/net/cci-nas-00/data/ceres_data/8uyb_42798/12_2024/8uyb_42798.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uyb_42798/12_2024/8uyb_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-5532/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: 8.85, per 1000 atoms: 0.64 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: 3.53 Conformation dependent library (CDL) restraints added in 1.8 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: 1.95 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: 5.21 Time building geometry restraints manager: 3.89 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: 3.250 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: 0.560 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 33.760 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.030 ------------------------------------------------------------------------------- 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 : 1.492 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: 0.2126 time to fit residues: 76.1148 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 : 1.733 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- 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 : 1.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ASN cc_start: 0.7847 (t0) cc_final: 0.7102 (t0) REVERT: A 104 LEU cc_start: 0.9313 (mm) cc_final: 0.9108 (mp) REVERT: A 127 MET cc_start: 0.8825 (mmp) cc_final: 0.8491 (mmm) REVERT: A 326 VAL cc_start: 0.9404 (t) cc_final: 0.9201 (t) REVERT: A 737 TYR cc_start: 0.8544 (t80) cc_final: 0.8130 (t80) REVERT: A 741 GLN cc_start: 0.9151 (mm110) cc_final: 0.8925 (mm110) REVERT: A 747 ASP cc_start: 0.8829 (t0) cc_final: 0.8603 (t0) REVERT: A 787 MET cc_start: 0.8770 (mmm) cc_final: 0.8434 (mmp) REVERT: A 840 MET cc_start: 0.8659 (mmt) cc_final: 0.7957 (mmm) REVERT: B 79 ASN cc_start: 0.7749 (t0) cc_final: 0.6836 (t0) REVERT: B 99 ASN cc_start: 0.8771 (OUTLIER) cc_final: 0.8570 (p0) REVERT: B 299 MET cc_start: 0.9254 (mtp) cc_final: 0.8696 (mmm) REVERT: B 737 TYR cc_start: 0.8484 (t80) cc_final: 0.8150 (t80) REVERT: B 838 MET cc_start: 0.9083 (OUTLIER) cc_final: 0.8868 (mtm) outliers start: 20 outliers final: 11 residues processed: 157 average time/residue: 0.1941 time to fit residues: 50.5520 Evaluate side-chains 126 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 1.769 ------------------------------------------------------------------------------- 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 89 optimal weight: 20.0000 chunk 50 optimal weight: 5.9990 chunk 134 optimal weight: 9.9990 chunk 110 optimal weight: 9.9990 chunk 44 optimal weight: 0.8980 chunk 161 optimal weight: 7.9990 chunk 174 optimal weight: 8.9990 chunk 144 optimal weight: 3.9990 chunk 160 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 129 optimal weight: 6.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN B 506 ASN B 734 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 14120 Z= 0.365 Angle : 0.663 14.494 19250 Z= 0.334 Chirality : 0.043 0.153 2281 Planarity : 0.005 0.051 2444 Dihedral : 5.564 73.425 1941 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.25 % Allowed : 10.10 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.05 (0.21), residues: 1792 helix: 1.63 (0.18), residues: 956 sheet: 0.40 (0.41), residues: 166 loop : -0.55 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 806 HIS 0.006 0.001 HIS B 819 PHE 0.022 0.002 PHE B 101 TYR 0.027 0.002 TYR B 698 ARG 0.005 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 144 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 111 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ASN cc_start: 0.8038 (t0) cc_final: 0.7235 (t0) REVERT: A 725 MET cc_start: 0.9049 (tpp) cc_final: 0.8799 (tpp) REVERT: A 840 MET cc_start: 0.8664 (mmt) cc_final: 0.7979 (mmm) REVERT: B 79 ASN cc_start: 0.7956 (t0) cc_final: 0.7160 (t0) REVERT: B 299 MET cc_start: 0.9173 (mtp) cc_final: 0.8887 (mmm) REVERT: B 326 VAL cc_start: 0.9415 (t) cc_final: 0.9185 (m) REVERT: B 725 MET cc_start: 0.9160 (ttm) cc_final: 0.8907 (ttm) REVERT: B 730 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8437 (mp) REVERT: B 775 ILE cc_start: 0.9411 (pt) cc_final: 0.8944 (mm) REVERT: B 787 MET cc_start: 0.8772 (mmm) cc_final: 0.8507 (mmm) REVERT: B 838 MET cc_start: 0.9139 (OUTLIER) cc_final: 0.8916 (mtm) outliers start: 33 outliers final: 17 residues processed: 137 average time/residue: 0.1956 time to fit residues: 44.7306 Evaluate side-chains 116 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 657 SER 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 304 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 