Starting phenix.real_space_refine on Tue Mar 19 10:04:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwk_23548/03_2024/7lwk_23548.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwk_23548/03_2024/7lwk_23548.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwk_23548/03_2024/7lwk_23548.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwk_23548/03_2024/7lwk_23548.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwk_23548/03_2024/7lwk_23548.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwk_23548/03_2024/7lwk_23548.pdb" } resolution = 2.92 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= -0.001 sd= 0.087 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: 4 Type Number sf(0) Gaussians S 105 5.16 5 C 15204 2.51 5 N 3924 2.21 5 O 4614 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23847 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7809 Classifications: {'peptide': 1001} Link IDs: {'PTRANS': 47, 'TRANS': 953} Chain breaks: 7 Chain: "B" Number of atoms: 7809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7809 Classifications: {'peptide': 1001} Link IDs: {'PTRANS': 47, 'TRANS': 953} Chain breaks: 7 Chain: "C" Number of atoms: 7809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7809 Classifications: {'peptide': 1001} Link IDs: {'PTRANS': 47, 'TRANS': 953} Chain breaks: 7 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 11.79, per 1000 atoms: 0.49 Number of scatterers: 23847 At special positions: 0 Unit cell: (133.625, 137.901, 176.385, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 105 16.00 O 4614 8.00 N 3924 7.00 C 15204 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.01 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=1.94 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.01 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.00 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.05 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.01 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.01 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 Links applied NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 603 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 657 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A1074 " " NAG A1310 " - " ASN A 165 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 603 " " NAG B1303 " - " ASN B 61 " " NAG B1304 " - " ASN B 657 " " NAG B1305 " - " ASN B 122 " " NAG B1306 " - " ASN B 282 " " NAG B1307 " - " ASN B 165 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 603 " " NAG C1305 " - " ASN C1074 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 165 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C 709 " " NAG C1310 " - " ASN C 122 " Time building additional restraints: 9.46 Conformation dependent library (CDL) restraints added in 4.3 seconds 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5622 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 49 sheets defined 26.9% alpha, 27.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.11 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.710A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 388 removed outlier: 4.519A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.671A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.544A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.639A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.746A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 939 Processing helix chain 'A' and resid 941 through 944 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.021A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 197 through 200 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.772A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.936A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.816A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.725A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 