Starting phenix.real_space_refine on Wed Sep 25 15:06:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b6g_44258/09_2024/9b6g_44258_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b6g_44258/09_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_44258/09_2024/9b6g_44258.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b6g_44258/09_2024/9b6g_44258.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b6g_44258/09_2024/9b6g_44258_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b6g_44258/09_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): 0.72s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 19.42, 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: 10.54 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: 3.31 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: 18.82 Time building geometry restraints manager: 13.02 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: 1.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.740 Extract box with map and model: 1.500 Check model and map are aligned: 0.300 Set scattering table: 0.390 Process input model: 86.670 Find NCS groups from input model: 1.620 Set up NCS constraints: 0.180 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 : 3.122 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: 1.5991 time to fit residues: 1013.9120 Evaluate side-chains 314 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 310 time to evaluate : 3.082 ------------------------------------------------------------------------------- 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 : 3.067 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: 1.7570 time to fit residues: 828.6812 Evaluate side-chains 320 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 308 time to evaluate : 3.097 ------------------------------------------------------------------------------- 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: 1.9990 chunk 225 optimal weight: 2.9990 chunk 91 optimal weight: 20.0000 chunk 331 optimal weight: 1.9990 chunk 357 optimal weight: 4.9990 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: 3.1990 ------------------------------------------------------------------------------- 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: 0.7391 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.104 29208 Z= 0.429 Angle : 0.613 8.261 39956 Z= 0.328 Chirality : 0.042 0.176 4688 Planarity : 0.005 0.062 4876 Dihedral : 7.811 57.749 5388 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.20 % Allowed : 12.77 % 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: 1.82 (0.14), residues: 3572 helix: 2.22 (0.10), residues: 2508 sheet: -2.71 (0.33), residues: 180 loop : -0.93 (0.19), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 682 HIS 0.007 0.001 HIS A 185 PHE 0.021 0.002 PHE A 677 TYR 0.026 0.002 TYR A 186 ARG 0.005 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 382 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 324 time to evaluate : 3.090 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 310 ARG cc_start: 0.7231 (ttt180) cc_final: 0.6611 (ttm-80) REVERT: A 615 GLU cc_start: 0.8589 (pt0) cc_final: 0.8192 (mm-30) REVERT: A 658 GLU cc_start: 0.8248 (mp0) cc_final: 0.7888 (mp0) REVERT: A 680 LYS cc_start: 0.7563 (mttt) cc_final: 0.7073 (mptt) REVERT: A 1000 PHE cc_start: 0.8242 (m-80) cc_final: 0.7933 (m-80) REVERT: A 1006 CYS cc_start: 0.7836 (m) cc_final: 0.7592 (m) REVERT: A 1020 TYR cc_start: 0.7518 (m-10) cc_final: 0.6024 (t80) REVERT: B 310 ARG cc_start: 0.7215 (ttt180) cc_final: 0.6603 (ttm-80) REVERT: B 615 GLU cc_start: 0.8561 (pt0) cc_final: 0.8162 (mm-30) REVERT: B 658 GLU cc_start: 0.8249 (mp0) cc_final: 0.7893 (mp0) REVERT: B 680 LYS cc_start: 0.7563 (mttt) cc_final: 0.7072 (mptt) REVERT: B 1000 PHE cc_start: 0.8240 (m-80) cc_final: 0.7930 (m-80) REVERT: B 1006 CYS cc_start: 0.7835 (m) cc_final: 0.7593 (m) REVERT: B 1020 TYR cc_start: 0.7516 (m-10) cc_final: 0.6012 (t80) REVERT: C 310 ARG cc_start: 0.7219 (ttt180) cc_final: 0.6604 (ttm-80) REVERT: C 615 GLU cc_start: 0.8562 (pt0) cc_final: 0.8163 (mm-30) REVERT: C 658 GLU cc_start: 0.8250 (mp0) cc_final: 0.7892 (mp0) REVERT: C 680 LYS cc_start: 0.7563 (mttt) cc_final: 0.7073 (mptt) REVERT: C 1000 PHE cc_start: 0.8241 (m-80) cc_final: 0.7932 (m-80) REVERT: C 1006 CYS cc_start: 0.7834 (m) cc_final: 0.7590 (m) REVERT: C 1020 TYR cc_start: 0.7515 (m-10) cc_final: 0.6010 (t80) REVERT: D 310 ARG cc_start: 0.7220 (ttt180) cc_final: 0.6607 (ttm-80) REVERT: D 615 GLU cc_start: 0.8560 (pt0) cc_final: 0.8162 (mm-30) REVERT: D 658 GLU cc_start: 0.8250 (mp0) cc_final: 0.7892 (mp0) REVERT: D 680 LYS cc_start: 0.7563 (mttt) cc_final: 0.7072 (mptt) REVERT: D 1000 PHE cc_start: 0.8243 (m-80) cc_final: 0.7932 (m-80) REVERT: D 1006 CYS cc_start: 0.7833 (m) cc_final: 0.7589 (m) REVERT: D 1020 TYR cc_start: 0.7514 (m-10) cc_final: 0.6011 (t80) outliers start: 58 outliers final: 20 residues processed: 363 average time/residue: 1.6161 time to fit residues: 736.9313 Evaluate side-chains 331 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 311 time to evaluate : 3.