159 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 162 optimal weight: 3.9990 chunk 172 optimal weight: 3.9990 chunk 154 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 143 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 734 ASN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 734 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2133 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= 0.213 Angle : 0.586 13.017 19250 Z= 0.290 Chirality : 0.041 0.129 2281 Planarity : 0.004 0.055 2444 Dihedral : 5.483 69.149 1941 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.98 % Allowed : 12.08 % Favored : 85.94 % 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: 1.17 (0.21), residues: 1792 helix: 1.82 (0.18), residues: 942 sheet: 0.38 (0.40), residues: 170 loop : -0.57 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 806 HIS 0.003 0.001 HIS B 19 PHE 0.015 0.001 PHE A 802 TYR 0.032 0.002 TYR A 737 ARG 0.003 0.000 ARG A 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 137 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 1.574 Fit side-chains revert: symmetry clash REVERT: A 45 MET cc_start: 0.8994 (mmm) cc_final: 0.8755 (mpp) REVERT: A 79 ASN cc_start: 0.7928 (t0) cc_final: 0.7165 (t0) REVERT: A 299 MET cc_start: 0.8872 (mtp) cc_final: 0.8502 (ttm) REVERT: A 725 MET cc_start: 0.9030 (tpp) cc_final: 0.8758 (tpp) REVERT: A 840 MET cc_start: 0.8685 (mmt) cc_final: 0.8012 (mmm) REVERT: B 45 MET cc_start: 0.9038 (mmm) cc_final: 0.8742 (mpp) REVERT: B 79 ASN cc_start: 0.7834 (t0) cc_final: 0.6993 (t0) REVERT: B 299 MET cc_start: 0.9139 (mtp) cc_final: 0.8881 (mmm) REVERT: B 714 LEU cc_start: 0.9725 (tt) cc_final: 0.9475 (tp) REVERT: B 730 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8429 (mp) REVERT: B 775 ILE cc_start: 0.9367 (pt) cc_final: 0.8934 (mm) REVERT: B 787 MET cc_start: 0.8849 (mmm) cc_final: 0.8599 (mmm) REVERT: B 840 MET cc_start: 0.9150 (mmm) cc_final: 0.8416 (mmm) outliers start: 29 outliers final: 15 residues processed: 132 average time/residue: 0.2027 time to fit residues: 44.7808 Evaluate side-chains 118 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 1.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 290 MET 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 816 LEU Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 488 VAL 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 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 97 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 128 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 146 optimal weight: 8.9990 chunk 118 optimal weight: 0.8980 chunk 0 optimal weight: 30.0000 chunk 87 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 734 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14120 Z= 0.237 Angle : 0.595 13.353 19250 Z= 0.293 Chirality : 0.041 0.153 2281 Planarity : 0.004 0.055 2444 Dihedral : 5.412 69.282 1941 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.05 % Allowed : 12.35 % Favored : 85.60 % 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: 1.16 (0.21), residues: 1792 helix: 1.75 (0.18), residues: 952 sheet: 0.36 (0.46), residues: 134 loop : -0.47 (0.24), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 806 HIS 0.004 0.001 HIS A 19 PHE 0.016 0.002 PHE A 802 TYR 0.023 0.002 TYR B 698 ARG 0.002 0.000 ARG A 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 143 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 113 time to evaluate : 1.602 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 MET cc_start: 0.8992 (mmm) cc_final: 0.8791 (mpp) REVERT: A 79 ASN cc_start: 0.7938 (t0) cc_final: 0.7137 (t0) REVERT: A 106 THR cc_start: 0.9332 (m) cc_final: 0.9098 (p) REVERT: A 840 MET cc_start: 0.8685 (mmt) cc_final: 0.8034 (mmm) REVERT: B 45 MET cc_start: 0.9006 (mmm) cc_final: 0.8776 (mpp) REVERT: B 79 ASN cc_start: 0.7881 (t0) cc_final: 0.7067 (t0) REVERT: B 326 VAL cc_start: 0.9398 (t) cc_final: 0.9171 (m) REVERT: B 775 ILE cc_start: 0.9428 (pt) cc_final: 0.8957 (mm) REVERT: B 840 MET cc_start: 0.9142 (mmm) cc_final: 0.8409 (mmm) outliers start: 30 outliers final: 19 residues processed: 137 average time/residue: 0.1953 time to fit residues: 44.8802 Evaluate side-chains 124 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 1.