939 Processing helix chain 'B' and resid 941 through 944 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.603A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.262A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.784A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.715A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.814A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.010A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.820A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.640A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.506A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) Processing helix chain 'C' and resid 941 through 944 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.538A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.190A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.215A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.505A pdb=" N ARG C 567 " --> pdb=" O PHE A 43 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.749A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 5.998A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.524A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 3.771A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.532A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.722A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.467A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.726A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.801A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.962A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.457A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 790 removed outlier: 6.112A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.602A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.720A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.736A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.590A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.269A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.284A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.284A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.874A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.713A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.484A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.636A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.824A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.484A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.509A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 28 through 30 removed outlier: 7.876A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.716A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.624A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.866A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE6, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.964A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE8, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.472A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.742A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.026A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.499A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.569A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1068 hydrogen bonds defined for protein. 2907 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: 11.53 Time building geometry restraints manager: 10.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6434 1.33 - 1.46: 4509 1.46 - 1.58: 13294 1.58 - 1.70: 0 1.70 - 1.83: 129 Bond restraints: 24366 Sorted by residual: bond pdb=" CA PRO A 862 " pdb=" C PRO A 862 " ideal model delta sigma weight residual 1.517 1.544 -0.027 6.70e-03 2.23e+04 1.60e+01 bond pdb=" C5 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.413 1.489 -0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" CA PRO C 862 " pdb=" C PRO C 862 " ideal model delta sigma weight residual 1.517 1.542 -0.025 6.70e-03 2.23e+04 1.42e+01 bond pdb=" C5 NAG A1306 " pdb=" O5 NAG A1306 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" C5 NAG B1305 " pdb=" O5 NAG B1305 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.41e+01 ... (remaining 24361 not shown) Histogram of bond angle deviations from ideal: 98.10 - 105.54: 525 105.54 - 112.98: 11719 112.98 - 120.43: 12097 120.43 - 127.87: 8694 127.87 - 135.31: 109 Bond angle restraints: 33144 Sorted by residual: angle pdb=" CA PHE C 133 " pdb=" CB PHE C 133 " pdb=" CG PHE C 133 " ideal model delta sigma weight residual 113.80 119.63 -5.83 1.00e+00 1.00e+00 3.40e+01 angle pdb=" CA ASP C 796 " pdb=" CB ASP C 796 " pdb=" CG ASP C 796 " ideal model delta sigma weight residual 112.60 118.40 -5.80 1.00e+00 1.00e+00 3.37e+01 angle pdb=" CA PHE C 135 " pdb=" CB PHE C 135 " pdb=" CG PHE C 135 " ideal model delta sigma weight residual 113.80 119.47 -5.67 1.00e+00 1.00e+00 3.22e+01 angle pdb=" N MET C1050 " pdb=" CA MET C1050 " pdb=" CB MET C1050 " ideal model delta sigma weight residual 111.56 103.09 8.47 1.52e+00 4.33e-01 3.10e+01 angle pdb=" CA ASP A 796 " pdb=" CB ASP A 796 " pdb=" CG ASP A 796 " ideal model delta sigma weight residual 112.60 118.16 -5.56 1.00e+00 1.00e+00 3.09e+01 ... (remaining 33139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 13923 17.97 - 35.95: 775 35.95 - 53.92: 124 53.92 - 71.89: 57 71.89 - 89.87: 28 Dihedral angle restraints: 14907 sinusoidal: 6180 harmonic: 8727 Sorted by residual: dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -171.38 85.38 1 1.00e+01 1.00e-02 8.83e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -163.90 77.90 1 1.00e+01 1.00e-02 7.59e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -157.64 71.64 1 1.00e+01 1.00e-02 6.58e+01 ... (remaining 14904 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 2220 0.078 - 0.157: 1322 0.157 - 0.235: 274 0.235 - 0.314: 51 0.314 - 0.392: 9 Chirality restraints: 3876 Sorted by residual: chirality pdb=" CA ALA B 123 " pdb=" N ALA B 123 " pdb=" C ALA B 123 " pdb=" CB ALA B 123 " both_signs ideal model delta sigma weight residual False 2.48 2.09 0.39 2.00e-01 2.50e+01 3.85e+00 chirality pdb=" CA SER C 112 " pdb=" N SER C 112 " pdb=" C SER C 112 " pdb=" CB SER C 112 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.55e+00 chirality pdb=" CA ASP A 571 " pdb=" N ASP A 571 " pdb=" C ASP A 571 " pdb=" CB ASP A 571 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.54e+00 ... (remaining 3873 not shown) Planarity restraints: 4281 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 165 " -0.143 2.00e-02 2.50e+03 1.50e-01 2.80e+02 pdb=" CG ASN C 165 " 0.085 2.00e-02 2.50e+03 pdb=" OD1 ASN C 165 " 0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN C 165 " 0.226 2.00e-02 2.50e+03 pdb=" C1 NAG C1307 " -0.182 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 331 " 0.137 2.00e-02 2.50e+03 1.46e-01 2.68e+02 pdb=" CG ASN C 331 " -0.080 2.00e-02 2.50e+03 pdb=" OD1 ASN C 331 " -0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN C 331 " -0.226 2.00e-02 2.50e+03 pdb=" C1 NAG C1303 " 0.175 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 709 " -0.102 2.00e-02 2.50e+03 1.06e-01 1.41e+02 pdb=" CG ASN A 709 " 0.056 2.00e-02 2.50e+03 pdb=" OD1 ASN A 709 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN A 709 " 0.160 2.00e-02 2.50e+03 pdb=" C1 NAG A1308 " -0.129 2.00e-02 2.50e+03 ... (remaining 4278 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 11189 2.99 - 3.46: 22366 3.46 - 3.94: 39653 3.94 - 4.42: 44137 4.42 - 4.90: 75147 Nonbonded interactions: 192492 Sorted by model distance: nonbonded pdb=" OD1 ASP C 364 " pdb=" OG SER C 366 " model vdw 2.508 2.440 nonbonded pdb=" OD1 ASP A 364 " pdb=" OG SER A 366 " model vdw 2.510 2.440 nonbonded pdb=" OD1 ASP B 364 " pdb=" OG SER B 366 " model vdw 2.519 2.440 nonbonded pdb=" OE2 GLU A 918 " pdb=" OG SER C1123 " model vdw 2.535 2.440 nonbonded pdb=" OG SER B1123 " pdb=" OE2 GLU C 918 " model vdw 2.540 2.440 ... (remaining 192487 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 1.