Starting phenix.real_space_refine on Fri Oct 11 12:59:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b6g_44258/10_2024/9b6g_44258_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b6g_44258/10_2024/9b6g_44258.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b6g_44258/10_2024/9b6g_44258.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b6g_44258/10_2024/9b6g_44258.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b6g_44258/10_2024/9b6g_44258_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b6g_44258/10_2024/9b6g_44258_trim.cif" } resolution = 2.81 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= 0.002 sd= 0.050 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 116 5.16 5 C 18840 2.51 5 N 4564 2.21 5 O 4964 1.98 5 H 25668 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.85s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 54152 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 13321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 915, 13321 Classifications: {'peptide': 915} Link IDs: {'PTRANS': 22, 'TRANS': 892} Chain breaks: 10 Unresolved non-hydrogen bonds: 577 Unresolved non-hydrogen angles: 709 Unresolved non-hydrogen dihedrals: 463 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 12, 'ASP:plan': 16, 'PHE:plan': 4, 'GLU:plan': 25, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 338 Chain: "B" Number of atoms: 13321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 915, 13321 Classifications: {'peptide': 915} Link IDs: {'PTRANS': 22, 'TRANS': 892} Chain breaks: 10 Unresolved non-hydrogen bonds: 577 Unresolved non-hydrogen angles: 709 Unresolved non-hydrogen dihedrals: 463 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 12, 'ASP:plan': 16, 'PHE:plan': 4, 'GLU:plan': 25, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 338 Chain: "C" Number of atoms: 13321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 915, 13321 Classifications: {'peptide': 915} Link IDs: {'PTRANS': 22, 'TRANS': 892} Chain breaks: 10 Unresolved non-hydrogen bonds: 577 Unresolved non-hydrogen angles: 709 Unresolved non-hydrogen dihedrals: 463 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 12, 'ASP:plan': 16, 'PHE:plan': 4, 'GLU:plan': 25, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 338 Chain: "D" Number of atoms: 13321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 915, 13321 Classifications: {'peptide': 915} Link IDs: {'PTRANS': 22, 'TRANS': 892} Chain breaks: 10 Unresolved non-hydrogen bonds: 577 Unresolved non-hydrogen angles: 709 Unresolved non-hydrogen dihedrals: 463 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 12, 'ASP:plan': 16, 'PHE:plan': 4, 'GLU:plan': 25, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 338 Chain: "A" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 217 Unusual residues: {'LQ7': 1, 'NAG': 1, 'Y01': 5} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 217 Unusual residues: {'LQ7': 1, 'NAG': 1, 'Y01': 5} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 217 Unusual residues: {'LQ7': 1, 'NAG': 1, 'Y01': 5} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 217 Unusual residues: {'LQ7': 1, 'NAG': 1, 'Y01': 5} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 19.36, per 1000 atoms: 0.36 Number of scatterers: 54152 At special positions: 0 Unit cell: (150.12, 150.12, 157.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 116 16.00 O 4964 8.00 N 4564 7.00 C 18840 6.00 H 25668 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 303 " - pdb=" SG CYS A 326 " distance=2.04 Simple disulfide: pdb=" SG CYS A 929 " - pdb=" SG CYS A 940 " distance=2.03 Simple disulfide: pdb=" SG CYS B 303 " - pdb=" SG CYS B 326 " distance=2.04 Simple disulfide: pdb=" SG CYS B 929 " - pdb=" SG CYS B 940 " distance=2.03 Simple disulfide: pdb=" SG CYS C 303 " - pdb=" SG CYS C 326 " distance=2.04 Simple disulfide: pdb=" SG CYS C 929 " - pdb=" SG CYS C 940 " distance=2.03 Simple disulfide: pdb=" SG CYS D 303 " - pdb=" SG CYS D 326 " distance=2.04 Simple disulfide: pdb=" SG CYS D 929 " - pdb=" SG CYS D 940 " distance=2.03 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: 10.75 Conformation dependent library (CDL) restraints added in 3.6 seconds 7144 Ramachandran restraints generated. 3572 Oldfield, 0 Emsley, 3572 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6984 Finding SS restraints... Secondary structure from input PDB file: 200 helices and 8 sheets defined 73.6% alpha, 1.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.38 Creating SS restraints... Processing helix chain 'A' and resid 40 through 49 removed outlier: 3.661A pdb=" N ALA A 47 " --> pdb=" O ASN A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 137 Processing helix chain 'A' and resid 158 through 176 Processing helix chain 'A' and resid 187 through 202 Processing helix chain 'A' and resid 276 through 288 Processing helix chain 'A' and resid 294 through 298 Processing helix chain 'A' and resid 309 through 322 removed outlier: 3.611A pdb=" N LEU A 313 " --> pdb=" O GLY A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 343 Processing helix chain 'A' and resid 351 through 362 Processing helix chain 'A' and resid 362 through 369 Processing helix chain 'A' and resid 370 through 387 removed outlier: 3.689A pdb=" N GLU A 375 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N SER A 387 " --> pdb=" O GLU A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 419 Processing helix chain 'A' and resid 425 through 436 removed outlier: 3.941A pdb=" N TRP A 436 " --> pdb=" O LEU A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 446 removed outlier: 3.789A pdb=" N ALA A 442 " --> pdb=" O GLN A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 457 No H-bonds generated for 'chain 'A' and resid 455 through 457' Processing helix chain 'A' and resid 458 through 469 removed outlier: 3.515A pdb=" N ASP A 469 " --> pdb=" O ALA A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 480 removed outlier: 3.533A pdb=" N VAL A 474 " --> pdb=" O ARG A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 488 Processing helix chain 'A' and resid 489 through 499 Processing helix chain 'A' and resid 502 through 516 Processing helix chain 'A' and resid 520 through 533 Processing helix chain 'A' and resid 559 through 571 removed outlier: 3.762A pdb=" N GLN A 571 " --> pdb=" O TRP A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 582 Processing helix chain 'A' and resid 586 through 605 removed outlier: 3.507A pdb=" N VAL A 604 " --> pdb=" O THR A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 634 removed outlier: 3.723A pdb=" N GLY A 612 " --> pdb=" O ILE A 608 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU A 613 " --> pdb=" O ASN A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 646 Processing helix chain 'A' and resid 655 through 663 Processing helix chain 'A' and resid 665 through 671 removed outlier: 3.505A pdb=" N ILE A 669 " --> pdb=" O ASP A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 684 Processing helix chain 'A' and resid 691 through 701 removed outlier: 3.653A pdb=" N PHE A 700 " --> pdb=" O ILE A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 706 Processing helix chain 'A' and resid 725 through 732 Processing helix chain 'A' and resid 733 through 759 Processing helix chain 'A' and resid 765 through 789 removed outlier: 3.579A pdb=" N VAL A 777 " --> pdb=" O ALA A 773 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A 778 " --> pdb=" O LEU A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 795 Processing helix chain 'A' and resid 796 through 817 removed outlier: 3.639A pdb=" N VAL A 800 " --> pdb=" O ASP A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 841 removed outlier: 3.550A pdb=" N LEU A 825 " --> pdb=" O ASN A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 847 Processing helix chain 'A' and resid 853 through 861 removed outlier: 3.867A pdb=" N GLN A 861 " --> pdb=" O ILE A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 890 removed outlier: 3.624A pdb=" N VAL A 867 " --> pdb=" O MET A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 904 Processing helix chain 'A' and resid 904 through 910 Processing helix chain 'A' and resid 911 through 913 No H-bonds generated for 'chain 'A' and resid 911 through 913' Processing helix chain 'A' and resid 952 through 969 removed outlier: 3.626A pdb=" N THR A 956 " --> pdb=" O PRO A 952 " (cutoff:3.500A) Proline residue: A 958 - end of helix removed outlier: 3.799A pdb=" N ILE A 969 " --> pdb=" O LEU A 965 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 987 Processing helix chain 'A' and resid 989 through 1008 Processing helix chain 'A' and resid 1012 through 1014 No H-bonds generated for 'chain 'A' and resid 1012 through 1014' Processing helix chain 'A' and resid 1015 through 1027 removed outlier: 4.400A pdb=" N ALA A1019 " --> pdb=" O PHE A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1051 through 1073 Processing helix chain 'A' and resid 1076 through 1104 removed outlier: 4.236A pdb=" N HIS A1080 " --> pdb=" O GLU A1076 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 49 removed outlier: 3.661A pdb=" N ALA B 47 " --> pdb=" O ASN B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 137 Processing helix chain 'B' and resid 158 through 176 Processing helix chain 'B' and resid 187 through 202 Processing helix chain 'B' and resid 276 through 288 Processing helix chain 'B' and resid 294 through 298 Processing helix chain 'B' and resid 309 through 322 removed outlier: 3.611A pdb=" N LEU B 313 " --> pdb=" O GLY B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 343 Processing helix chain 'B' and resid 351 through 362 Processing helix chain 'B' and resid 362 through 369 Processing helix chain 'B' and resid 370 through 387 removed outlier: 3.689A pdb=" N GLU B 375 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N SER B 387 " --> pdb=" O GLU B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 419 Processing helix chain 'B' and resid 425 through 436 removed outlier: 3.941A pdb=" N TRP B 436 " --> pdb=" O LEU B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 446 removed outlier: 3.790A pdb=" N ALA B 442 " --> pdb=" O GLN B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 457 No H-bonds generated for 'chain 'B' and resid 455 through 457' Processing helix chain 'B' and resid 458 through 469 removed outlier: 3.515A pdb=" N ASP B 469 " --> pdb=" O ALA B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 480 removed outlier: 3.533A pdb=" N VAL B 474 " --> pdb=" O ARG B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 488 Processing helix chain 'B' and resid 489 through 499 Processing helix