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 816 LEU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 154 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 101 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 172 optimal weight: 7.9990 chunk 142 optimal weight: 9.9990 chunk 79 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 166 optimal weight: 0.8980 overall best weight: 1.7584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14120 Z= 0.220 Angle : 0.590 13.389 19250 Z= 0.288 Chirality : 0.041 0.181 2281 Planarity : 0.004 0.055 2444 Dihedral : 5.367 68.085 1941 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.25 % Allowed : 13.11 % Favored : 84.64 % 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: 1.11 (0.21), residues: 1792 helix: 1.67 (0.18), residues: 964 sheet: 0.16 (0.45), residues: 136 loop : -0.42 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 806 HIS 0.004 0.001 HIS B 19 PHE 0.015 0.001 PHE A 802 TYR 0.023 0.002 TYR B 698 ARG 0.002 0.000 ARG B 822 *********************** 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 147 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 114 time to evaluate : 1.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 ASN cc_start: 0.7919 (t0) cc_final: 0.7083 (t0) REVERT: A 106 THR cc_start: 0.9313 (m) cc_final: 0.9085 (p) REVERT: A 299 MET cc_start: 0.8853 (mtp) cc_final: 0.8572 (ttm) REVERT: A 840 MET cc_start: 0.8698 (mmt) cc_final: 0.8037 (mmm) REVERT: B 45 MET cc_start: 0.8993 (mmm) cc_final: 0.8766 (mpp) REVERT: B 79 ASN cc_start: 0.7911 (t0) cc_final: 0.7092 (t0) REVERT: B 104 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.9149 (tt) REVERT: B 106 THR cc_start: 0.9334 (m) cc_final: 0.9091 (p) REVERT: B 242 MET cc_start: 0.8625 (mmm) cc_final: 0.8257 (mmm) REVERT: B 326 VAL cc_start: 0.9412 (OUTLIER) cc_final: 0.9175 (m) REVERT: B 840 MET cc_start: 0.9123 (mmm) cc_final: 0.8378 (mmm) outliers start: 33 outliers final: 21 residues processed: 139 average time/residue: 0.1808 time to fit residues: 42.2640 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 : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 290 MET 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 816 LEU 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 104 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 657 SER Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain B residue 849 ILE Chi-restraints excluded: chain B residue 873 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 19 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 125 optimal weight: 0.6980 chunk 97 optimal weight: 5.9990 chunk 144 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 171 optimal weight: 8.9990 chunk 107 optimal weight: 0.6980 chunk 104 optimal weight: 6.9990 chunk 79 optimal weight: 7.9990 chunk 106 optimal weight: 7.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14120 Z= 0.174 Angle : 0.579 14.841 19250 Z= 0.281 Chirality : 0.040 0.141 2281 Planarity : 0.004 0.054 2444 Dihedral : 5.239 65.909 1941 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.46 % Allowed : 13.86 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.70 (0.18), residues: 964 sheet: 0.14 (0.44), residues: 136 loop : -0.39 (0.25), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 806 HIS 0.012 0.001 HIS A 41 PHE 0.014 0.001 PHE A 802 TYR 0.020 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 150 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 114 time to evaluate : 1.968 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8513 (tmm) cc_final: 0.8220 (tmm) REVERT: A 79 ASN cc_start: 0.7920 (t0) cc_final: 0.7108 (t0) REVERT: A 106 THR cc_start: 0.9291 (m) cc_final: 0.9064 (p) REVERT: A 299 MET cc_start: 0.8851 (mtp) cc_final: 0.8585 (ttm) REVERT: A 725 MET cc_start: 0.8940 (tpp) cc_final: 0.8735 (tpp) REVERT: A 840 MET cc_start: 0.8692 (mmt) cc_final: 0.8052 (mmm) REVERT: B 79 ASN cc_start: 0.7872 (t0) cc_final: 0.7058 (t0) REVERT: B 104 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.9122 (tt) REVERT: B 106 THR cc_start: 0.9307 (m) cc_final: 0.9076 (p) REVERT: B 299 MET cc_start: 0.8907 (mtp) cc_final: 0.8584 (ttm) REVERT: B 840 MET cc_start: 0.9115 (mmm) cc_final: 0.8415 (mmm) outliers start: 36 outliers final: 22 residues processed: 141 average time/residue: 0.1972 time to fit residues: 46.4765 Evaluate side-chains 134 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 290 MET 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 654 ILE Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 388 HIS Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 654 ILE Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 800 THR Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain B residue 849 ILE Chi-restraints excluded: chain B residue 873 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 68 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 33 optimal weight: 0.4980 chunk 109 optimal weight: 6.9990 chunk 116 optimal weight: 0.2980 chunk 