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.210 Check model and map are aligned: 0.370 Set scattering table: 0.240 Process input model: 66.240 Find NCS groups from input model: 1.450 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 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 : 0.013 0.076 24366 Z= 0.858 Angle : 1.774 9.539 33144 Z= 1.197 Chirality : 0.096 0.392 3876 Planarity : 0.013 0.159 4251 Dihedral : 12.788 89.865 9168 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 0.06 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.26 % Favored : 95.60 % Rotamer: Outliers : 0.65 % Allowed : 1.98 % Favored : 97.37 % Cbeta Deviations : 0.11 % 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: -0.78 (0.14), residues: 2955 helix: -1.14 (0.16), residues: 693 sheet: 0.68 (0.20), residues: 576 loop : -0.62 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.020 TRP A 104 HIS 0.010 0.002 HIS A1083 PHE 0.101 0.012 PHE C 718 TYR 0.148 0.019 TYR B 396 ARG 0.010 0.001 ARG C 577 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 389 time to evaluate : 2.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 HIS cc_start: 0.6923 (p90) cc_final: 0.6099 (p90) REVERT: A 237 ARG cc_start: 0.7509 (mtt90) cc_final: 0.6957 (ttm-80) REVERT: A 239 GLN cc_start: 0.8417 (tt0) cc_final: 0.8005 (tt0) REVERT: A 529 LYS cc_start: 0.7741 (mttt) cc_final: 0.7477 (tptt) REVERT: A 533 LEU cc_start: 0.8255 (tp) cc_final: 0.7651 (mt) REVERT: A 933 LYS cc_start: 0.8313 (mttt) cc_final: 0.7994 (mtpm) REVERT: A 954 GLN cc_start: 0.7921 (mt0) cc_final: 0.7719 (mt0) REVERT: A 1029 MET cc_start: 0.9104 (tpp) cc_final: 0.8764 (tpp) REVERT: B 202 LYS cc_start: 0.7619 (mttm) cc_final: 0.7088 (mttp) REVERT: B 230 PRO cc_start: 0.7918 (Cg_endo) cc_final: 0.7660 (Cg_exo) REVERT: B 239 GLN cc_start: 0.7312 (tt0) cc_final: 0.7025 (tp40) REVERT: B 362 VAL cc_start: 0.7729 (t) cc_final: 0.7483 (m) REVERT: B 436 TRP cc_start: 0.7545 (p90) cc_final: 0.6663 (p90) REVERT: B 511 VAL cc_start: 0.7580 (t) cc_final: 0.7329 (m) REVERT: B 529 LYS cc_start: 0.8125 (mttt) cc_final: 0.7682 (ttpp) REVERT: B 532 ASN cc_start: 0.8057 (t0) cc_final: 0.7647 (p0) REVERT: B 540 ASN cc_start: 0.7980 (t0) cc_final: 0.7764 (t0) REVERT: C 41 LYS cc_start: 0.7989 (mttt) cc_final: 0.7600 (mttp) REVERT: C 129 LYS cc_start: 0.6816 (mttm) cc_final: 0.6455 (mmtp) REVERT: C 205 SER cc_start: 0.9245 (p) cc_final: 0.8806 (t) REVERT: C 383 SER cc_start: 0.7556 (OUTLIER) cc_final: 0.6902 (p) REVERT: C 394 ASN cc_start: 0.5500 (m-40) cc_final: 0.5257 (m-40) REVERT: C 425 LEU cc_start: 0.7774 (mt) cc_final: 0.7354 (mt) REVERT: C 434 ILE cc_start: 0.8810 (mt) cc_final: 0.8130 (tp) REVERT: C 529 LYS cc_start: 0.7554 (mttt) cc_final: 0.7212 (mmmm) REVERT: C 586 ASP cc_start: 0.7747 (m-30) cc_final: 0.7380 (m-30) REVERT: C 747 THR cc_start: 0.8584 (m) cc_final: 0.8376 (p) REVERT: C 1029 MET cc_start: 0.9082 (tpp) cc_final: 0.8788 (tpp) outliers start: 17 outliers final: 4 residues processed: 404 average time/residue: 1.1671 time to fit residues: 550.9257 Evaluate side-chains 216 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 211 time to evaluate : 2.