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 288 ARG Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 440 ASP 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 B residue 440 ASP Chi-restraints excluded: chain B residue 488 LEU 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 C residue 440 ASP Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 288 ARG Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 488 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 327 optimal weight: 4.9990 chunk 248 optimal weight: 0.9980 chunk 171 optimal weight: 0.5980 chunk 36 optimal weight: 7.9990 chunk 158 optimal weight: 0.9990 chunk 222 optimal weight: 4.9990 chunk 332 optimal weight: 0.9980 chunk 351 optimal weight: 0.8980 chunk 173 optimal weight: 0.6980 chunk 314 optimal weight: 3.9990 chunk 94 optimal weight: 8.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 510 GLN C 510 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 29208 Z= 0.167 Angle : 0.484 8.109 39956 Z= 0.261 Chirality : 0.036 0.164 4688 Planarity : 0.003 0.041 4876 Dihedral : 7.025 56.529 5388 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.05 % Allowed : 13.18 % Favored : 84.77 % 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: 2.26 (0.14), residues: 3572 helix: 2.57 (0.10), residues: 2484 sheet: -2.75 (0.32), residues: 180 loop : -0.66 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 682 HIS 0.005 0.001 HIS C 136 PHE 0.011 0.001 PHE A 165 TYR 0.013 0.001 TYR A 999 ARG 0.003 0.000 ARG A 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 383 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 329 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: A 310 ARG cc_start: 0.7204 (ttt180) cc_final: 0.6597 (ttm-80) REVERT: A 615 GLU cc_start: 0.8559 (pt0) cc_final: 0.8164 (mm-30) REVERT: A 658 GLU cc_start: 0.8288 (mp0) cc_final: 0.7780 (mp0) REVERT: A 680 LYS cc_start: 0.7530 (mttt) cc_final: 0.7036 (mptt) REVERT: A 1000 PHE cc_start: 0.8167 (m-80) cc_final: 0.7866 (m-80) REVERT: A 1004 GLU cc_start: 0.7446 (tm-30) cc_final: 0.7148 (pt0) REVERT: A 1005 TYR cc_start: 0.6982 (OUTLIER) cc_final: 0.6639 (m-80) REVERT: A 1006 CYS cc_start: 0.7646 (m) cc_final: 0.7430 (m) REVERT: A 1020 TYR cc_start: 0.7389 (m-10) cc_final: 0.6001 (t80) REVERT: A 1061 GLU cc_start: 0.7695 (mt-10) cc_final: 0.7406 (mp0) REVERT: B 310 ARG cc_start: 0.7150 (ttt180) cc_final: 0.6538 (ttm-80) REVERT: B 615 GLU cc_start: 0.8531 (pt0) cc_final: 0.8137 (mm-30) REVERT: B 658 GLU cc_start: 0.8286 (mp0) cc_final: 0.7779 (mp0) REVERT: B 680 LYS cc_start: 0.7529 (mttt) cc_final: 0.7034 (mptt) REVERT: B 1000 PHE cc_start: 0.8164 (m-80) cc_final: 0.7862 (m-80) REVERT: B 1006 CYS cc_start: 0.7631 (m) cc_final: 0.7410 (m) REVERT: B 1020 TYR cc_start: 0.7438 (m-10) cc_final: 0.6040 (t80) REVERT: B 1061 GLU cc_start: 0.7696 (mt-10) cc_final: 0.7407 (mp0) REVERT: C 310 ARG cc_start: 0.7153 (ttt180) cc_final: 0.6540 (ttm-80) REVERT: C 615 GLU cc_start: 0.8531 (pt0) cc_final: 0.8139 (mm-30) REVERT: C 658 GLU cc_start: 0.8286 (mp0) cc_final: 0.7779 (mp0) REVERT: C 680 LYS cc_start: 0.7531 (mttt) cc_final: 0.7036 (mptt) REVERT: C 1000 PHE cc_start: 0.8166 (m-80) cc_final: 0.7858 (m-80) REVERT: C 1006 CYS cc_start: 0.7628 (m) cc_final: 0.7406 (m) REVERT: C 1020 TYR cc_start: 0.7436 (m-10) cc_final: 0.6039 (t80) REVERT: C 1061 GLU cc_start: 0.7695 (mt-10) cc_final: 0.7407 (mp0) REVERT: D 310 ARG cc_start: 0.7152 (ttt180) cc_final: 0.6540 (ttm-80) REVERT: D 615 GLU cc_start: 0.8531 (pt0) cc_final: 0.8138 (mm-30) REVERT: D 658 GLU cc_start: 0.8287 (mp0) cc_final: 0.7779 (mp0) REVERT: D 680 LYS cc_start: 0.7530 (mttt) cc_final: 0.7035 (mptt) REVERT: D 1000 PHE cc_start: 0.8166 (m-80) cc_final: 0.7863 (m-80) REVERT: D 1006 CYS cc_start: 0.7626 (m) cc_final: 0.7404 (m) REVERT: D 1020 TYR cc_start: 0.7434 (m-10) cc_final: 0.6038 (t80) REVERT: D 1061 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7407 (mp0) outliers start: 54 outliers final: 32 residues processed: 364 average time/residue: 1.7604 time to fit residues: 802.2168 Evaluate side-chains 340 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 307 time to evaluate : 3.204 ------------------------------------------------------------------------------- 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 920 ASP Chi-restraints excluded: chain A residue 1005 TYR Chi-restraints excluded: chain A residue 1069 THR 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 440 ASP Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 920 ASP Chi-restraints excluded: chain B residue 1069 THR 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 440 ASP Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 920 ASP Chi-restraints excluded: chain C residue 1069 THR 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 440 ASP Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 920 ASP 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: 0.5980 chunk 199 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 chunk 261 optimal weight: 0.9990 chunk 145 optimal weight: 5.9990 chunk 300 optimal weight: 5.9990 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: 2.3188 ------------------------------------------------------------------------------- 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: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 29208 Z= 0.311 Angle : 0.529 7.636 39956 Z= 0.284 Chirality : 0.038 0.157 4688 Planarity : 0.004 0.048 4876 Dihedral : 7.312 58.446 5388 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.64 % Favored : 96.25 % Rotamer: Outliers : 2.01 % Allowed : 14.58 % Favored : 83.41 % 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: 2.11 (0.14), residues: 3572 helix: 2.48 (0.10), residues: 2484 sheet: -2.87 (0.32), residues: 180 loop : -0.80 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 682 HIS 0.004 0.001 HIS A 185 PHE 0.014 0.001 PHE A 874 TYR 0.017 0.001 TYR B 186 ARG 0.002 0.000 ARG A 998 *********************** 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 382 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 329 time to evaluate : 3.128 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: 0.7155 (ttt180) cc_final: 0.6505 (ttm-80) REVERT: A 615 GLU cc_start: 0.8587 (pt0) cc_final: 0.8171 (mm-30) REVERT: A 658 GLU cc_start: 0.8367 (mp0) cc_final: 0.7816 (mp0) REVERT: A 680 LYS cc_start: 0.7561 (mttt) cc_final: 0.7079 (mptt) REVERT: A 1000 PHE cc_start: 0.8169 (m-80) cc_final: 0.7823 (m-80) REVERT: A 1005 TYR cc_start: 0.7032 (OUTLIER) cc_final: 0.6340 (t80) REVERT: A 1020 TYR cc_start: 0.7417 (m-10) cc_final: 0.5998 (t80) REVERT: B 310 ARG cc_start: 0.7141 (ttt180) cc_final: 0.6498 (ttm-80) REVERT: B 615 GLU cc_start: 0.8559 (pt0) cc_final: 0.8144 (mm-30) REVERT: B 658 GLU cc_start: 0.8365 (mp0) cc_final: 0.7814 (mp0) REVERT: B 680 LYS cc_start: 0.7560 (mttt) cc_final: 0.7078 (mptt) REVERT: B 1000 PHE cc_start: 0.8186 (m-80) cc_final: 0.7846 (m-80) REVERT: B 1006 CYS cc_start: 0.7682 (m) cc_final: 0.7479 (m) REVERT: B 1020 TYR cc_start: 0.7465 (m-10) cc_final: 0.6038 (t80) REVERT: C 310 ARG cc_start: 0.7142 (ttt180) cc_final: 0.6500 (ttm-80) REVERT: C 615 GLU cc_start: 0.8560 (pt0) cc_final: 0.8145 (mm-30) REVERT: C 658 GLU cc_start: 0.8363 (mp0) cc_final: 0.7813 (mp0) REVERT: C 680 LYS cc_start: 0.7561 (mttt) cc_final: 0.7078 (mptt) REVERT: C 1000 PHE cc_start: 0.8187 (m-80) cc_final: 0.7847 (m-80) REVERT: C 1006 CYS cc_start: 0.7682 (m) cc_final: 0.7479 (m) REVERT: C 1020 TYR cc_start: 0.7462 (m-10) cc_final: 0.6036 (t80) REVERT: D 310 ARG cc_start: 0.7142 (ttt180) cc_final: 0.6500 (ttm-80) REVERT: D 615 GLU cc_start: 0.8558 (pt0) cc_final: 0.8145 (mm-30) REVERT: D 658 GLU cc_start: 0.8366 (mp0) cc_final: 0.7815 (mp0) REVERT: D 680 LYS cc_start: 0.7562 (mttt) cc_final: 0.7080 (mptt) REVERT: D 1000 PHE cc_start: 0.8186 (m-80) cc_final: 0.7846 (m-80) REVERT: D 1006 CYS cc_start: 0.7679 (m) cc_final: 0.7475 (m) REVERT: D 1020 TYR cc_start: 0.7461 (m-10) cc_final: 0.6036 (t80) outliers start: 53 outliers final: 33 residues processed: 361 average time/residue: 1.6828 time to fit residues: 757.1628 Evaluate side-chains 339 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 305 time to evaluate : 3.113 ------------------------------------------------------------------------------- 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 997 GLN 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 488 LEU Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 997 GLN Chi-restraints excluded: chain B residue 1007 ASN 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 440 ASP Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 997 GLN 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 488 LEU Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 997 GLN Chi-restraints excluded: chain D residue 1007 ASN 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: 1.9990 chunk 206 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 chunk 352 optimal weight: 0.9990 chunk 292 optimal weight: 7.9990 chunk 163 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 116 optimal weight: 5.9990 chunk 184 optimal weight: 10.