84 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 134 optimal weight: 4.9990 chunk 156 optimal weight: 0.8980 chunk 164 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 14120 Z= 0.159 Angle : 0.582 13.738 19250 Z= 0.282 Chirality : 0.040 0.131 2281 Planarity : 0.004 0.055 2444 Dihedral : 5.125 64.183 1941 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.46 % Allowed : 14.06 % Favored : 83.48 % 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: 1.20 (0.21), residues: 1792 helix: 1.74 (0.18), residues: 962 sheet: 0.17 (0.44), residues: 136 loop : -0.37 (0.25), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 806 HIS 0.020 0.001 HIS B 76 PHE 0.014 0.001 PHE A 802 TYR 0.018 0.002 TYR B 698 ARG 0.003 0.000 ARG B 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 150 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 114 time to evaluate : 1.607 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8444 (tmm) cc_final: 0.8155 (tmm) REVERT: A 79 ASN cc_start: 0.7928 (t0) cc_final: 0.7133 (t0) REVERT: A 106 THR cc_start: 0.9283 (m) cc_final: 0.9047 (p) REVERT: A 299 MET cc_start: 0.8834 (mtp) cc_final: 0.8574 (ttm) REVERT: A 701 MET cc_start: 0.8089 (mmp) cc_final: 0.7856 (mmt) REVERT: A 725 MET cc_start: 0.8918 (tpp) cc_final: 0.8656 (tpp) REVERT: A 840 MET cc_start: 0.8671 (mmt) cc_final: 0.8049 (mmm) REVERT: B 79 ASN cc_start: 0.7838 (t0) cc_final: 0.7044 (t0) REVERT: B 104 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.9119 (tt) REVERT: B 106 THR cc_start: 0.9302 (m) cc_final: 0.9071 (p) REVERT: B 299 MET cc_start: 0.8804 (mtp) cc_final: 0.8601 (ttm) REVERT: B 840 MET cc_start: 0.9103 (mmm) cc_final: 0.8439 (mmm) outliers start: 36 outliers final: 26 residues processed: 139 average time/residue: 0.1943 time to fit residues: 45.2944 Evaluate side-chains 138 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 1.592 ------------------------------------------------------------------------------- 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 290 MET 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 654 ILE Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 838 MET Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 388 HIS Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 654 ILE Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 800 THR Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain B residue 873 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 149 optimal weight: 7.9990 chunk 159 optimal weight: 4.9990 chunk 164 optimal weight: 0.0570 chunk 96 optimal weight: 6.9990 chunk 69 optimal weight: 0.6980 chunk 125 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 151 optimal weight: 0.8980 chunk 104 optimal weight: 10.0000 chunk 169 optimal weight: 0.9990 overall best weight: 0.6900 ------------------------------------------------------------------------------- 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** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 734 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 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 0.048 14120 Z= 0.156 Angle : 0.594 13.252 19250 Z= 0.288 Chirality : 0.040 0.162 2281 Planarity : 0.004 0.055 2444 Dihedral : 5.045 62.495 1941 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.12 % Allowed : 14.61 % Favored : 83.28 % 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: 1.23 (0.21), residues: 1792 helix: 1.81 (0.18), residues: 940 sheet: 0.05 (0.42), residues: 146 loop : -0.33 (0.25), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 806 HIS 0.016 0.001 HIS B 76 PHE 0.014 0.001 PHE B 802 TYR 0.019 0.002 TYR B 698 ARG 0.001 0.000 ARG B 20 *********************** 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 144 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 113 time to evaluate : 1.677 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8489 (tmm) cc_final: 0.8189 (tmm) REVERT: A 79 ASN cc_start: 0.7932 (t0) cc_final: 0.7151 (t0) REVERT: A 106 THR cc_start: 0.9273 (m) cc_final: 0.9040 (p) REVERT: A 127 MET cc_start: 0.8598 (mmp) cc_final: 0.8353 (tpt) REVERT: A 299 MET cc_start: 0.8810 (mtp) cc_final: 0.8569 (ttm) REVERT: A 725 MET cc_start: 0.8918 (tpp) cc_final: 0.8687 (tpp) REVERT: A 840 MET cc_start: 0.8673 (mmt) cc_final: 0.7873 (mmm) REVERT: B 79 ASN cc_start: 0.7896 (t0) cc_final: 0.7087 (t0) REVERT: B 104 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.9129 (tt) REVERT: B 106 THR cc_start: 0.9295 (m) cc_final: 0.9066 (p) REVERT: B 254 MET cc_start: 0.8110 (tpp) cc_final: 0.7895 (tpp) REVERT: B 299 MET cc_start: 0.8835 (mtp) cc_final: 0.8585 (ttm) REVERT: B 840 MET cc_start: 