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 253 optimal weight: 0.8980 chunk 227 optimal weight: 10.0000 chunk 126 optimal weight: 7.9990 chunk 77 optimal weight: 0.9990 chunk 153 optimal weight: 5.9990 chunk 121 optimal weight: 0.8980 chunk 235 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 chunk 142 optimal weight: 5.9990 chunk 175 optimal weight: 0.6980 chunk 272 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 188 ASN A 519 HIS A 580 GLN A 641 ASN A 675 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN B 755 GLN B 914 ASN B 965 GLN C 121 ASN C 207 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 ASN C 935 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 24366 Z= 0.200 Angle : 0.622 8.318 33144 Z= 0.335 Chirality : 0.047 0.202 3876 Planarity : 0.004 0.033 4251 Dihedral : 6.123 52.822 3836 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.03 % Favored : 97.94 % Rotamer: Outliers : 2.44 % Allowed : 7.74 % Favored : 89.82 % 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: 0.36 (0.15), residues: 2955 helix: 1.05 (0.20), residues: 687 sheet: 0.90 (0.19), residues: 621 loop : -0.33 (0.15), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 436 HIS 0.005 0.001 HIS C 207 PHE 0.025 0.002 PHE C 855 TYR 0.023 0.002 TYR C 369 ARG 0.004 0.000 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 264 time to evaluate : 2.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.7049 (p0) cc_final: 0.6737 (p0) REVERT: A 190 ARG cc_start: 0.7035 (OUTLIER) cc_final: 0.6709 (mmt-90) REVERT: A 207 HIS cc_start: 0.7065 (p90) cc_final: 0.6699 (p90) REVERT: A 237 ARG cc_start: 0.7417 (mtt90) cc_final: 0.6945 (ttm-80) REVERT: A 239 GLN cc_start: 0.8392 (tt0) cc_final: 0.8040 (tt0) REVERT: A 383 SER cc_start: 0.6428 (OUTLIER) cc_final: 0.6033 (t) REVERT: A 394 ASN cc_start: 0.6151 (m-40) cc_final: 0.5927 (m-40) REVERT: A 529 LYS cc_start: 0.7808 (mttt) cc_final: 0.7525 (tptt) REVERT: A 533 LEU cc_start: 0.8149 (tp) cc_final: 0.7906 (mt) REVERT: A 954 GLN cc_start: 0.7774 (mt0) cc_final: 0.7548 (mt0) REVERT: A 994 ASP cc_start: 0.7648 (OUTLIER) cc_final: 0.7306 (m-30) REVERT: A 1029 MET cc_start: 0.8903 (tpp) cc_final: 0.8625 (tpp) REVERT: B 33 THR cc_start: 0.8147 (p) cc_final: 0.7757 (p) REVERT: B 202 LYS cc_start: 0.7437 (mttm) cc_final: 0.6995 (mttp) REVERT: B 230 PRO cc_start: 0.7546 (Cg_endo) cc_final: 0.7146 (Cg_exo) REVERT: B 239 GLN cc_start: 0.7399 (tt0) cc_final: 0.7059 (tt0) REVERT: B 436 TRP cc_start: 0.7297 (p90) cc_final: 0.6818 (p-90) REVERT: B 462 LYS cc_start: 0.7483 (mptp) cc_final: 0.6786 (pptt) REVERT: B 529 LYS cc_start: 0.8102 (mttt) cc_final: 0.7764 (ttpp) REVERT: C 41 LYS cc_start: 0.8000 (mttt) cc_final: 0.7694 (mttp) REVERT: C 129 LYS cc_start: 0.6619 (mttm) cc_final: 0.6333 (mttp) REVERT: C 205 SER cc_start: 0.9146 (p) cc_final: 0.8816 (t) REVERT: C 383 SER cc_start: 0.7537 (OUTLIER) cc_final: 0.6900 (p) REVERT: C 396 TYR cc_start: 0.7060 (m-80) cc_final: 0.5837 (m-80) REVERT: C 529 LYS cc_start: 0.7505 (mttt) cc_final: 0.7218 (mmmm) REVERT: C 675 GLN cc_start: 0.7033 (mt0) cc_final: 0.6789 (tm-30) REVERT: C 988 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7503 (tm-30) REVERT: C 1010 GLN cc_start: 0.7457 (mt0) cc_final: 0.7154 (pt0) outliers start: 64 outliers final: 20 residues processed: 300 average time/residue: 1.0593 time to fit residues: 376.5019 Evaluate side-chains 218 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 193 time to evaluate : 2.