chain 'B' and resid 502 through 516 Processing helix chain 'B' and resid 520 through 533 Processing helix chain 'B' and resid 559 through 571 removed outlier: 3.761A pdb=" N GLN B 571 " --> pdb=" O TRP B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 582 Processing helix chain 'B' and resid 586 through 605 removed outlier: 3.507A pdb=" N VAL B 604 " --> pdb=" O THR B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 634 removed outlier: 3.723A pdb=" N GLY B 612 " --> pdb=" O ILE B 608 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU B 613 " --> pdb=" O ASN B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 646 Processing helix chain 'B' and resid 655 through 663 Processing helix chain 'B' and resid 665 through 671 removed outlier: 3.505A pdb=" N ILE B 669 " --> pdb=" O ASP B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 684 Processing helix chain 'B' and resid 691 through 701 removed outlier: 3.654A pdb=" N PHE B 700 " --> pdb=" O ILE B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 706 Processing helix chain 'B' and resid 725 through 732 Processing helix chain 'B' and resid 733 through 759 Processing helix chain 'B' and resid 765 through 789 removed outlier: 3.579A pdb=" N VAL B 777 " --> pdb=" O ALA B 773 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU B 778 " --> pdb=" O LEU B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 790 through 795 Processing helix chain 'B' and resid 796 through 817 removed outlier: 3.639A pdb=" N VAL B 800 " --> pdb=" O ASP B 796 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 841 removed outlier: 3.550A pdb=" N LEU B 825 " --> pdb=" O ASN B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 847 Processing helix chain 'B' and resid 853 through 861 removed outlier: 3.866A pdb=" N GLN B 861 " --> pdb=" O ILE B 857 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 890 removed outlier: 3.624A pdb=" N VAL B 867 " --> pdb=" O MET B 863 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 904 Processing helix chain 'B' and resid 904 through 910 Processing helix chain 'B' and resid 911 through 913 No H-bonds generated for 'chain 'B' and resid 911 through 913' Processing helix chain 'B' and resid 952 through 969 removed outlier: 3.625A pdb=" N THR B 956 " --> pdb=" O PRO B 952 " (cutoff:3.500A) Proline residue: B 958 - end of helix removed outlier: 3.799A pdb=" N ILE B 969 " --> pdb=" O LEU B 965 " (cutoff:3.500A) Processing helix chain 'B' and resid 969 through 987 Processing helix chain 'B' and resid 989 through 1008 Processing helix chain 'B' and resid 1012 through 1014 No H-bonds generated for 'chain 'B' and resid 1012 through 1014' Processing helix chain 'B' and resid 1015 through 1027 removed outlier: 4.400A pdb=" N ALA B1019 " --> pdb=" O PHE B1015 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1073 Processing helix chain 'B' and resid 1076 through 1104 removed outlier: 4.235A pdb=" N HIS B1080 " --> pdb=" O GLU B1076 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 49 removed outlier: 3.662A pdb=" N ALA C 47 " --> pdb=" O ASN C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 137 Processing helix chain 'C' and resid 158 through 176 Processing helix chain 'C' and resid 187 through 202 Processing helix chain 'C' and resid 276 through 288 Processing helix chain 'C' and resid 294 through 298 Processing helix chain 'C' and resid 309 through 322 removed outlier: 3.611A pdb=" N LEU C 313 " --> pdb=" O GLY C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 343 Processing helix chain 'C' and resid 351 through 362 Processing helix chain 'C' and resid 362 through 369 Processing helix chain 'C' and resid 370 through 387 removed outlier: 3.689A pdb=" N GLU C 375 " --> pdb=" O GLU C 371 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N SER C 387 " --> pdb=" O GLU C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 419 Processing helix chain 'C' and resid 425 through 436 removed outlier: 3.941A pdb=" N TRP C 436 " --> pdb=" O LEU C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 446 removed outlier: 3.789A pdb=" N ALA C 442 " --> pdb=" O GLN C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 457 No H-bonds generated for 'chain 'C' and resid 455 through 457' Processing helix chain 'C' and resid 458 through 469 removed outlier: 3.516A pdb=" N ASP C 469 " --> pdb=" O ALA C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 480 removed outlier: 3.533A pdb=" N VAL C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 488 Processing helix chain 'C' and resid 489 through 499 Processing helix chain 'C' and resid 502 through 516 Processing helix chain 'C' and resid 520 through 533 Processing helix chain 'C' and resid 559 through 571 removed outlier: 3.762A pdb=" N GLN C 571 " --> pdb=" O TRP C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 582 Processing helix chain 'C' and resid 586 through 605 removed outlier: 3.507A pdb=" N VAL C 604 " --> pdb=" O THR C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 634 removed outlier: 3.723A pdb=" N GLY C 612 " --> pdb=" O ILE C 608 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU C 613 " --> pdb=" O ASN C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 646 Processing helix chain 'C' and resid 655 through 663 Processing helix chain 'C' and resid 665 through 671 removed outlier: 3.505A pdb=" N ILE C 669 " --> pdb=" O ASP C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 684 Processing helix chain 'C' and resid 691 through 701 removed outlier: 3.654A pdb=" N PHE C 700 " --> pdb=" O ILE C 696 " (cutoff:3.500A) Processing helix chain 'C' and resid 702 through 706 Processing helix chain 'C' and resid 725 through 732 Processing helix chain 'C' and resid 733 through 759 Processing helix chain 'C' and resid 765 through 789 removed outlier: 3.579A pdb=" N VAL C 777 " --> pdb=" O ALA C 773 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU C 778 " --> pdb=" O LEU C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 790 through 795 Processing helix chain 'C' and resid 796 through 817 removed outlier: 3.639A pdb=" N VAL C 800 " --> pdb=" O ASP C 796 " (cutoff:3.500A) Processing helix chain 'C' and resid 821 through 841 removed outlier: 3.550A pdb=" N LEU C 825 " --> pdb=" O ASN C 821 " (cutoff:3.500A) Processing helix chain 'C' and resid 842 through 847 Processing helix chain 'C' and resid 853 through 861 removed outlier: 3.867A pdb=" N GLN C 861 " --> pdb=" O ILE C 857 " (cutoff:3.500A) Processing helix chain 'C' and resid 863 through 890 removed outlier: 3.624A pdb=" N VAL C 867 " --> pdb=" O MET C 863 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 904 Processing helix chain 'C' and resid 904 through 910 Processing helix chain 'C' and resid 911 through 913 No H-bonds generated for 'chain 'C' and resid 911 through 913' Processing helix chain 'C' and resid 952 through 969 removed outlier: 3.626A pdb=" N THR C 956 " --> pdb=" O PRO C 952 " (cutoff:3.500A) Proline residue: C 958 - end of helix removed outlier: 3.799A pdb=" N ILE C 969 " --> pdb=" O LEU C 965 " (cutoff:3.500A) Processing helix chain 'C' and resid 969 through 987 Processing helix chain 'C' and resid 989 through 1008 Processing helix chain 'C' and resid 1012 through 1014 No H-bonds generated for 'chain 'C' and resid 1012 through 1014' Processing helix chain 'C' and resid 1015 through 1027 removed outlier: 4.401A pdb=" N ALA C1019 " --> pdb=" O PHE C1015 " (cutoff:3.500A) Processing helix chain 'C' and resid 1051 through 1073 Processing helix chain 'C' and resid 1076 through 1104 removed outlier: 4.235A pdb=" N HIS C1080 " --> pdb=" O GLU C1076 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 49 removed outlier: 3.661A pdb=" N ALA D 47 " --> pdb=" O ASN D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 137 Processing helix chain 'D' and resid 158 through 176 Processing helix chain 'D' and resid 187 through 202 Processing helix chain 'D' and resid 276 through 288 Processing helix chain 'D' and resid 294 through 298 Processing helix chain 'D' and resid 309 through 322 removed outlier: 3.611A pdb=" N LEU D 313 " --> pdb=" O GLY D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 343 Processing helix chain 'D' and resid 351 through 362 Processing helix chain 'D' and resid 362 through 369 Processing helix chain 'D' and resid 370 through 387 removed outlier: 3.689A pdb=" N GLU D 375 " --> pdb=" O GLU D 371 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N SER D 387 " --> pdb=" O GLU D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 419 Processing helix chain 'D' and resid 425 through 436 removed outlier: 3.941A pdb=" N TRP D 436 " --> pdb=" O LEU D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 446 removed outlier: 3.790A pdb=" N ALA D 442 " --> pdb=" O GLN D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 457 No H-bonds generated for 'chain 'D' and resid 455 through 457' Processing helix chain 'D' and resid 458 through 469 removed outlier: 3.515A pdb=" N ASP D 469 " --> pdb=" O ALA D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 480 removed outlier: 3.533A pdb=" N VAL D 474 " --> pdb=" O ARG D 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 488 Processing helix chain 'D' and resid 489 through 499 Processing helix chain 'D' and resid 502 through 516 Processing helix chain 'D' and resid 520 through 533 Processing helix chain 'D' and resid 559 through 571 removed outlier: 3.761A pdb=" N GLN D 571 " --> pdb=" O TRP D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 582 Processing helix chain 'D' and resid 586 through 605 removed outlier: 3.507A pdb=" N VAL D 604 " --> pdb=" O THR D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 634 removed outlier: 3.723A pdb=" N GLY D 612 " --> pdb=" O ILE D 608 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU D 613 " --> pdb=" O ASN D 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 646 Processing helix chain 'D' and resid 655 through 663 Processing helix chain 'D' and resid 665 through 671 removed outlier: 3.505A pdb=" N ILE D 669 " --> pdb=" O ASP D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 671 through 684 Processing helix chain 'D' and resid 691 through 701 removed outlier: 3.654A pdb=" N PHE D 700 " --> pdb=" O ILE D 696 " (cutoff:3.500A) Processing helix chain 'D' and resid 702 through 706 Processing helix chain 'D' and resid 725 through 732 Processing helix chain 'D' and resid 733 through 759 Processing helix chain 'D' and resid 765 through 789 removed outlier: 3.579A pdb=" N VAL D 777 " --> pdb=" O ALA D 773 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU D 778 " --> pdb=" O LEU D 774 " (cutoff:3.500A) Processing helix chain 'D' and resid 790 