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 429 GLN B 429 GLN C 429 GLN D 429 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 29208 Z= 0.317 Angle : 0.528 7.860 39956 Z= 0.285 Chirality : 0.038 0.168 4688 Planarity : 0.004 0.049 4876 Dihedral : 7.319 59.175 5388 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.92 % Favored : 95.97 % Rotamer: Outliers : 2.12 % Allowed : 14.89 % Favored : 82.99 % 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: 1.97 (0.14), residues: 3572 helix: 2.41 (0.10), residues: 2488 sheet: -3.02 (0.32), residues: 180 loop : -0.93 (0.20), residues: 904 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 0.013 0.001 PHE A 874 TYR 0.012 0.001 TYR A1005 ARG 0.002 0.000 ARG C 278 *********************** 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 388 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 332 time to evaluate : 3.128 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: 0.7195 (ttt180) cc_final: 0.6531 (ttm-80) REVERT: A 615 GLU cc_start: 0.8602 (pt0) cc_final: 0.8180 (mm-30) REVERT: A 658 GLU cc_start: 0.8383 (mp0) cc_final: 0.7957 (mp0) REVERT: A 680 LYS cc_start: 0.7549 (mttt) cc_final: 0.7059 (mptt) REVERT: A 1000 PHE cc_start: 0.8152 (m-80) cc_final: 0.7799 (m-80) REVERT: A 1005 TYR cc_start: 0.7045 (OUTLIER) cc_final: 0.6253 (t80) REVERT: A 1020 TYR cc_start: 0.7416 (m-10) cc_final: 0.6024 (t80) REVERT: B 310 ARG cc_start: 0.7185 (ttt180) cc_final: 0.6527 (ttm-80) REVERT: B 615 GLU cc_start: 0.8590 (pt0) cc_final: 0.8177 (mm-30) REVERT: B 658 GLU cc_start: 0.8383 (mp0) cc_final: 0.7956 (mp0) REVERT: B 680 LYS cc_start: 0.7550 (mttt) cc_final: 0.7061 (mptt) REVERT: B 1000 PHE cc_start: 0.8151 (m-80) cc_final: 0.7798 (m-80) REVERT: B 1005 TYR cc_start: 0.6958 (OUTLIER) cc_final: 0.6338 (t80) REVERT: B 1020 TYR cc_start: 0.7413 (m-10) cc_final: 0.6014 (t80) REVERT: C 310 ARG cc_start: 0.7185 (ttt180) cc_final: 0.6527 (ttm-80) REVERT: C 615 GLU cc_start: 0.8591 (pt0) cc_final: 0.8179 (mm-30) REVERT: C 658 GLU cc_start: 0.8383 (mp0) cc_final: 0.7956 (mp0) REVERT: C 680 LYS cc_start: 0.7552 (mttt) cc_final: 0.7061 (mptt) REVERT: C 1000 PHE cc_start: 0.8152 (m-80) cc_final: 0.7799 (m-80) REVERT: C 1005 TYR cc_start: 0.6960 (OUTLIER) cc_final: 0.6340 (t80) REVERT: C 1020 TYR cc_start: 0.7412 (m-10) cc_final: 0.6015 (t80) REVERT: D 310 ARG cc_start: 0.7186 (ttt180) cc_final: 0.6528 (ttm-80) REVERT: D 615 GLU cc_start: 0.8590 (pt0) cc_final: 0.8179 (mm-30) REVERT: D 658 GLU cc_start: 0.8383 (mp0) cc_final: 0.7954 (mp0) REVERT: D 680 LYS cc_start: 0.7552 (mttt) cc_final: 0.7062 (mptt) REVERT: D 1000 PHE cc_start: 0.8153 (m-80) cc_final: 0.7800 (m-80) REVERT: D 1005 TYR cc_start: 0.6958 (OUTLIER) cc_final: 0.6340 (t80) REVERT: D 1020 TYR cc_start: 0.7412 (m-10) cc_final: 0.6014 (t80) outliers start: 56 outliers final: 38 residues processed: 367 average time/residue: 1.7063 time to fit residues: 776.6672 Evaluate side-chains 358 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 316 time to evaluate : 3.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 262 LEU 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 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 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 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 339 optimal weight: 0.9990 chunk 39 optimal weight: 7.9990 chunk 200 optimal weight: 4.9990 chunk 257 optimal weight: 3.9990 chunk 199 optimal weight: 0.8980 chunk 296 optimal weight: 4.9990 chunk 196 optimal weight: 9.9990 chunk 350 optimal weight: 0.7980 chunk 219 optimal weight: 1.9990 chunk 213 optimal weight: 9.9990 chunk 161 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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: 0.7351 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29208 Z= 0.184 Angle : 0.491 9.267 39956 Z= 0.264 Chirality : 0.036 0.162 4688 Planarity : 0.003 0.046 4876 Dihedral : 6.982 58.332 5388 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.39 % Favored : 96.50 % Rotamer: Outliers : 1.74 % Allowed : 16.21 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.14), residues: 3572 helix: 2.51 (0.10), residues: 2476 sheet: -2.97 (0.32), residues: 180 loop : -0.84 (0.20), residues: 916 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 874 TYR 0.013 0.001 TYR A 999 ARG 0.002 0.000 ARG C 