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1123 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 151 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 226 optimal weight: 0.9980 chunk 185 optimal weight: 2.9990 chunk 75 optimal weight: 0.3980 chunk 272 optimal weight: 1.9990 chunk 294 optimal weight: 1.9990 chunk 243 optimal weight: 20.0000 chunk 270 optimal weight: 0.9980 chunk 93 optimal weight: 0.5980 chunk 218 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 532 ASN A 613 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN B 334 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN B 935 GLN C 66 HIS ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN C1101 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 24366 Z= 0.168 Angle : 0.554 14.123 33144 Z= 0.292 Chirality : 0.045 0.167 3876 Planarity : 0.003 0.041 4251 Dihedral : 5.718 59.721 3833 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.48 % Allowed : 9.73 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.63 (0.15), residues: 2955 helix: 1.62 (0.21), residues: 669 sheet: 0.81 (0.20), residues: 594 loop : -0.18 (0.15), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 436 HIS 0.006 0.001 HIS C 207 PHE 0.024 0.001 PHE C 855 TYR 0.022 0.001 TYR B 170 ARG 0.004 0.000 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 222 time to evaluate : 2.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.7351 (OUTLIER) cc_final: 0.6689 (p0) REVERT: A 190 ARG cc_start: 0.7214 (OUTLIER) cc_final: 0.6973 (mmt-90) REVERT: A 207 HIS cc_start: 0.6973 (p90) cc_final: 0.6707 (p90) REVERT: A 237 ARG cc_start: 0.7481 (mtt90) cc_final: 0.7027 (ttm-80) REVERT: A 239 GLN cc_start: 0.8469 (tt0) cc_final: 0.7806 (tm-30) REVERT: A 347 PHE cc_start: 0.3735 (OUTLIER) cc_final: 0.3410 (t80) REVERT: A 529 LYS cc_start: 0.7758 (mttt) cc_final: 0.7508 (tptt) REVERT: A 531 THR cc_start: 0.8237 (t) cc_final: 0.7994 (p) REVERT: A 533 LEU cc_start: 0.8227 (tp) cc_final: 0.7915 (mt) REVERT: A 954 GLN cc_start: 0.7776 (mt0) cc_final: 0.7525 (mt0) REVERT: A 994 ASP cc_start: 0.7574 (OUTLIER) cc_final: 0.7282 (m-30) REVERT: B 33 THR cc_start: 0.8080 (p) cc_final: 0.7873 (p) REVERT: B 202 LYS cc_start: 0.7322 (mttm) cc_final: 0.6937 (mttp) REVERT: B 239 GLN cc_start: 0.7480 (tt0) cc_final: 0.7195 (tt0) REVERT: B 436 TRP cc_start: 0.7325 (p90) cc_final: 0.6942 (p-90) REVERT: B 462 LYS cc_start: 0.7432 (OUTLIER) cc_final: 0.6763 (pptt) REVERT: B 529 LYS cc_start: 0.8078 (mttt) cc_final: 0.7762 (ttpp) REVERT: B 740 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.7944 (ttt) REVERT: B 900 MET cc_start: 0.8495 (mtp) cc_final: 0.8279 (mtt) REVERT: B 957 GLN cc_start: 0.7694 (OUTLIER) cc_final: 0.7485 (tp-100) REVERT: C 41 LYS cc_start: 0.8124 (mttt) cc_final: 0.7842 (mttp) REVERT: C 102 ARG cc_start: 0.5961 (OUTLIER) cc_final: 0.5606 (ttm170) REVERT: C 129 LYS cc_start: 0.6666 (mttm) cc_final: 0.6385 (mttp) REVERT: C 205 SER cc_start: 0.9022 (p) cc_final: 0.8797 (t) REVERT: C 424 LYS cc_start: 0.7198 (tppt) cc_final: 0.6639 (tttm) REVERT: C 529 LYS cc_start: 0.7550 (mttt) cc_final: 0.7175 (mmmm) REVERT: C 675 GLN cc_start: 0.7059 (mt0) cc_final: 0.6818 (tm-30) REVERT: C 1010 GLN cc_start: 0.7433 (mt0) cc_final: 0.7182 (pt0) outliers start: 65 outliers final: 29 residues processed: 257 average time/residue: 1.0212 time to fit residues: 313.8419 Evaluate side-chains 227 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 190 time to evaluate : 2.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1142 GLN Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 723 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 269 optimal weight: 2.9990 chunk 205 optimal weight: 10.0000 chunk 141 optimal weight: 0.6980 chunk 30 optimal weight: 7.9990 chunk 130 optimal weight: 9.9990 chunk 183 optimal weight: 0.9990 chunk 273 optimal weight: 4.9990 chunk 289 optimal weight: 3.9990 chunk 143 optimal weight: 0.5980 chunk 259 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN C 207 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN C 856 ASN C1002 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 24366 Z= 0.206 Angle : 0.547 11.365 33144 Z= 0.286 Chirality : 0.045 0.294 3876 Planarity : 0.004 0.060 4251 Dihedral : 5.378 56.683 3832 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.32 % Allowed : 9.84 % Favored : 86.84 % 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: 0.75 (0.15), residues: 2955 helix: 1.87 (0.21), residues: 651 sheet: 0.88 (0.20), residues: 576 loop : -0.14 (0.15), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.006 0.001 HIS C 207 PHE 0.013 0.001 PHE A 643 TYR 0.023 0.001 TYR B 170 ARG 0.004 0.000 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 196 time to evaluate : 3.