through 795 Processing helix chain 'D' and resid 796 through 817 removed outlier: 3.639A pdb=" N VAL D 800 " --> pdb=" O ASP D 796 " (cutoff:3.500A) Processing helix chain 'D' and resid 821 through 841 removed outlier: 3.550A pdb=" N LEU D 825 " --> pdb=" O ASN D 821 " (cutoff:3.500A) Processing helix chain 'D' and resid 842 through 847 Processing helix chain 'D' and resid 853 through 861 removed outlier: 3.866A pdb=" N GLN D 861 " --> pdb=" O ILE D 857 " (cutoff:3.500A) Processing helix chain 'D' and resid 863 through 890 removed outlier: 3.624A pdb=" N VAL D 867 " --> pdb=" O MET D 863 " (cutoff:3.500A) Processing helix chain 'D' and resid 895 through 904 Processing helix chain 'D' and resid 904 through 910 Processing helix chain 'D' and resid 911 through 913 No H-bonds generated for 'chain 'D' and resid 911 through 913' Processing helix chain 'D' and resid 952 through 969 removed outlier: 3.625A pdb=" N THR D 956 " --> pdb=" O PRO D 952 " (cutoff:3.500A) Proline residue: D 958 - end of helix removed outlier: 3.799A pdb=" N ILE D 969 " --> pdb=" O LEU D 965 " (cutoff:3.500A) Processing helix chain 'D' and resid 969 through 987 Processing helix chain 'D' and resid 989 through 1008 Processing helix chain 'D' and resid 1012 through 1014 No H-bonds generated for 'chain 'D' and resid 1012 through 1014' Processing helix chain 'D' and resid 1015 through 1027 removed outlier: 4.401A pdb=" N ALA D1019 " --> pdb=" O PHE D1015 " (cutoff:3.500A) Processing helix chain 'D' and resid 1051 through 1073 Processing helix chain 'D' and resid 1076 through 1104 removed outlier: 4.235A pdb=" N HIS D1080 " --> pdb=" O GLU D1076 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 178 through 180 removed outlier: 3.527A pdb=" N LEU A 180 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N PHE A 304 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ILE A 146 " --> pdb=" O PHE A 304 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N CYS A 303 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 8.536A pdb=" N VAL A 329 " --> pdb=" O CYS A 303 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ALA A 305 " --> pdb=" O VAL A 329 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N CYS A 326 " --> pdb=" O THR A 392 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N ILE A 394 " --> pdb=" O CYS A 326 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N VAL A 328 " --> pdb=" O ILE A 394 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 214 through 216 Processing sheet with id=AA3, first strand: chain 'B' and resid 178 through 180 removed outlier: 3.527A pdb=" N LEU B 180 " --> pdb=" O VAL B 145 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N PHE B 304 " --> pdb=" O LEU B 144 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ILE B 146 " --> pdb=" O PHE B 304 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N CYS B 303 " --> pdb=" O VAL B 327 " (cutoff:3.500A) removed outlier: 8.536A pdb=" N VAL B 329 " --> pdb=" O CYS B 303 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ALA B 305 " --> pdb=" O VAL B 329 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N CYS B 326 " --> pdb=" O THR B 392 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N ILE B 394 " --> pdb=" O CYS B 326 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N VAL B 328 " --> pdb=" O ILE B 394 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 214 through 216 Processing sheet with id=AA5, first strand: chain 'C' and resid 178 through 180 removed outlier: 3.528A pdb=" N LEU C 180 " --> pdb=" O VAL C 145 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N PHE C 304 " --> pdb=" O LEU C 144 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ILE C 146 " --> pdb=" O PHE C 304 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N CYS C 303 " --> pdb=" O VAL C 327 " (cutoff:3.500A) removed outlier: 8.536A pdb=" N VAL C 329 " --> pdb=" O CYS C 303 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N ALA C 305 " --> pdb=" O VAL C 329 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N CYS C 326 " --> pdb=" O THR C 392 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N ILE C 394 " --> pdb=" O CYS C 326 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N VAL C 328 " --> pdb=" O ILE C 394 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 214 through 216 Processing sheet with id=AA7, first strand: chain 'D' and resid 178 through 180 removed outlier: 3.527A pdb=" N LEU D 180 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N PHE D 304 " --> pdb=" O LEU D 144 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ILE D 146 " --> pdb=" O PHE D 304 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N CYS D 303 " --> pdb=" O VAL D 327 " (cutoff:3.500A) removed outlier: 8.536A pdb=" N VAL D 329 " --> pdb=" O CYS D 303 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ALA D 305 " --> pdb=" O VAL D 329 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N CYS D 326 " --> pdb=" O THR D 392 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N ILE D 394 " --> pdb=" O CYS D 326 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N VAL D 328 " --> pdb=" O ILE D 394 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 214 through 216 1825 hydrogen bonds defined for protein. 5391 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: 19.41 Time building geometry restraints manager: 13.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 25624 1.03 - 1.23: 421 1.23 - 1.43: 12011 1.43 - 1.62: 16652 1.62 - 1.82: 168 Bond restraints: 54876 Sorted by residual: bond pdb=" ND2 ASN A 947 " pdb="HD21 ASN A 947 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.63e+01 bond pdb=" ND2 ASN B 947 " pdb="HD21 ASN B 947 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.63e+01 bond pdb=" ND2 ASN C 947 " pdb="HD21 ASN C 947 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.63e+01 bond pdb=" ND2 ASN D 947 " pdb="HD21 ASN D 947 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.63e+01 bond pdb=" ND2 ASN C 947 " pdb="HD22 ASN C 947 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.58e+01 ... (remaining 54871 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 97406 2.66 - 5.31: 626 5.31 - 7.97: 100 7.97 - 10.62: 52 10.62 - 13.28: 20 Bond angle restraints: 98204 Sorted by residual: angle pdb=" N ARG A 950 " pdb=" CA ARG A 950 " pdb=" C ARG A 950 " ideal model delta sigma weight residual 113.23 118.98 -5.75 1.24e+00 6.50e-01 2.15e+01 angle pdb=" N ARG D 950 " pdb=" CA ARG D 950 " pdb=" C ARG D 950 " ideal model delta sigma weight residual 113.23 118.98 -5.75 1.24e+00 6.50e-01 2.15e+01 angle pdb=" N ARG B 950 " pdb=" CA ARG B 950 " pdb=" C ARG B 950 " ideal model delta sigma weight residual 113.23 118.98 -5.75 1.24e+00 6.50e-01 2.15e+01 angle pdb=" N ARG C 950 " pdb=" CA ARG C 950 " pdb=" C ARG C 950 " ideal model delta sigma weight residual 113.23 118.98 -5.75 1.24e+00 6.50e-01 2.15e+01 angle pdb=" CAT Y01 D1203 " pdb=" CBH Y01 D1203 " pdb=" CBF Y01 D1203 " ideal model delta sigma weight residual 108.46 95.18 13.28 3.00e+00 1.11e-01 1.96e+01 ... (remaining 98199 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.01: 25353 17.01 - 34.02: 1367 34.02 - 51.02: 396 51.02 - 68.03: 188 68.03 - 85.04: 20 Dihedral angle restraints: 27324 sinusoidal: 14160 harmonic: 13164 Sorted by residual: dihedral pdb=" SG CYS C 303 " pdb=" CB CYS C 326 " pdb=" SG CYS C 326 " pdb=" CA CYS C 326 " ideal model delta sinusoidal sigma weight residual -73.00 -0.97 -72.03 1 2.00e+01 2.50e-03 1.66e+01 dihedral pdb=" SG CYS B 303 " pdb=" CB CYS B 326 " pdb=" SG CYS B 326 " pdb=" CA CYS B 326 " ideal model delta sinusoidal sigma weight residual -73.00 -1.00 -72.00 1 2.00e+01 2.50e-03 1.66e+01 dihedral pdb=" SG CYS D 303 " pdb=" CB CYS D 326 " pdb=" SG CYS D 326 " pdb=" CA CYS D 326 " ideal model delta sinusoidal sigma weight residual -73.00 -1.00 -72.00 1 2.00e+01 2.50e-03 1.66e+01 ... (remaining 27321 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 4378 0.085 - 0.169: 214 0.169 - 0.254: 27 0.254 - 0.338: 25 0.338 - 0.423: 44 Chirality restraints: 4688 Sorted by residual: chirality pdb=" CBH Y01 C1201 " pdb=" CAT Y01 C1201 " pdb=" CAZ Y01 C1201 " pdb=" CBF Y01 C1201 " both_signs ideal model delta sigma weight residual False -2.85 -3.28 0.42 2.00e-01 2.50e+01 4.47e+00 chirality pdb=" CBH Y01 A1201 " pdb=" CAT Y01 A1201 " pdb=" CAZ Y01 A1201 " pdb=" CBF Y01 A1201 " both_signs ideal model delta sigma weight residual False -2.85 -3.27 0.42 2.00e-01 2.50e+01 4.42e+00 chirality pdb=" CBF Y01 D1203 " pdb=" CAS Y01 D1203 " pdb=" CBD Y01 D1203 " pdb=" CBH Y01 D1203 " both_signs ideal model delta sigma weight residual False -2.45 -2.86 0.42 2.00e-01 2.50e+01 4.39e+00 ... (remaining 4685 not shown) Planarity restraints: 8400 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 947 " -0.259 2.00e-02 2.50e+03 2.67e-01 1.07e+03 pdb=" CG ASN C 947 " 0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN C 947 " 0.243 2.00e-02 2.50e+03 pdb=" ND2 ASN C 947 " 0.002 2.00e-02 2.50e+03 pdb="HD21 ASN C 947 " -0.395 2.00e-02 2.50e+03 pdb="HD22 ASN C 947 " 0.382 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 947 " -0.259 2.00e-02 2.50e+03 2.67e-01 1.07e+03 pdb=" CG ASN D 947 " 0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN D 947 " 0.243 2.00e-02 2.50e+03 pdb=" ND2 ASN D 947 " 0.002 2.00e-02 2.50e+03 pdb="HD21 ASN D 947 " -0.395 2.00e-02 2.50e+03 pdb="HD22 ASN D 947 " 0.382 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 947 " -0.259 2.00e-02 2.50e+03 2.67e-01 1.07e+03 pdb=" CG ASN B 947 " 0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN B 947 " 0.243 2.00e-02 2.50e+03 pdb=" ND2 ASN B 947 " 0.002 2.00e-02 2.50e+03 pdb="HD21 ASN B 947 " -0.395 2.00e-02 2.50e+03 pdb="HD22 ASN B 947 " 0.382 2.00e-02 2.50e+03 ... (remaining 8397 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.21: 3014 2.21 - 2.81: 108277 2.81 - 3.41: 140847 3.41 - 4.00: 178519 4.00 - 4.60: 284977 Nonbonded interactions: 715634 Sorted by model distance: nonbonded pdb=" OG SER C 679 " pdb="HH22 ARG C 998 " model vdw 1.618 2.450 nonbonded pdb=" OG SER B 679 " pdb="HH22 ARG B 998 " model vdw 1.619 2.450 nonbonded pdb=" OG SER D 679 " pdb="HH22 ARG D 998 " model vdw 1.619 2.450 nonbonded pdb=" OG SER A 679 " pdb="HH22 ARG A 998 " model vdw 1.619 2.450 nonbonded pdb=" OE1 GLN C 666 " pdb="HE22 GLN C 992 " model vdw 1.650 2.450 ... (remaining 715629 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.580 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: 0.760 Extract box with map and model: 1.520 Check model and map are aligned: 0.310 Set scattering table: 0.380 Process input model: 86.710 Find NCS groups from input model: 1.670 Set up NCS constraints: 0.200 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: 0.020 Load rotamer database and sin/cos tables:11.