0.9038 (mmm) cc_final: 0.8328 (mmm) outliers start: 31 outliers final: 26 residues processed: 135 average time/residue: 0.1911 time to fit residues: 43.5850 Evaluate side-chains 138 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 1.665 ------------------------------------------------------------------------------- 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 290 MET 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 654 ILE Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 838 MET Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 388 HIS Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 654 ILE Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 800 THR Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain B residue 838 MET 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 103 optimal weight: 0.9980 chunk 80 optimal weight: 6.9990 chunk 117 optimal weight: 0.1980 chunk 177 optimal weight: 0.9980 chunk 163 optimal weight: 4.9990 chunk 141 optimal weight: 7.9990 chunk 14 optimal weight: 0.9980 chunk 109 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 150 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14120 Z= 0.162 Angle : 0.605 13.065 19250 Z= 0.291 Chirality : 0.041 0.201 2281 Planarity : 0.004 0.055 2444 Dihedral : 4.951 61.312 1941 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.12 % Allowed : 14.61 % Favored : 83.28 % 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: 1.81 (0.18), residues: 942 sheet: 0.01 (0.39), residues: 166 loop : -0.29 (0.25), residues: 684 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 0.014 0.001 PHE A 802 TYR 0.019 0.002 TYR A 698 ARG 0.001 0.000 ARG A 451 ********************** 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 147 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 116 time to evaluate : 1.495 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 ASN cc_start: 0.7931 (t0) cc_final: 0.7140 (t0) REVERT: A 106 THR cc_start: 0.9275 (m) cc_final: 0.9056 (p) REVERT: A 299 MET cc_start: 0.8778 (mtp) cc_final: 0.8578 (ttm) REVERT: A 725 MET cc_start: 0.8931 (tpp) cc_final: 0.8698 (tpp) REVERT: A 840 MET cc_start: 0.8523 (mmt) cc_final: 0.7934 (mmm) REVERT: B 79 ASN cc_start: 0.7899 (t0) cc_final: 0.7078 (t0) REVERT: B 106 THR cc_start: 0.9303 (m) cc_final: 0.9066 (p) REVERT: B 242 MET cc_start: 0.8066 (mmm) cc_final: 0.7611 (mmm) REVERT: B 299 MET cc_start: 0.8855 (mtp) cc_final: 0.8566 (ttm) REVERT: B 636 VAL cc_start: 0.9592 (t) cc_final: 0.9364 (p) REVERT: B 840 MET cc_start: 0.9035 (mmm) cc_final: 0.8450 (mmm) outliers start: 31 outliers final: 25 residues processed: 138 average time/residue: 0.1937 time to fit residues: 44.5234 Evaluate side-chains 137 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 1.710 ------------------------------------------------------------------------------- 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 290 MET 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 654 ILE Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 800 THR Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 388 HIS Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 654 ILE Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 800 THR Chi-restraints excluded: chain B residue 838 MET 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 43 optimal weight: 4.9990 chunk 130 optimal weight: 0.0970 chunk 20 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 141 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 145 optimal weight: 6.9990 chunk 17 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.058980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.047160 restraints weight = 65570.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.048663 restraints weight = 34898.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.049676 restraints weight = 23053.467| |-----------------------------------------------------------------------------| r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 14120 Z= 0.156 Angle : 0.602 12.746 19250 Z= 0.290 Chirality : 0.041 0.195 2281 Planarity : 0.004 0.055 2444 Dihedral : 4.852 58.527 1941 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.77 % Allowed : 15.22 % Favored : 83.00 % 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: 1.90 (0.18), residues: 930 sheet: 0.12 (0.42), residues: 146 loop : -0.37 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 835 HIS 0.013 0.001 HIS B 76 PHE 0.014 0.001 PHE A 802 TYR 0.019 0.002 TYR B 698 ARG 0.002 0.000 ARG A 767 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2484.64 seconds wall clock time: 46 minutes 39.45 seconds (2799.45 seconds total)