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 366 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 320 time to evaluate : 3.090 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 209 ILE cc_start: 0.8364 (mp) cc_final: 0.8151 (mp) REVERT: A 310 ARG cc_start: 0.7187 (ttt180) cc_final: 0.6529 (ttm-80) REVERT: A 342 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8230 (mt) REVERT: A 615 GLU cc_start: 0.8575 (pt0) cc_final: 0.8183 (mm-30) REVERT: A 658 GLU cc_start: 0.8393 (mp0) cc_final: 0.7962 (mp0) REVERT: A 680 LYS cc_start: 0.7540 (mttt) cc_final: 0.7052 (mptt) REVERT: A 1000 PHE cc_start: 0.8089 (m-80) cc_final: 0.7745 (m-80) REVERT: A 1005 TYR cc_start: 0.6958 (OUTLIER) cc_final: 0.6400 (t80) REVERT: A 1020 TYR cc_start: 0.7390 (m-10) cc_final: 0.6030 (t80) REVERT: B 310 ARG cc_start: 0.7122 (ttt180) cc_final: 0.6472 (ttm-80) REVERT: B 342 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8239 (mt) REVERT: B 615 GLU cc_start: 0.8566 (pt0) cc_final: 0.8180 (mm-30) REVERT: B 658 GLU cc_start: 0.8392 (mp0) cc_final: 0.7960 (mp0) REVERT: B 680 LYS cc_start: 0.7540 (mttt) cc_final: 0.7052 (mptt) REVERT: B 1000 PHE cc_start: 0.8086 (m-80) cc_final: 0.7743 (m-80) REVERT: B 1005 TYR cc_start: 0.7004 (OUTLIER) cc_final: 0.6185 (t80) REVERT: B 1020 TYR cc_start: 0.7388 (m-10) cc_final: 0.6029 (t80) REVERT: C 310 ARG cc_start: 0.7122 (ttt180) cc_final: 0.6473 (ttm-80) REVERT: C 342 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8239 (mt) REVERT: C 615 GLU cc_start: 0.8567 (pt0) cc_final: 0.8180 (mm-30) REVERT: C 658 GLU cc_start: 0.8391 (mp0) cc_final: 0.7959 (mp0) REVERT: C 680 LYS cc_start: 0.7540 (mttt) cc_final: 0.7052 (mptt) REVERT: C 1000 PHE cc_start: 0.8088 (m-80) cc_final: 0.7744 (m-80) REVERT: C 1005 TYR cc_start: 0.7004 (OUTLIER) cc_final: 0.6184 (t80) REVERT: C 1020 TYR cc_start: 0.7389 (m-10) cc_final: 0.6031 (t80) REVERT: D 310 ARG cc_start: 0.7125 (ttt180) cc_final: 0.6475 (ttm-80) REVERT: D 342 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8239 (mt) REVERT: D 615 GLU cc_start: 0.8565 (pt0) cc_final: 0.8180 (mm-30) REVERT: D 658 GLU cc_start: 0.8391 (mp0) cc_final: 0.7958 (mp0) REVERT: D 680 LYS cc_start: 0.7538 (mttt) cc_final: 0.7049 (mptt) REVERT: D 1000 PHE cc_start: 0.8088 (m-80) cc_final: 0.7745 (m-80) REVERT: D 1005 TYR cc_start: 0.7005 (OUTLIER) cc_final: 0.6185 (t80) REVERT: D 1020 TYR cc_start: 0.7388 (m-10) cc_final: 0.6029 (t80) outliers start: 46 outliers final: 28 residues processed: 350 average time/residue: 1.6835 time to fit residues: 738.0200 Evaluate side-chains 350 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 314 time to evaluate : 3.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 262 LEU 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 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 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 217 optimal weight: 6.9990 chunk 140 optimal weight: 3.9990 chunk 209 optimal weight: 6.9990 chunk 105 optimal weight: 10.0000 chunk 68 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 chunk 223 optimal weight: 3.9990 chunk 239 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 275 optimal weight: 0.0870 overall best weight: 1.0962 ------------------------------------------------------------------------------- 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: 0.7348 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29208 Z= 0.180 Angle : 0.487 10.240 39956 Z= 0.261 Chirality : 0.036 0.166 4688 Planarity : 0.003 0.045 4876 Dihedral : 6.833 57.891 5388 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.36 % Favored : 96.53 % Rotamer: Outliers : 1.59 % Allowed : 16.86 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.16 (0.14), residues: 3572 helix: 2.55 (0.10), residues: 2476 sheet: -2.92 (0.32), residues: 180 loop : -0.83 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 525 HIS 0.005 0.001 HIS C 136 PHE 0.010 0.001 PHE D 874 TYR 0.013 0.001 TYR A 999 ARG 0.001 0.000 ARG A 278 *********************** 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 350 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 308 time to evaluate : 3.111 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 209 ILE cc_start: 0.8367 (mp) cc_final: 0.8165 (mp) REVERT: A 310 ARG cc_start: 0.7129 (ttt180) cc_final: 0.6478 (ttm-80) REVERT: A 342 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8235 (mt) REVERT: A 469 ASP cc_start: 0.7615 (t70) cc_final: 0.7239 (m-30) REVERT: A 615 GLU cc_start: 0.8595 (pt0) cc_final: 0.8204 (mm-30) REVERT: A 658 GLU cc_start: 0.8411 (mp0) cc_final: 0.7984 (mp0) REVERT: A 680 LYS cc_start: 0.7539 (mttt) cc_final: 0.7057 (mptt) REVERT: A 1000 PHE cc_start: 0.8073 (m-80) cc_final: 0.7713 (m-80) REVERT: A 1020 TYR cc_start: 0.7384 (m-10) cc_final: 0.6036 (t80) REVERT: B 310 ARG cc_start: 0.7109 (ttt180) cc_final: 0.6476 (ttm-80) REVERT: B 342 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8232 (mt) REVERT: B 469 ASP cc_start: 0.7619 (t70) cc_final: 0.7240 (m-30) REVERT: B 615 GLU cc_start: 0.8558 (pt0) cc_final: 0.8165 (mm-30) REVERT: B 658 GLU cc_start: 0.8410 (mp0) cc_final: 0.7982 (mp0) REVERT: B 680 LYS cc_start: 0.7539 (mttt) cc_final: 0.7056 (mptt) REVERT: B 1000 PHE cc_start: 0.8099 (m-80) cc_final: 0.7743 (m-80) REVERT: B 1005 TYR cc_start: 0.6800 (OUTLIER) cc_final: 0.6105 (t80) REVERT: B 1020 TYR cc_start: 0.7382 (m-10) cc_final: 0.6036 (t80) REVERT: C 310 ARG cc_start: 0.7110 (ttt180) cc_final: 0.6477 (ttm-80) REVERT: C 342 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8232 (mt) REVERT: C 469 ASP cc_start: 0.7614 (t70) cc_final: 0.7236 (m-30) REVERT: C 615 GLU cc_start: 0.8558 (pt0) cc_final: 0.8165 (mm-30) REVERT: C 658 GLU cc_start: 0.8409 (mp0) cc_final: 0.7981 (mp0) REVERT: C 680 LYS cc_start: 0.7540 (mttt) cc_final: 0.7057 (mptt) REVERT: C 1000 PHE cc_start: 0.8102 (m-80) cc_final: 0.7744 (m-80) REVERT: C 1005 TYR cc_start: 0.6801 (OUTLIER) cc_final: 0.6105 (t80) REVERT: C 1020 TYR cc_start: 0.7382 (m-10) cc_final: 0.6037 (t80) REVERT: D 310 ARG cc_start: 0.7110 (ttt180) cc_final: 0.6478 (ttm-80) REVERT: D 342 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8232 (mt) REVERT: D 469 ASP cc_start: 0.7619 (t70) cc_final: 0.7241 (m-30) REVERT: D 615 GLU cc_start: 0.8556 (pt0) cc_final: 0.8165 (mm-30) REVERT: D 658 GLU cc_start: 0.8410 (mp0) cc_final: 0.7982 (mp0) REVERT: D 680 LYS cc_start: 0.7538 (mttt) cc_final: 0.7055 (mptt) REVERT: D 1000 PHE cc_start: 0.8102 (m-80) cc_final: 0.7745 (m-80) REVERT: D 1005 TYR cc_start: 0.6799 (OUTLIER) cc_final: 0.6104 (t80) REVERT: D 1020 TYR cc_start: 0.7379 (m-10) cc_final: 0.6034 (t80) outliers start: 42 outliers final: 22 residues processed: 332 average time/residue: 1.6535 time to fit residues: 685.7455 Evaluate side-chains 330 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 301 time to evaluate : 3.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 262 LEU 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 849 VAL 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 849 VAL Chi-restraints excluded: chain B residue 1005 TYR Chi-restraints excluded: chain C residue 262 LEU 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: 2.9990 chunk 336 optimal weight: 0.6980 chunk 306 optimal weight: 4.9990 chunk 326 optimal weight: 0.0870 chunk 196 optimal weight: 7.9990 chunk 142 optimal weight: 2.9990 chunk 256 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 295 optimal weight: 6.9990 chunk 309 optimal weight: 2.9990 chunk 325 optimal weight: 2.9990 overall best weight: 1.5564 ------------------------------------------------------------------------------- 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: 0.7359 moved from start: 0.3378 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= 0.226 Angle : 0.494 9.098 39956 Z= 0.265 Chirality : 0.037 0.179 4688 Planarity : 0.004 0.045 4876 Dihedral : 6.834 57.809 5388 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.81 % Favored : 96.08 % Rotamer: Outliers : 1.48 % Allowed : 16.97 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.50 (0.10), residues: 2480 sheet: -2.93 (0.32), residues: 180 loop : -0.85 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 525 HIS 0.004 0.001 HIS C 136 PHE 0.013 0.001 PHE C 523 TYR 0.012 0.001 TYR D 999 ARG 0.004 0.000 ARG C 288 *********************** 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 353 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 314 time to evaluate : 3.126 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: 0.7136 (ttt180) cc_final: 0.6493 (ttm-80) REVERT: A 342 LEU cc_start: 0.8509 (mm) cc_final: 0.8229 (mt) REVERT: A 469 ASP cc_start: 0.7631 (t70) cc_final: 0.7250 (m-30) REVERT: A 615 GLU cc_start: 0.8599 (pt0) cc_final: 0.8209 (mm-30) REVERT: A 616 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8306 (tm-30) REVERT: A 658 GLU cc_start: 0.8417 (mp0) cc_final: 0.7985 (mp0) REVERT: A 680 LYS cc_start: 0.7549 (mttt) cc_final: 0.7065 (mptt) REVERT: A 1000 PHE cc_start: 0.8111 (m-80) cc_final: 0.7751 (m-80) REVERT: A 1020 TYR cc_start: 0.7407 (m-10) cc_final: 0.6036 (t80) REVERT: B 310 ARG cc_start: 0.7124 (ttt180) cc_final: 0.6487 (ttm-80) REVERT: B 342 LEU cc_start: 0.8510 (mm) cc_final: 0.8235 (mt) REVERT: B 469 ASP cc_start: 0.7631 (t70) cc_final: 0.7248 (m-30) REVERT: B 615 