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 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 : 0.007 0.117 29208 Z= 0.437 Angle : 0.821 13.275 39956 Z= 0.347 Chirality : 0.059 0.423 4688 Planarity : 0.003 0.074 4876 Dihedral : 11.769 85.038 10816 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.15 % Allowed : 6.52 % Favored : 93.33 % 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: 2.73 (0.15), residues: 3572 helix: 2.95 (0.11), residues: 2420 sheet: -2.00 (0.35), residues: 184 loop : -0.45 (0.20), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 954 HIS 0.004 0.001 HIS B 136 PHE 0.010 0.001 PHE D 869 TYR 0.007 0.001 TYR B 999 ARG 0.006 0.001 ARG A 950 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7144 Ramachandran restraints generated. 3572 Oldfield, 0 Emsley, 3572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7144 Ramachandran restraints generated. 3572 Oldfield, 0 Emsley, 3572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 374 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 573 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue LEU 1009 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 374 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 573 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue LEU 1009 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 374 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 573 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue LEU 1009 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 374 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 573 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue LEU 1009 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 506 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 502 time to evaluate : 3.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 ARG cc_start: 0.7256 (ttt180) cc_final: 0.6691 (ttm-80) REVERT: A 494 THR cc_start: 0.8607 (m) cc_final: 0.8395 (p) REVERT: A 527 LEU cc_start: 0.6721 (tt) cc_final: 0.6484 (tt) REVERT: A 680 LYS cc_start: 0.7770 (mttt) cc_final: 0.7058 (mptt) REVERT: A 947 ASN cc_start: 0.9015 (OUTLIER) cc_final: 0.8796 (m-40) REVERT: B 310 ARG cc_start: 0.7241 (ttt180) cc_final: 0.6686 (ttm-80) REVERT: B 494 THR cc_start: 0.8605 (m) cc_final: 0.8394 (p) REVERT: B 527 LEU cc_start: 0.6693 (tt) cc_final: 0.6453 (tt) REVERT: B 680 LYS cc_start: 0.7767 (mttt) cc_final: 0.7055 (mptt) REVERT: B 947 ASN cc_start: 0.9029 (OUTLIER) cc_final: 0.8798 (m-40) REVERT: C 310 ARG cc_start: 0.7243 (ttt180) cc_final: 0.6687 (ttm-80) REVERT: C 494 THR cc_start: 0.8603 (m) cc_final: 0.8393 (p) REVERT: C 527 LEU cc_start: 0.6695 (tt) cc_final: 0.6452 (tt) REVERT: C 680 LYS cc_start: 0.7768 (mttt) cc_final: 0.7056 (mptt) REVERT: C 947 ASN cc_start: 0.9027 (OUTLIER) cc_final: 0.8797 (m-40) REVERT: D 310 ARG cc_start: 0.7243 (ttt180) cc_final: 0.6686 (ttm-80) REVERT: D 494 THR cc_start: 0.8603 (m) cc_final: 0.8393 (p) REVERT: D 527 LEU cc_start: 0.6693 (tt) cc_final: 0.6451 (tt) REVERT: D 680 LYS cc_start: 0.7767 (mttt) cc_final: 0.7056 (mptt) REVERT: D 947 ASN cc_start: 0.9029 (OUTLIER) cc_final: 0.8797 (m-40) outliers start: 4 outliers final: 0 residues processed: 506 average time/residue: 1.5946 time to fit residues: 1008.8483 Evaluate side-chains 314 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 310 time to evaluate : 3.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 947 ASN Chi-restraints excluded: chain B residue 947 ASN Chi-restraints excluded: chain C residue 947 ASN Chi-restraints excluded: chain D residue 947 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 307 optimal weight: 5.9990 chunk 275 optimal weight: 20.0000 chunk 153 optimal weight: 3.9990 chunk 94 optimal weight: 9.9990 chunk 186 optimal weight: 0.3980 chunk 147 optimal weight: 0.7980 chunk 285 optimal weight: 6.9990 chunk 110 optimal weight: 0.4980 chunk 173 optimal weight: 1.9990 chunk 212 optimal weight: 7.9990 chunk 330 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN A 490 ASN A 947 ASN A 968 ASN B 199 ASN B 490 ASN B 947 ASN B 968 ASN C 199 ASN C 490 ASN C 947 ASN C 968 ASN D 199 ASN D 490 ASN D 947 ASN D 968 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 29208 Z= 0.184 Angle : 0.491 5.011 39956 Z= 0.258 Chirality : 0.036 0.157 4688 Planarity : 0.003 0.050 4876 Dihedral : 7.247 59.634 5396 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.55 % Allowed : 12.58 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.58 (0.14), residues: 3572 helix: 2.75 (0.10), residues: 2464 sheet: -2.16 (0.35), residues: 184 loop : -0.37 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 682 HIS 0.005 0.001 HIS C 136 PHE 0.011 0.001 PHE A 523 TYR 0.014 0.001 TYR B 186 ARG 0.002 0.000 ARG C 998 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7144 Ramachandran restraints generated. 3572 Oldfield, 0 Emsley, 3572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7144 Ramachandran restraints generated. 3572 Oldfield, 0 Emsley, 3572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 374 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 573 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue LEU 1009 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 374 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 573 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue LEU 1009 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 374 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 573 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue LEU 1009 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 374 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 573 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue LEU 1009 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 379 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 338 time to evaluate : 3.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 ARG cc_start: 0.7199 (ttt180) cc_final: 0.6616 (ttm-80) REVERT: A 494 THR cc_start: 0.8672 (m) cc_final: 0.8418 (p) REVERT: A 531 PHE cc_start: 0.7182 (m-80) cc_final: 0.6958 (m-80) REVERT: A 680 LYS cc_start: 0.7533 (mttt) cc_final: 0.6898 (mptt) REVERT: A 1000 PHE cc_start: 0.8266 (m-80) cc_final: 0.8014 (m-80) REVERT: A 1004 GLU cc_start: 0.7719 (tp30) cc_final: 0.7331 (pt0) REVERT: A 1020 TYR cc_start: 0.7563 (m-10) cc_final: 0.5929 (t80) REVERT: A 1061 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7383 (mp0) REVERT: B 310 ARG cc_start: 0.7182 (ttt180) cc_final: 0.6607 (ttm-80) REVERT: B 494 THR cc_start: 0.8671 (m) cc_final: 0.8419 (p) REVERT: B 531 PHE cc_start: 0.7180 (m-80) cc_final: 0.6960 (m-80) REVERT: B 680 LYS cc_start: 0.7525 (mttt) cc_final: 0.6883 (mptt) REVERT: B 1000 PHE cc_start: 0.8266 (m-80) cc_final: 0.8012 (m-80) REVERT: B 1004 GLU cc_start: 0.7724 (tp30) cc_final: 0.7330 (pt0) REVERT: B 1020 TYR cc_start: 0.7247 (m-10) cc_final: 0.5884 (t80) REVERT: B 1061 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7383 (mp0) REVERT: C 310 ARG cc_start: 0.7185 (ttt180) cc_final: 0.6610 (ttm-80) REVERT: C 494 THR cc_start: 0.8669 (m) cc_final: 0.8417 (p) REVERT: C 531 PHE cc_start: 0.7177 (m-80) cc_final: 0.6958 (m-80) REVERT: C 680 LYS cc_start: 0.7527 (mttt) cc_final: 0.6884 (mptt) REVERT: C 1000 PHE cc_start: 0.8266 (m-80) cc_final: 0.8014 (m-80) REVERT: C 1004 GLU cc_start: 0.7721 (tp30) cc_final: 0.7330 (pt0) REVERT: C 1020 TYR cc_start: 0.7248 (m-10) cc_final: 0.5885 (t80) REVERT: C 1061 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7382 (mp0) REVERT: D 310 ARG cc_start: 0.7183 (ttt180) cc_final: 0.6608 (ttm-80) REVERT: D 494 THR cc_start: 0.8669 (m) cc_final: 0.8417 (p) REVERT: D 531 PHE cc_start: 0.7183 (m-80) cc_final: 0.6963 (m-80) REVERT: D 680 LYS cc_start: 0.7527 (mttt) cc_final: 0.6884 (mptt) REVERT: D 1000 PHE cc_start: 0.8265 (m-80) cc_final: 0.8012 (m-80) REVERT: D 1004 GLU cc_start: 0.7723 (tp30) cc_final: 0.7330 (pt0) REVERT: D 1020 TYR cc_start: 0.7247 (m-10) cc_final: 0.5883 (t80) REVERT: D 1061 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7383 (mp0) outliers start: 41 outliers final: 12 residues processed: 370 average time/residue: 1.7330 time to fit residues: 813.4390 Evaluate side-chains 320 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 308 time to evaluate : 3.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 1069 THR Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 1069 THR Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 1069 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 183 optimal weight: 20.0000 chunk 102 optimal weight: 8.9990 chunk 275 optimal weight: 0.0470 chunk 225 optimal weight: 2.9990 chunk 91 optimal weight: 20.0000 chunk 331 optimal weight: 1.9990 chunk 357 optimal weight: 3.9990 chunk 294 optimal weight: 9.9990 chunk 328 optimal weight: 6.9990 chunk 112 optimal weight: 10.0000 chunk 265 optimal weight: 3.9990 overall best weight: 2.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 29208 Z= 0.372 Angle : 0.567 7.435 39956 Z= 0.304 Chirality : 0.040 0.156 4688 Planarity : 0.004 0.059 4876 Dihedral : 7.536 59.985 5388 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.01 % Allowed : 12.95 % Favored : 85.04 % 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: 2.10 (0.14), residues: 3572 helix: 2.45 (0.10), residues: 2480 sheet: -2.57 (0.33), residues: 180 loop : -0.79 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 682 HIS 0.006 0.001 HIS A 185 PHE 0.018 0.002 PHE B 874 TYR 0.023 0.002 TYR A 186 ARG 0.004 0.001 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7144 Ramachandran restraints generated. 3572 Oldfield, 0 Emsley, 3572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7144 Ramachandran restraints generated. 3572 Oldfield, 0 Emsley, 3572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 374 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 573 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue LEU 1009 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 374 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 573 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue LEU 1009 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 374 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 573 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue LEU 1009 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 374 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 573 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue LEU 1009 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 378 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 325 time to evaluate : 3.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 ARG cc_start: 0.7201 (ttt180) cc_final: 0.6594 (ttm-80) REVERT: A 615 GLU cc_start: 0.8574 (pt0) cc_final: 0.8152 (mm-30) REVERT: A 658 GLU cc_start: 0.8259 (mp0) cc_final: 0.7842 (mp0) REVERT: A 680 LYS cc_start: 0.7524 (mttt) cc_final: 0.7004 (mptt) REVERT: A 1000 PHE cc_start: 0.8286 (m-80) cc_final: 0.7955 (m-80) REVERT: A 1006 CYS cc_start: 0.7768 (m) cc_final: 0.7486 (m) REVERT: A 1020 TYR cc_start: 0.7450 (m-10) cc_final: 0.6016 (t80) REVERT: A 1061 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7446 (mp0) REVERT: B 310 ARG cc_start: 0.7199 (ttt180) cc_final: 0.6586 (ttm-80) REVERT: B 615 GLU cc_start: 0.8539 (pt0) cc_final: 0.8136 (mm-30) REVERT: B 658 GLU cc_start: 0.8262 (mp0) cc_final: 0.7845 (mp0) REVERT: B 680 LYS cc_start: 0.7523 (mttt) cc_final: 0.7003 (mptt) REVERT: B 1000 PHE cc_start: 0.8285 (m-80) cc_final: 0.7954 (m-80) REVERT: B 1006 CYS cc_start: 0.7766 (m) cc_final: 0.7486 (m) REVERT: B 1020 TYR cc_start: 0.7404 (m-10) cc_final: 0.5989 (t80) REVERT: B 1061 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7445 (mp0) REVERT: C 310 ARG cc_start: 0.7204 (ttt180) cc_final: 0.6588 (ttm-80) REVERT: C 615 GLU cc_start: 0.8540 (pt0) cc_final: 0.8137 (mm-30) REVERT: C 658 GLU cc_start: 0.8260 (mp0) cc_final: 0.7844 (mp0) REVERT: C 680 LYS cc_start: 0.7524 (mttt) cc_final: 0.7003 (mptt) REVERT: C 1000 PHE cc_start: 0.8286 (m-80) cc_final: 0.7954 (m-80) REVERT: C 1006 CYS cc_start: 0.7767 (m) cc_final: 0.7488 (m) REVERT: C 1020 TYR cc_start: 0.7403 (m-10) cc_final: 0.5989 (t80) REVERT: C 1061 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7445 (mp0) REVERT: D 310 ARG cc_start: 0.7203 (ttt180) cc_final: 0.6588 (ttm-80) REVERT: D 615 GLU cc_start: 0.8539 (pt0) cc_final: 0.8137 (mm-30) REVERT: D 658 GLU cc_start: 0.8260 (mp0) cc_final: 0.7843 (mp0) REVERT: D 680 LYS cc_start: 0.7524 (mttt) cc_final: 0.7002 (mptt) REVERT: D 1000 PHE cc_start: 0.8286 (m-80) cc_final: 0.7954 (m-80) REVERT: D 1006 CYS cc_start: 0.7767 (m) cc_final: 0.7486 (m) REVERT: D 1020 TYR cc_start: 0.7401 (m-10) cc_final: 0.5988 (t80) REVERT: D 1061 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7448 (mp0) outliers start: 53 outliers final: 12 residues processed: 360 average time/residue: 1.6465 time to fit residues: 740.4935 Evaluate side-chains 325 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 313 time to evaluate : 3.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 ARG Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 288 ARG Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 288 ARG Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 288 ARG Chi-restraints excluded: chain D residue 329 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 327 optimal weight: 5.9990 chunk 248 optimal weight: 1.9990 chunk 171 optimal weight: 0.5980 chunk 36 optimal weight: 5.9990 chunk 158 optimal weight: 0.9980 chunk 222 optimal weight: 4.9990 chunk 332 optimal weight: 0.2980 chunk 351 optimal weight: 0.9990 chunk 173 optimal weight: 0.8980 chunk 314 optimal weight: 3.9990 chunk 94 optimal weight: 9.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 510 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 29208 Z= 0.152 Angle : 0.470 7.995 39956 Z= 0.251 Chirality : 0.036 0.165 4688 Planarity : 0.003 0.040 4876 Dihedral : 6.871 57.598 5388 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.67 % Allowed : 12.73 % Favored : 85.61 % 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: 2.45 (0.15), residues: 3572 helix: 2.69 (0.10), residues: 2484 sheet: -2.59 (0.32), residues: 180 loop : -0.53 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 682 HIS 0.005 0.001 HIS C 185 PHE 0.012 0.001 PHE A 165 TYR 0.013 0.001 TYR A 999 ARG 0.004 0.000 ARG C 197 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7144 Ramachandran restraints generated. 3572 Oldfield, 0 Emsley, 3572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7144 Ramachandran restraints generated. 3572 Oldfield, 0 Emsley, 3572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 374 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 573 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue LEU 1009 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 374 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 573 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue LEU 1009 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 374 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 573 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue LEU 1009 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 374 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 573 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue LEU 1009 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 372 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 328 time to evaluate : 3.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 ILE cc_start: 0.8211 (mp) cc_final: 0.8002 (mp) REVERT: A 310 ARG cc_start: 0.7131 (ttt180) cc_final: 0.6525 (ttm-80) REVERT: A 615 GLU cc_start: 0.8544 (pt0) cc_final: 0.8153 (mm-30) REVERT: A 658 GLU cc_start: 0.8346 (mp0) cc_final: 0.7869 (mp0) REVERT: A 680 LYS cc_start: 0.7494 (mttt) cc_final: 0.6999 (mptt) REVERT: A 1000 PHE cc_start: 0.8192 (m-80) cc_final: 0.7872 (m-80) REVERT: A 1006 CYS cc_start: 0.7655 (m) cc_final: 0.7427 (m) REVERT: A 1020 TYR cc_start: 0.7369 (m-10) cc_final: 0.5984 (t80) REVERT: A 1061 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7430 (mp0) REVERT: B 209 ILE cc_start: 0.8218 (mp) cc_final: 0.8017 (mp) REVERT: B 310 ARG cc_start: 0.7103 (ttt180) cc_final: 0.6526 (ttm-80) REVERT: B 615 GLU cc_start: 0.8516 (pt0) cc_final: 0.8126 (mm-30) REVERT: B 658 GLU cc_start: 0.8346 (mp0) cc_final: 0.7870 (mp0) REVERT: B 680 LYS cc_start: 0.7494 (mttt) cc_final: 0.6998 (mptt) REVERT: B 1000 PHE cc_start: 0.8190 (m-80) cc_final: 0.7870 (m-80) REVERT: B 1006 CYS cc_start: 0.7653 (m) cc_final: 0.7427 (m) REVERT: B 1020 TYR cc_start: 0.7370 (m-10) cc_final: 0.6007 (t80) REVERT: B 1061 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7429 (mp0) REVERT: C 209 ILE cc_start: 0.8217 (mp) cc_final: 0.8015 (mp) REVERT: C 310 ARG cc_start: 0.7104 (ttt180) cc_final: 0.6527 (ttm-80) REVERT: C 615 GLU cc_start: 0.8516 (pt0) cc_final: 0.8126 (mm-30) REVERT: C 658 GLU cc_start: 0.8345 (mp0) cc_final: 0.7869 (mp0) REVERT: C 680 LYS cc_start: 0.7495 (mttt) cc_final: 0.6999 (mptt) REVERT: C 1000 PHE cc_start: 0.8193 (m-80) cc_final: 0.7871 (m-80) REVERT: C 1006 CYS cc_start: 0.7650 (m) cc_final: 0.7424 (m) REVERT: C 1020 TYR cc_start: 0.7368 (m-10) cc_final: 0.6005 (t80) REVERT: C 1061 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7429 (mp0) REVERT: D 209 ILE cc_start: 0.8221 (mp) cc_final: 0.8019 (mp) REVERT: D 310 ARG cc_start: 0.7105 (ttt180) cc_final: 0.6528 (ttm-80) REVERT: D 615 GLU cc_start: 0.8515 (pt0) cc_final: 0.8126 (mm-30) REVERT: D 658 GLU cc_start: 0.8346 (mp0) cc_final: 0.7870 (mp0) REVERT: D 680 LYS cc_start: 0.7495 (mttt) cc_final: 0.6999 (mptt) REVERT: D 1000 PHE cc_start: 0.8193 (m-80) cc_final: 0.7871 (m-80) REVERT: D 1006 CYS cc_start: 0.7649 (m) cc_final: 0.7424 (m) REVERT: D 1020 TYR cc_start: 0.7366 (m-10) cc_final: 0.6005 (t80) REVERT: D 1061 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7429 (mp0) outliers start: 44 outliers final: 30 residues processed: 356 average time/residue: 1.7320 time to fit residues: 765.3646 Evaluate side-chains 337 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 307 time to evaluate : 3.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 ARG Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 920 ASP Chi-restraints excluded: chain A residue 1007 ASN Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain B residue 288 ARG Chi-restraints excluded: chain B residue 326 CYS Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 920 ASP Chi-restraints excluded: chain B residue 1007 ASN Chi-restraints excluded: chain B residue 1069 THR Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 288 ARG Chi-restraints excluded: chain C residue 326 CYS Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 920 ASP Chi-restraints excluded: chain C residue 1007 ASN Chi-restraints excluded: chain C residue 1069 THR Chi-restraints excluded: chain D residue 288 ARG Chi-restraints excluded: chain D residue 326 CYS Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 920 ASP Chi-restraints excluded: chain D residue 1007 ASN Chi-restraints excluded: chain D residue 1069 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 293 optimal weight: 6.9990 chunk 199 optimal weight: 0.5980 chunk 5 optimal weight: 7.9990 chunk 261 optimal weight: 0.9990 chunk 145 optimal weight: 5.9990 chunk 300 optimal weight: 6.9990 chunk 243 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 179 optimal weight: 9.9990 chunk 315 optimal weight: 4.9990 chunk 88 optimal weight: 10.0000 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 510 GLN B 429 GLN B 510 GLN C 429 GLN D 429 GLN D 510 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 29208 Z= 0.382 Angle : 0.564 6.394 39956 Z= 0.303 Chirality : 0.040 0.167 4688 Planarity : 0.004 0.050 4876 Dihedral : 7.499 58.651 5388 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.81 % Favored : 96.08 % Rotamer: Outliers : 2.31 % Allowed : 14.02 % Favored : 83.67 % 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: 2.00 (0.14), residues: 3572 helix: 2.37 (0.10), residues: 2516 sheet: -2.79 (0.34), residues: 180 loop : -0.87 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 682 HIS 0.005 0.001 HIS D 761 PHE 0.016 0.002 PHE C 677 TYR 0.014 0.002 TYR A1005 ARG 0.002 0.000 ARG A 278 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7144 Ramachandran restraints generated. 3572 Oldfield, 0 Emsley, 3572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7144 Ramachandran restraints generated. 3572 Oldfield, 0 Emsley, 3572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 374 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 573 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue LEU 1009 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 374 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 573 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue LEU 1009 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 374 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 573 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue LEU 1009 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 374 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 573 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue LEU 1009 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 395 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 334 time to evaluate : 3.