GLU cc_start: 0.8560 (pt0) cc_final: 0.8170 (mm-30) REVERT: B 616 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8305 (tm-30) REVERT: B 658 GLU cc_start: 0.8418 (mp0) cc_final: 0.7892 (mp0) REVERT: B 680 LYS cc_start: 0.7549 (mttt) cc_final: 0.7065 (mptt) REVERT: B 1000 PHE cc_start: 0.8119 (m-80) cc_final: 0.7757 (m-80) REVERT: B 1005 TYR cc_start: 0.6738 (OUTLIER) cc_final: 0.6056 (t80) REVERT: B 1020 TYR cc_start: 0.7376 (m-10) cc_final: 0.6039 (t80) REVERT: C 310 ARG cc_start: 0.7126 (ttt180) cc_final: 0.6489 (ttm-80) REVERT: C 342 LEU cc_start: 0.8510 (mm) cc_final: 0.8209 (mt) REVERT: C 469 ASP cc_start: 0.7631 (t70) cc_final: 0.7248 (m-30) REVERT: C 615 GLU cc_start: 0.8561 (pt0) cc_final: 0.8171 (mm-30) REVERT: C 616 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8305 (tm-30) REVERT: C 658 GLU cc_start: 0.8417 (mp0) cc_final: 0.7891 (mp0) REVERT: C 680 LYS cc_start: 0.7551 (mttt) cc_final: 0.7066 (mptt) REVERT: C 1000 PHE cc_start: 0.8121 (m-80) cc_final: 0.7758 (m-80) REVERT: C 1005 TYR cc_start: 0.6738 (OUTLIER) cc_final: 0.6057 (t80) REVERT: C 1020 TYR cc_start: 0.7378 (m-10) cc_final: 0.6040 (t80) REVERT: D 310 ARG cc_start: 0.7127 (ttt180) cc_final: 0.6491 (ttm-80) REVERT: D 342 LEU cc_start: 0.8512 (mm) cc_final: 0.8236 (mt) REVERT: D 469 ASP cc_start: 0.7634 (t70) cc_final: 0.7252 (m-30) REVERT: D 615 GLU cc_start: 0.8561 (pt0) cc_final: 0.8171 (mm-30) REVERT: D 616 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8305 (tm-30) REVERT: D 658 GLU cc_start: 0.8418 (mp0) cc_final: 0.7892 (mp0) REVERT: D 680 LYS cc_start: 0.7551 (mttt) cc_final: 0.7067 (mptt) REVERT: D 1000 PHE cc_start: 0.8122 (m-80) cc_final: 0.7759 (m-80) REVERT: D 1005 TYR cc_start: 0.6739 (OUTLIER) cc_final: 0.6055 (t80) REVERT: D 1020 TYR cc_start: 0.7376 (m-10) cc_final: 0.6039 (t80) outliers start: 39 outliers final: 32 residues processed: 338 average time/residue: 1.7242 time to fit residues: 729.1628 Evaluate side-chains 343 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 304 time to evaluate : 3.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 262 LEU 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 440 ASP Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain B residue 262 LEU 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 381 LEU Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 920 ASP Chi-restraints excluded: chain B residue 997 GLN Chi-restraints excluded: chain B residue 1005 TYR Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 326 CYS Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 616 GLU Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 920 ASP Chi-restraints excluded: chain C residue 997 GLN Chi-restraints excluded: chain C residue 1005 TYR Chi-restraints excluded: chain D residue 262 LEU 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 381 LEU Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 616 GLU Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 920 ASP 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: 0.9980 chunk 345 optimal weight: 2.9990 chunk 211 optimal weight: 2.9990 chunk 164 optimal weight: 0.8980 chunk 240 optimal weight: 0.9990 chunk 362 optimal weight: 9.9990 chunk 333 optimal weight: 0.8980 chunk 288 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 223 optimal weight: 3.9990 chunk 177 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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: 0.7355 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29208 Z= 0.204 Angle : 0.502 12.811 39956 Z= 0.269 Chirality : 0.036 0.179 4688 Planarity : 0.003 0.045 4876 Dihedral : 6.740 58.474 5388 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.81 % Favored : 96.08 % Rotamer: Outliers : 1.21 % Allowed : 17.23 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.09 (0.14), residues: 3572 helix: 2.50 (0.10), residues: 2480 sheet: -2.94 (0.32), residues: 180 loop : -0.87 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 525 HIS 0.004 0.001 HIS D 136 PHE 0.016 0.001 PHE C 523 TYR 0.013 0.001 TYR A 999 ARG 0.003 0.000 ARG C 288 ********************** 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 351 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 319 time to evaluate : 3.157 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: 0.7212 (ttt180) cc_final: 0.6583 (ttm-80) REVERT: A 342 LEU cc_start: 0.8508 (mm) cc_final: 0.8207 (mt) REVERT: A 469 ASP cc_start: 0.7598 (t70) cc_final: 0.7225 (m-30) REVERT: A 615 GLU cc_start: 0.8593 (pt0) cc_final: 0.8207 (mm-30) REVERT: A 616 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8302 (tm-30) REVERT: A 658 GLU cc_start: 0.8420 (mp0) cc_final: 0.7896 (mp0) REVERT: A 680 LYS cc_start: 0.7543 (mttt) cc_final: 0.7061 (mptt) REVERT: A 1000 PHE cc_start: 0.8094 (m-80) cc_final: 0.7719 (m-80) REVERT: A 1020 TYR cc_start: 0.7397 (m-10) cc_final: 0.6043 (t80) REVERT: B 310 ARG cc_start: 0.7208 (ttt180) cc_final: 0.6576 (ttm-80) REVERT: B 342 LEU cc_start: 0.8509 (mm) cc_final: 0.8212 (mt) REVERT: B 469 ASP cc_start: 0.7599 (t70) cc_final: 0.7224 (m-30) REVERT: B 615 GLU cc_start: 0.8554 (pt0) cc_final: 0.8167 (mm-30) REVERT: B 616 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8302 (tm-30) REVERT: B 658 GLU cc_start: 0.8418 (mp0) cc_final: 0.7894 (mp0) REVERT: B 680 LYS cc_start: 0.7542 (mttt) cc_final: 0.7061 (mptt) REVERT: B 1000 PHE cc_start: 0.8103 (m-80) cc_final: 0.7727 (m-80) REVERT: B 1005 TYR cc_start: 0.6706 (OUTLIER) cc_final: 0.6048 (t80) REVERT: B 1020 TYR cc_start: 0.7366 (m-10) cc_final: 0.6046 (t80) REVERT: C 310 ARG cc_start: 0.7211 (ttt180) cc_final: 0.6578 (ttm-80) REVERT: C 342 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8212 (mt) REVERT: C 469 ASP cc_start: 0.7599 (t70) cc_final: 0.7224 (m-30) REVERT: C 615 GLU cc_start: 0.8555 (pt0) cc_final: 0.8168 (mm-30) REVERT: C 616 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8302 (tm-30) REVERT: C 658 GLU cc_start: 0.8417 (mp0) cc_final: 0.7893 (mp0) REVERT: C 680 LYS cc_start: 0.7543 (mttt) cc_final: 0.7061 (mptt) REVERT: C 1000 PHE cc_start: 0.8105 (m-80) cc_final: 0.7729 (m-80) REVERT: C 1005 TYR cc_start: 0.6706 (OUTLIER) cc_final: 0.6049 (t80) REVERT: C 1020 TYR cc_start: 0.7366 (m-10) cc_final: 0.6047 (t80) REVERT: D 310 ARG cc_start: 0.7212 (ttt180) cc_final: 0.6580 (ttm-80) REVERT: D 342 LEU cc_start: 0.8511 (mm) cc_final: 0.8214 (mt) REVERT: D 469 ASP cc_start: 0.7600 (t70) cc_final: 0.7225 (m-30) REVERT: D 615 GLU cc_start: 0.8554 (pt0) cc_final: 0.8169 (mm-30) REVERT: D 616 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8303 (tm-30) REVERT: D 658 GLU cc_start: 0.8418 (mp0) cc_final: 0.7892 (mp0) REVERT: D 680 LYS cc_start: 0.7543 (mttt) cc_final: 0.7061 (mptt) REVERT: D 1000 PHE cc_start: 0.8106 (m-80) cc_final: 0.7730 (m-80) REVERT: D 1005 TYR cc_start: 0.6707 (OUTLIER) cc_final: 0.6050 (t80) REVERT: D 1020 TYR cc_start: 0.7365 (m-10) cc_final: 0.6045 (t80) outliers start: 32 outliers final: 24 residues processed: 331 average time/residue: 1.7643 time to fit residues: 736.8672 Evaluate side-chains 337 residues out of total 3276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 305 time to evaluate : 3.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 262 LEU 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 616 GLU Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain B residue 262 LEU 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 616 GLU Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 920 ASP Chi-restraints excluded: chain B residue 1005 TYR Chi-restraints excluded: chain C residue 262 LEU 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 385 LEU Chi-restraints excluded: chain C residue 616 GLU 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 262 LEU 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 616 GLU Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 920 ASP 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: 2.9990 chunk 307 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 266 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 80 optimal weight: 0.5980 chunk 289 optimal weight: 9.9990 chunk 121 optimal weight: 7.9990 chunk 296 optimal weight: 0.0470 chunk 36 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.7284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.171889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.103314 restraints weight = 106547.981| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.96 r_work: 0.3233 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.3542 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 : 0.512 12.082 39956 Z= 0.274 Chirality : 0.037 0.182 4688 Planarity : 0.004 0.045 4876 Dihedral : 6.783 58.710 5388 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.23 % Favored : 95.66 % Rotamer: Outliers : 1.52 % Allowed : 17.16 % 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: 2.05 (0.14), residues: 3572 helix: 2.46 (0.10), residues: 2484 sheet: -2.98 (0.32), residues: 180 loop : -0.89 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP C 525 HIS 0.007 0.001 HIS A 185 PHE 0.013 0.001 PHE D 523 TYR 0.013 0.001 TYR D 186 ARG 0.002 0.000 ARG C 288 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14593.35 seconds wall clock time: 247 minutes 45.66 seconds (14865.66 seconds total)