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 ARG cc_start: 0.7938 (mmp80) cc_final: 0.7510 (mmp-170) REVERT: A 310 ARG cc_start: 0.7161 (ttt180) cc_final: 0.6510 (ttm-80) REVERT: A 615 GLU cc_start: 0.8595 (pt0) cc_final: 0.8177 (mm-30) REVERT: A 658 GLU cc_start: 0.8378 (mp0) cc_final: 0.7978 (mp0) REVERT: A 680 LYS cc_start: 0.7550 (mttt) cc_final: 0.7067 (mptt) REVERT: A 1000 PHE cc_start: 0.8185 (m-80) cc_final: 0.7855 (m-80) REVERT: A 1006 CYS cc_start: 0.7686 (m) cc_final: 0.7470 (m) REVERT: A 1020 TYR cc_start: 0.7434 (m-10) cc_final: 0.5993 (t80) REVERT: B 310 ARG cc_start: 0.7147 (ttt180) cc_final: 0.6504 (ttm-80) REVERT: B 615 GLU cc_start: 0.8566 (pt0) cc_final: 0.8148 (mm-30) REVERT: B 658 GLU cc_start: 0.8377 (mp0) cc_final: 0.7977 (mp0) REVERT: B 680 LYS cc_start: 0.7549 (mttt) cc_final: 0.7066 (mptt) REVERT: B 1000 PHE cc_start: 0.8184 (m-80) cc_final: 0.7855 (m-80) REVERT: B 1006 CYS cc_start: 0.7687 (m) cc_final: 0.7472 (m) REVERT: B 1020 TYR cc_start: 0.7438 (m-10) cc_final: 0.5991 (t80) REVERT: C 310 ARG cc_start: 0.7150 (ttt180) cc_final: 0.6505 (ttm-80) REVERT: C 615 GLU cc_start: 0.8568 (pt0) cc_final: 0.8149 (mm-30) REVERT: C 658 GLU cc_start: 0.8377 (mp0) cc_final: 0.7978 (mp0) REVERT: C 680 LYS cc_start: 0.7551 (mttt) cc_final: 0.7068 (mptt) REVERT: C 1000 PHE cc_start: 0.8187 (m-80) cc_final: 0.7857 (m-80) REVERT: C 1006 CYS cc_start: 0.7684 (m) cc_final: 0.7468 (m) REVERT: C 1020 TYR cc_start: 0.7435 (m-10) cc_final: 0.5990 (t80) REVERT: D 310 ARG cc_start: 0.7148 (ttt180) cc_final: 0.6504 (ttm-80) REVERT: D 615 GLU cc_start: 0.8566 (pt0) cc_final: 0.8149 (mm-30) REVERT: D 658 GLU cc_start: 0.8377 (mp0) cc_final: 0.7978 (mp0) REVERT: D 680 LYS cc_start: 0.7550 (mttt) cc_final: 0.7066 (mptt) REVERT: D 1000 PHE cc_start: 0.8185 (m-80) cc_final: 0.7856 (m-80) REVERT: D 1006 CYS cc_start: 0.7683 (m) cc_final: 0.7467 (m) REVERT: D 1020 TYR cc_start: 0.7433 (m-10) cc_final: 0.5989 (t80) outliers start: 61 outliers final: 31 residues processed: 375 average time/residue: 1.6850 time to fit residues: 794.8213 Evaluate side-chains 348 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 317 time to evaluate : 3.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 288 ARG Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 920 ASP Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 288 ARG Chi-restraints excluded: chain B residue 326 CYS Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 920 ASP Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 288 ARG Chi-restraints excluded: chain C residue 326 CYS Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 920 ASP Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 288 ARG Chi-restraints excluded: chain D residue 326 CYS Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 920 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 118 optimal weight: 6.9990 chunk 316 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 206 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 352 optimal weight: 0.6980 chunk 292 optimal weight: 3.9990 chunk 163 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 chunk 184 optimal weight: 8.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 29208 Z= 0.286 Angle : 0.520 8.951 39956 Z= 0.280 Chirality : 0.037 0.163 4688 Planarity : 0.004 0.048 4876 Dihedral : 7.284 59.521 5388 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.42 % Favored : 96.47 % Rotamer: Outliers : 1.97 % Allowed : 14.89 % Favored : 83.14 % 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: 2.04 (0.14), residues: 3572 helix: 2.44 (0.10), residues: 2488 sheet: -2.85 (0.33), residues: 180 loop : -0.90 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 682 HIS 0.004 0.001 HIS D 136 PHE 0.013 0.001 PHE C 874 TYR 0.018 0.001 TYR A 186 ARG 0.002 0.000 ARG D 998 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7144 Ramachandran restraints generated. 3572 Oldfield, 0 Emsley, 3572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7144 Ramachandran restraints generated. 3572 Oldfield, 0 Emsley, 3572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 374 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 573 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue LEU 1009 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 374 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 573 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue LEU 1009 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 374 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 573 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue LEU 1009 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 374 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 573 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue LEU 1009 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 392 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 340 time to evaluate : 3.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 ARG cc_start: 0.7179 (ttt180) cc_final: 0.6521 (ttm-80) REVERT: A 469 ASP cc_start: 0.7651 (t70) cc_final: 0.7299 (m-30) REVERT: A 615 GLU cc_start: 0.8587 (pt0) cc_final: 0.8187 (mm-30) REVERT: A 658 GLU cc_start: 0.8382 (mp0) cc_final: 0.7886 (mp0) REVERT: A 680 LYS cc_start: 0.7543 (mttt) cc_final: 0.7055 (mptt) REVERT: A 1000 PHE cc_start: 0.8144 (m-80) cc_final: 0.7787 (m-80) REVERT: A 1005 TYR cc_start: 0.6940 (OUTLIER) cc_final: 0.6318 (t80) REVERT: A 1020 TYR cc_start: 0.7417 (m-10) cc_final: 0.6018 (t80) REVERT: B 310 ARG cc_start: 0.7167 (ttt180) cc_final: 0.6516 (ttm-80) REVERT: B 615 GLU cc_start: 0.8580 (pt0) cc_final: 0.8171 (mm-30) REVERT: B 658 GLU cc_start: 0.8380 (mp0) cc_final: 0.7884 (mp0) REVERT: B 680 LYS cc_start: 0.7542 (mttt) cc_final: 0.7054 (mptt) REVERT: B 1000 PHE cc_start: 0.8143 (m-80) cc_final: 0.7786 (m-80) REVERT: B 1005 TYR cc_start: 0.6938 (OUTLIER) cc_final: 0.6318 (t80) REVERT: B 1020 TYR cc_start: 0.7415 (m-10) cc_final: 0.6017 (t80) REVERT: C 310 ARG cc_start: 0.7169 (ttt180) cc_final: 0.6517 (ttm-80) REVERT: C 469 ASP cc_start: 0.7654 (t70) cc_final: 0.7313 (m-30) REVERT: C 510 GLN cc_start: 0.6078 (OUTLIER) cc_final: 0.5814 (mp10) REVERT: C 615 GLU cc_start: 0.8582 (pt0) cc_final: 0.8172 (mm-30) REVERT: C 658 GLU cc_start: 0.8380 (mp0) cc_final: 0.7885 (mp0) REVERT: C 680 LYS cc_start: 0.7543 (mttt) cc_final: 0.7054 (mptt) REVERT: C 1000 PHE cc_start: 0.8144 (m-80) cc_final: 0.7786 (m-80) REVERT: C 1005 TYR cc_start: 0.6938 (OUTLIER) cc_final: 0.6315 (t80) REVERT: C 1020 TYR cc_start: 0.7413 (m-10) cc_final: 0.6017 (t80) REVERT: D 310 ARG cc_start: 0.7169 (ttt180) cc_final: 0.6517 (ttm-80) REVERT: D 615 GLU cc_start: 0.8581 (pt0) cc_final: 0.8172 (mm-30) REVERT: D 658 GLU cc_start: 0.8380 (mp0) cc_final: 0.7885 (mp0) REVERT: D 680 LYS cc_start: 0.7543 (mttt) cc_final: 0.7054 (mptt) REVERT: D 1000 PHE cc_start: 0.8144 (m-80) cc_final: 0.7786 (m-80) REVERT: D 1005 TYR cc_start: 0.6938 (OUTLIER) cc_final: 0.6319 (t80) REVERT: D 1020 TYR cc_start: 0.7413 (m-10) cc_final: 0.6018 (t80) outliers start: 52 outliers final: 29 residues processed: 370 average time/residue: 1.6759 time to fit residues: 773.1629 Evaluate side-chains 343 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 309 time to evaluate : 3.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 288 ARG Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 1005 TYR Chi-restraints excluded: chain A residue 1007 ASN Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 288 ARG Chi-restraints excluded: chain B residue 326 CYS Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 1005 TYR Chi-restraints excluded: chain B residue 1007 ASN Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 288 ARG Chi-restraints excluded: chain C residue 326 CYS Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 510 GLN Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 1005 TYR Chi-restraints excluded: chain C residue 1007 ASN Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 288 ARG Chi-restraints excluded: chain D residue 326 CYS Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 1005 TYR Chi-restraints excluded: chain D residue 1007 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 339 optimal weight: 0.9980 chunk 39 optimal weight: 7.9990 chunk 200 optimal weight: 6.9990 chunk 257 optimal weight: 3.9990 chunk 199 optimal weight: 3.9990 chunk 296 optimal weight: 7.9990 chunk 196 optimal weight: 10.0000 chunk 350 optimal weight: 2.9990 chunk 219 optimal weight: 4.9990 chunk 213 optimal weight: 9.9990 chunk 161 optimal weight: 0.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 429 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 29208 Z= 0.347 Angle : 0.548 9.016 39956 Z= 0.295 Chirality : 0.039 0.190 4688 Planarity : 0.004 0.050 4876 Dihedral : 7.413 59.757 5388 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.37 % Favored : 95.52 % Rotamer: Outliers : 2.27 % Allowed : 16.02 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.86 (0.14), residues: 3572 helix: 2.39 (0.10), residues: 2472 sheet: -2.95 (0.33), residues: 180 loop : -1.16 (0.19), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 682 HIS 0.004 0.001 HIS A 185 PHE 0.014 0.002 PHE D 165 TYR 0.014 0.002 TYR C1005 ARG 0.002 0.000 ARG A 278 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7144 Ramachandran restraints generated. 3572 Oldfield, 0 Emsley, 3572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7144 Ramachandran restraints generated. 3572 Oldfield, 0 Emsley, 3572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 374 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 573 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue LEU 1009 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 374 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 573 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue LEU 1009 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 374 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 573 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue LEU 1009 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 374 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 573 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue LEU 1009 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 384 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 324 time to evaluate : 3.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 ARG cc_start: 0.7234 (ttt180) cc_final: 0.6558 (ttm-80) REVERT: A 615 GLU cc_start: 0.8602 (pt0) cc_final: 0.8183 (mm-30) REVERT: A 658 GLU cc_start: 0.8399 (mp0) cc_final: 0.7960 (mp0) REVERT: A 680 LYS cc_start: 0.7560 (mttt) cc_final: 0.7065 (mptt) REVERT: A 1000 PHE cc_start: 0.8164 (m-80) cc_final: 0.7811 (m-80) REVERT: A 1005 TYR cc_start: 0.7052 (OUTLIER) cc_final: 0.6223 (t80) REVERT: A 1020 TYR cc_start: 0.7419 (m-10) cc_final: 0.6029 (t80) REVERT: B 310 ARG cc_start: 0.7206 (ttt180) cc_final: 0.6541 (ttm-80) REVERT: B 615 GLU cc_start: 0.8581 (pt0) cc_final: 0.8186 (mm-30) REVERT: B 658 GLU cc_start: 0.8398 (mp0) cc_final: 0.7959 (mp0) REVERT: B 680 LYS cc_start: 0.7560 (mttt) cc_final: 0.7064 (mptt) REVERT: B 1000 PHE cc_start: 0.8161 (m-80) cc_final: 0.7808 (m-80) REVERT: B 1005 TYR cc_start: 0.7050 (OUTLIER) cc_final: 0.6225 (t80) REVERT: B 1020 TYR cc_start: 0.7419 (m-10) cc_final: 0.6019 (t80) REVERT: C 310 ARG cc_start: 0.7206 (ttt180) cc_final: 0.6541 (ttm-80) REVERT: C 444 ASP cc_start: 0.7926 (m-30) cc_final: 0.7699 (m-30) REVERT: C 615 GLU cc_start: 0.8582 (pt0) cc_final: 0.8188 (mm-30) REVERT: C 658 GLU cc_start: 0.8398 (mp0) cc_final: 0.7959 (mp0) REVERT: C 680 LYS cc_start: 0.7561 (mttt) cc_final: 0.7063 (mptt) REVERT: C 1000 PHE cc_start: 0.8167 (m-80) cc_final: 0.7814 (m-80) REVERT: C 1005 TYR cc_start: 0.7050 (OUTLIER) cc_final: 0.6228 (t80) REVERT: C 1020 TYR cc_start: 0.7418 (m-10) cc_final: 0.6020 (t80) REVERT: D 310 ARG cc_start: 0.7207 (ttt180) cc_final: 0.6543 (ttm-80) REVERT: D 615 GLU cc_start: 0.8581 (pt0) cc_final: 0.8188 (mm-30) REVERT: D 658 GLU cc_start: 0.8396 (mp0) cc_final: 0.7958 (mp0) REVERT: D 680 LYS cc_start: 0.7561 (mttt) cc_final: 0.7064 (mptt) REVERT: D 1000 PHE cc_start: 0.8163 (m-80) cc_final: 0.7811 (m-80) REVERT: D 1005 TYR cc_start: 0.7051 (OUTLIER) cc_final: 0.6226 (t80) REVERT: D 1020 TYR cc_start: 0.7418 (m-10) cc_final: 0.6020 (t80) outliers start: 60 outliers final: 39 residues processed: 360 average time/residue: 1.7248 time to fit residues: 771.4617 Evaluate side-chains 358 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 315 time to evaluate : 3.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 288 ARG Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 997 GLN Chi-restraints excluded: chain A residue 1005 TYR Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 288 ARG Chi-restraints excluded: chain B residue 326 CYS Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 846 ILE Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 997 GLN Chi-restraints excluded: chain B residue 1005 TYR Chi-restraints excluded: chain C residue 288 ARG Chi-restraints excluded: chain C residue 326 CYS Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 846 ILE Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 997 GLN Chi-restraints excluded: chain C residue 1005 TYR Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 288 ARG Chi-restraints excluded: chain D residue 326 CYS Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 846 ILE Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 997 GLN Chi-restraints excluded: chain D residue 1005 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 217 optimal weight: 5.9990 chunk 140 optimal weight: 6.9990 chunk 209 optimal weight: 5.9990 chunk 105 optimal weight: 10.0000 chunk 68 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 223 optimal weight: 0.9980 chunk 239 optimal weight: 1.9990 chunk 173 optimal weight: 0.3980 chunk 32 optimal weight: 1.9990 chunk 275 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 500 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 29208 Z= 0.146 Angle : 0.486 10.862 39956 Z= 0.261 Chirality : 0.036 0.167 4688 Planarity : 0.003 0.047 4876 Dihedral : 6.869 58.259 5388 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.64 % Favored : 96.25 % Rotamer: Outliers : 1.48 % Allowed : 16.78 % Favored : 81.74 % 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: 2.18 (0.14), residues: 3572 helix: 2.57 (0.10), residues: 2480 sheet: -2.91 (0.32), residues: 180 loop : -0.87 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 682 HIS 0.005 0.001 HIS C 136 PHE 0.011 0.001 PHE D 165 TYR 0.015 0.001 TYR B 999 ARG 0.002 0.000 ARG A 851 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7144 Ramachandran restraints generated. 3572 Oldfield, 0 Emsley, 3572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7144 Ramachandran restraints generated. 3572 Oldfield, 0 Emsley, 3572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 374 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 573 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue LEU 1009 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 374 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 573 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue LEU 1009 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 374 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 573 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue LEU 1009 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 374 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 573 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue LEU 1009 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 371 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 332 time to evaluate : 3.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 ILE cc_start: 0.8364 (mp) cc_final: 0.8163 (mp) REVERT: A 310 ARG cc_start: 0.7198 (ttt180) cc_final: 0.6536 (ttm-80) REVERT: A 342 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8230 (mt) REVERT: A 615 GLU cc_start: 0.8586 (pt0) cc_final: 0.8204 (mm-30) REVERT: A 658 GLU cc_start: 0.8405 (mp0) cc_final: 0.7977 (mp0) REVERT: A 680 LYS cc_start: 0.7529 (mttt) cc_final: 0.7040 (mptt) REVERT: A 1000 PHE cc_start: 0.8075 (m-80) cc_final: 0.7725 (m-80) REVERT: A 1005 TYR cc_start: 0.6875 (OUTLIER) cc_final: 0.6221 (t80) REVERT: A 1020 TYR cc_start: 0.7416 (m-10) cc_final: 0.6034 (t80) REVERT: B 209 ILE cc_start: 0.8385 (mp) cc_final: 0.8185 (mp) REVERT: B 310 ARG cc_start: 0.7178 (ttt180) cc_final: 0.6535 (ttm-80) REVERT: B 342 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8230 (mt) REVERT: B 658 GLU cc_start: 0.8407 (mp0) cc_final: 0.7978 (mp0) REVERT: B 680 LYS cc_start: 0.7527 (mttt) cc_final: 0.7038 (mptt) REVERT: B 1000 PHE cc_start: 0.8073 (m-80) cc_final: 0.7723 (m-80) REVERT: B 1005 TYR cc_start: 0.6861 (OUTLIER) cc_final: 0.6208 (t80) REVERT: B 1020 TYR cc_start: 0.7386 (m-10) cc_final: 0.6039 (t80) REVERT: C 209 ILE cc_start: 0.8385 (mp) cc_final: 0.8183 (mp) REVERT: C 310 ARG cc_start: 0.7180 (ttt180) cc_final: 0.6537 (ttm-80) REVERT: C 342 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8229 (mt) REVERT: C 658 GLU cc_start: 0.8404 (mp0) cc_final: 0.7976 (mp0) REVERT: C 680 LYS cc_start: 0.7528 (mttt) cc_final: 0.7039 (mptt) REVERT: C 1000 PHE cc_start: 0.8090 (m-80) cc_final: 0.7742 (m-80) REVERT: C 1005 TYR cc_start: 0.6861 (OUTLIER) cc_final: 0.6211 (t80) REVERT: C 1020 TYR cc_start: 0.7384 (m-10) cc_final: 0.6039 (t80) REVERT: D 209 ILE cc_start: 0.8385 (mp) cc_final: 0.8184 (mp) REVERT: D 310 ARG cc_start: 0.7180 (ttt180) cc_final: 0.6538 (ttm-80) REVERT: D 342 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8229 (mt) REVERT: D 658 GLU cc_start: 0.8404 (mp0) cc_final: 0.7975 (mp0) REVERT: D 680 LYS cc_start: 0.7530 (mttt) cc_final: 0.7040 (mptt) REVERT: D 1000 PHE cc_start: 0.8075 (m-80) cc_final: 0.7724 (m-80) REVERT: D 1005 TYR cc_start: 0.6860 (OUTLIER) cc_final: 0.6206 (t80) REVERT: D 1020 TYR cc_start: 0.7382 (m-10) cc_final: 0.6038 (t80) outliers start: 39 outliers final: 23 residues processed: 355 average time/residue: 1.7604 time to fit residues: 768.7465 Evaluate side-chains 338 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 307 time to evaluate : 3.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 288 ARG Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 1005 TYR Chi-restraints excluded: chain B residue 288 ARG Chi-restraints excluded: chain B residue 326 CYS Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 1005 TYR Chi-restraints excluded: chain C residue 288 ARG Chi-restraints excluded: chain C residue 326 CYS Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 1005 TYR Chi-restraints excluded: chain D residue 288 ARG Chi-restraints excluded: chain D residue 326 CYS Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 1005 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 319 optimal weight: 3.9990 chunk 336 optimal weight: 2.9990 chunk 306 optimal weight: 5.9990 chunk 326 optimal weight: 3.9990 chunk 196 optimal weight: 10.0000 chunk 142 optimal weight: 1.9990 chunk 256 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 295 optimal weight: 6.9990 chunk 309 optimal weight: 7.9990 chunk 325 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 761 HIS C 761 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 29208 Z= 0.352 Angle : 0.544 9.296 39956 Z= 0.291 Chirality : 0.039 0.177 4688 Planarity : 0.004 0.049 4876 Dihedral : 7.231 59.357 5388 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.48 % Favored : 95.41 % Rotamer: Outliers : 1.78 % Allowed : 16.86 % Favored : 81.36 % 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: 2.01 (0.14), residues: 3572 helix: 2.50 (0.10), residues: 2472 sheet: -2.93 (0.34), residues: 180 loop : -1.09 (0.19), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 682 HIS 0.004 0.001 HIS D 136 PHE 0.014 0.002 PHE D 874 TYR 0.014 0.002 TYR C1005 ARG 0.002 0.000 ARG B 901 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7144 Ramachandran restraints generated. 3572 Oldfield, 0 Emsley, 3572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7144 Ramachandran restraints generated. 3572 Oldfield, 0 Emsley, 3572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 374 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 573 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue LEU 1009 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 374 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 573 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue LEU 1009 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 374 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 573 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue LEU 1009 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 374 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 573 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue LEU 1009 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 357 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 310 time to evaluate : 3.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 ARG cc_start: 0.7315 (ttt180) cc_final: 0.6652 (ttm-80) REVERT: A 342 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8229 (mt) REVERT: A 615 GLU cc_start: 0.8597 (pt0) cc_final: 0.8186 (mm-30) REVERT: A 658 GLU cc_start: 0.8389 (mp0) cc_final: 0.7942 (mp0) REVERT: A 680 LYS cc_start: 0.7577 (mttt) cc_final: 0.7079 (mptt) REVERT: A 1000 PHE cc_start: 0.8158 (m-80) cc_final: 0.7831 (m-80) REVERT: A 1005 TYR cc_start: 0.6961 (OUTLIER) cc_final: 0.6224 (t80) REVERT: A 1020 TYR cc_start: 0.7437 (m-10) cc_final: 0.6033 (t80) REVERT: B 310 ARG cc_start: 0.7305 (ttt180) cc_final: 0.6648 (ttm-80) REVERT: B 342 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8232 (mt) REVERT: B 615 GLU cc_start: 0.8573 (pt0) cc_final: 0.8166 (mm-30) REVERT: B 658 GLU cc_start: 0.8390 (mp0) cc_final: 0.7942 (mp0) REVERT: B 680 LYS cc_start: 0.7576 (mttt) cc_final: 0.7078 (mptt) REVERT: B 1000 PHE cc_start: 0.8155 (m-80) cc_final: 0.7827 (m-80) REVERT: B 1005 TYR cc_start: 0.6959 (OUTLIER) cc_final: 0.6225 (t80) REVERT: B 1020 TYR cc_start: 0.7404 (m-10) cc_final: 0.6036 (t80) REVERT: C 310 ARG cc_start: 0.7308 (ttt180) cc_final: 0.6649 (ttm-80) REVERT: C 342 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8231 (mt) REVERT: C 469 ASP cc_start: 0.7657 (t70) cc_final: 0.7255 (m-30) REVERT: C 615 GLU cc_start: 0.8574 (pt0) cc_final: 0.8166 (mm-30) REVERT: C 658 GLU cc_start: 0.8388 (mp0) cc_final: 0.7941 (mp0) REVERT: C 680 LYS cc_start: 0.7578 (mttt) cc_final: 0.7079 (mptt) REVERT: C 1000 PHE cc_start: 0.8161 (m-80) cc_final: 0.7835 (m-80) REVERT: C 1005 TYR cc_start: 0.6964 (OUTLIER) cc_final: 0.6152 (t80) REVERT: C 1020 TYR cc_start: 0.7403 (m-10) cc_final: 0.6036 (t80) REVERT: D 310 ARG cc_start: 0.7308 (ttt180) cc_final: 0.6650 (ttm-80) REVERT: D 342 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8231 (mt) REVERT: D 615 GLU cc_start: 0.8573 (pt0) cc_final: 0.8166 (mm-30) REVERT: D 658 GLU cc_start: 0.8389 (mp0) cc_final: 0.7941 (mp0) REVERT: D 680 LYS cc_start: 0.7577 (mttt) cc_final: 0.7079 (mptt) REVERT: D 1000 PHE cc_start: 0.8158 (m-80) cc_final: 0.7831 (m-80) REVERT: D 1005 TYR cc_start: 0.6959 (OUTLIER) cc_final: 0.6226 (t80) REVERT: D 1020 TYR cc_start: 0.7402 (m-10) cc_final: 0.6035 (t80) outliers start: 47 outliers final: 27 residues processed: 333 average time/residue: 1.7369 time to fit residues: 721.9497 Evaluate side-chains 342 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 307 time to evaluate : 3.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 288 ARG Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 997 GLN Chi-restraints excluded: chain A residue 1005 TYR Chi-restraints excluded: chain B residue 288 ARG Chi-restraints excluded: chain B residue 326 CYS Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 997 GLN Chi-restraints excluded: chain B residue 1005 TYR Chi-restraints excluded: chain C residue 288 ARG Chi-restraints excluded: chain C residue 326 CYS Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 997 GLN Chi-restraints excluded: chain C residue 1005 TYR Chi-restraints excluded: chain D residue 288 ARG Chi-restraints excluded: chain D residue 326 CYS Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 997 GLN Chi-restraints excluded: chain D residue 1005 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 214 optimal weight: 2.9990 chunk 345 optimal weight: 1.9990 chunk 211 optimal weight: 3.9990 chunk 164 optimal weight: 0.6980 chunk 240 optimal weight: 0.9990 chunk 362 optimal weight: 8.9990 chunk 333 optimal weight: 0.9990 chunk 288 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 223 optimal weight: 3.9990 chunk 177 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29208 Z= 0.220 Angle : 0.514 13.320 39956 Z= 0.276 Chirality : 0.037 0.168 4688 Planarity : 0.004 0.048 4876 Dihedral : 6.942 58.798 5388 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.78 % Favored : 96.11 % Rotamer: Outliers : 1.21 % Allowed : 17.46 % Favored : 81.33 % 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: 2.08 (0.14), residues: 3572 helix: 2.53 (0.10), residues: 2476 sheet: -2.95 (0.33), residues: 180 loop : -1.01 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 682 HIS 0.004 0.001 HIS C 136 PHE 0.010 0.001 PHE A 874 TYR 0.018 0.001 TYR D 186 ARG 0.002 0.000 ARG B 851 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7144 Ramachandran restraints generated. 3572 Oldfield, 0 Emsley, 3572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7144 Ramachandran restraints generated. 3572 Oldfield, 0 Emsley, 3572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 374 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 573 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue LEU 1009 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 374 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 573 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue LEU 1009 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 374 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 573 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue LEU 1009 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue VAL 148 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue SER 221 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue VAL 354 is missing expected H atoms. Skipping. Residue LYS 357 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue VAL 366 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue ILE 374 is missing expected H atoms. Skipping. Residue ILE 378 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue THR 448 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue THR 557 is missing expected H atoms. Skipping. Residue LYS 573 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 704 is missing expected H atoms. Skipping. Residue LEU 709 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue LEU 724 is missing expected H atoms. Skipping. Residue THR 923 is missing expected H atoms. Skipping. Residue LEU 1009 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 342 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 310 time to evaluate : 3.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 ARG cc_start: 0.7318 (ttt180) cc_final: 0.6654 (ttm-80) REVERT: A 342 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8221 (mt) REVERT: A 469 ASP cc_start: 0.7600 (t70) cc_final: 0.7219 (m-30) REVERT: A 615 GLU cc_start: 0.8598 (pt0) cc_final: 0.8206 (mm-30) REVERT: A 658 GLU cc_start: 0.8412 (mp0) cc_final: 0.8028 (mp0) REVERT: A 680 LYS cc_start: 0.7555 (mttt) cc_final: 0.7062 (mptt) REVERT: A 1000 PHE cc_start: 0.8116 (m-80) cc_final: 0.7768 (m-80) REVERT: A 1005 TYR cc_start: 0.6905 (OUTLIER) cc_final: 0.6225 (t80) REVERT: A 1020 TYR cc_start: 0.7418 (m-10) cc_final: 0.6044 (t80) REVERT: B 310 ARG cc_start: 0.7306 (ttt180) cc_final: 0.6654 (ttm-80) REVERT: B 342 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8224 (mt) REVERT: B 615 GLU cc_start: 0.8558 (pt0) cc_final: 0.8166 (mm-30) REVERT: B 658 GLU cc_start: 0.8401 (mp0) cc_final: 0.8014 (mp0) REVERT: B 680 LYS cc_start: 0.7556 (mttt) cc_final: 0.7063 (mptt) REVERT: B 1000 PHE cc_start: 0.8115 (m-80) cc_final: 0.7766 (m-80) REVERT: B 1005 TYR cc_start: 0.6904 (OUTLIER) cc_final: 0.6227 (t80) REVERT: B 1020 TYR cc_start: 0.7386 (m-10) cc_final: 0.6046 (t80) REVERT: C 310 ARG cc_start: 0.7301 (ttt180) cc_final: 0.6656 (ttm-80) REVERT: C 342 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8223 (mt) REVERT: C 469 ASP cc_start: 0.7595 (t70) cc_final: 0.7212 (m-30) REVERT: C 615 GLU cc_start: 0.8559 (pt0) cc_final: 0.8167 (mm-30) REVERT: C 658 GLU cc_start: 0.8399 (mp0) cc_final: 0.8013 (mp0) REVERT: C 680 LYS cc_start: 0.7556 (mttt) cc_final: 0.7062 (mptt) REVERT: C 1000 PHE cc_start: 0.8102 (m-80) cc_final: 0.7691 (m-80) REVERT: C 1005 TYR cc_start: 0.6771 (OUTLIER) cc_final: 0.6090 (t80) REVERT: C 1020 TYR cc_start: 0.7385 (m-10) cc_final: 0.6048 (t80) REVERT: D 310 ARG cc_start: 0.7302 (ttt180) cc_final: 0.6657 (ttm-80) REVERT: D 342 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8225 (mt) REVERT: D 615 GLU cc_start: 0.8557 (pt0) cc_final: 0.8167 (mm-30) REVERT: D 658 GLU cc_start: 0.8400 (mp0) cc_final: 0.8013 (mp0) REVERT: D 680 LYS cc_start: 0.7556 (mttt) cc_final: 0.7062 (mptt) REVERT: D 1000 PHE cc_start: 0.8116 (m-80) cc_final: 0.7768 (m-80) REVERT: D 1005 TYR cc_start: 0.6904 (OUTLIER) cc_final: 0.6227 (t80) REVERT: D 1020 TYR cc_start: 0.7383 (m-10) cc_final: 0.6045 (t80) outliers start: 32 outliers final: 23 residues processed: 322 average time/residue: 1.7216 time to fit residues: 696.5981 Evaluate side-chains 340 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 309 time to evaluate : 3.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 ARG Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 920 ASP Chi-restraints excluded: chain A residue 1005 TYR Chi-restraints excluded: chain B residue 288 ARG Chi-restraints excluded: chain B residue 326 CYS Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 1005 TYR Chi-restraints excluded: chain C residue 288 ARG Chi-restraints excluded: chain C residue 326 CYS Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 920 ASP Chi-restraints excluded: chain C residue 1005 TYR Chi-restraints excluded: chain D residue 288 ARG Chi-restraints excluded: chain D residue 326 CYS Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 1005 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 229 optimal weight: 3.9990 chunk 307 optimal weight: 4.9990 chunk 88 optimal weight: 9.9990 chunk 266 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 80 optimal weight: 0.5980 chunk 289 optimal weight: 1.9990 chunk 121 optimal weight: 8.9990 chunk 296 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 500 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.171471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.102913 restraints weight = 106834.264| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.97 r_work: 0.3255 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 29208 Z= 0.243 Angle : 0.514 12.203 39956 Z= 0.276 Chirality : 0.037 0.169 4688 Planarity : 0.004 0.048 4876 Dihedral : 6.885 58.559 5388 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.37 % Favored : 95.52 % Rotamer: Outliers : 1.33 % Allowed : 17.35 % Favored : 81.33 % 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: 2.08 (0.14), residues: 3572 helix: 2.53 (0.10), residues: 2476 sheet: -2.93 (0.33), residues: 180 loop : -1.03 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 682 HIS 0.004 0.001 HIS C 136 PHE 0.011 0.001 PHE A 874 TYR 0.012 0.001 TYR C 999 ARG 0.001 0.000 ARG C 532 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14288.87 seconds wall clock time: 245 minutes 17.46 seconds (14717.46 seconds total)