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.7308 (p0) cc_final: 0.7069 (m-40) REVERT: A 190 ARG cc_start: 0.7214 (OUTLIER) cc_final: 0.6962 (mmt-90) REVERT: A 207 HIS cc_start: 0.7032 (p90) cc_final: 0.6752 (p90) REVERT: A 237 ARG cc_start: 0.7512 (mtt90) cc_final: 0.6975 (ttm-80) REVERT: A 239 GLN cc_start: 0.8434 (tt0) cc_final: 0.7881 (tm-30) REVERT: A 347 PHE cc_start: 0.3838 (OUTLIER) cc_final: 0.3453 (t80) REVERT: A 529 LYS cc_start: 0.7795 (mttt) cc_final: 0.7591 (tptt) REVERT: A 651 ILE cc_start: 0.9291 (OUTLIER) cc_final: 0.9008 (mm) REVERT: A 954 GLN cc_start: 0.7783 (mt0) cc_final: 0.7570 (mt0) REVERT: A 994 ASP cc_start: 0.7570 (OUTLIER) cc_final: 0.7284 (m-30) REVERT: B 33 THR cc_start: 0.8093 (p) cc_final: 0.7865 (p) REVERT: B 52 GLN cc_start: 0.8065 (OUTLIER) cc_final: 0.7636 (tt0) REVERT: B 202 LYS cc_start: 0.7321 (mttm) cc_final: 0.6804 (mttp) REVERT: B 239 GLN cc_start: 0.7411 (tt0) cc_final: 0.7123 (tt0) REVERT: B 436 TRP cc_start: 0.7310 (p90) cc_final: 0.6943 (p-90) REVERT: B 462 LYS cc_start: 0.7455 (OUTLIER) cc_final: 0.6710 (pptt) REVERT: B 529 LYS cc_start: 0.8051 (mttt) cc_final: 0.7743 (ttpp) REVERT: B 740 MET cc_start: 0.8221 (OUTLIER) cc_final: 0.7830 (ttp) REVERT: B 957 GLN cc_start: 0.7734 (OUTLIER) cc_final: 0.7524 (tp-100) REVERT: C 41 LYS cc_start: 0.8163 (mttt) cc_final: 0.7894 (mttp) REVERT: C 102 ARG cc_start: 0.5757 (OUTLIER) cc_final: 0.5435 (ttm170) REVERT: C 205 SER cc_start: 0.9091 (p) cc_final: 0.8864 (t) REVERT: C 231 ILE cc_start: 0.8476 (OUTLIER) cc_final: 0.8231 (pt) REVERT: C 424 LYS cc_start: 0.7221 (tppt) cc_final: 0.6791 (tttm) REVERT: C 675 GLN cc_start: 0.7129 (mt0) cc_final: 0.6798 (pt0) outliers start: 87 outliers final: 43 residues processed: 252 average time/residue: 1.0277 time to fit residues: 311.1883 Evaluate side-chains 230 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 177 time to evaluate : 2.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1142 GLN Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1123 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 241 optimal weight: 0.9990 chunk 164 optimal weight: 0.6980 chunk 4 optimal weight: 6.9990 chunk 215 optimal weight: 0.8980 chunk 119 optimal weight: 0.5980 chunk 247 optimal weight: 7.9990 chunk 200 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 148 optimal weight: 10.0000 chunk 260 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1083 HIS B 188 ASN B 207 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN C1002 GLN C1010 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 24366 Z= 0.154 Angle : 0.518 9.450 33144 Z= 0.270 Chirality : 0.045 0.350 3876 Planarity : 0.003 0.047 4251 Dihedral : 5.014 52.268 3831 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.97 % Allowed : 10.83 % Favored : 86.19 % 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: 0.80 (0.15), residues: 2955 helix: 2.04 (0.21), residues: 648 sheet: 0.60 (0.19), residues: 642 loop : -0.06 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.006 0.001 HIS C 207 PHE 0.021 0.001 PHE C 855 TYR 0.020 0.001 TYR B 380 ARG 0.007 0.000 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 200 time to evaluate : 2.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7406 (t0) cc_final: 0.7039 (t70) REVERT: A 190 ARG cc_start: 0.7212 (OUTLIER) cc_final: 0.6978 (mmt-90) REVERT: A 207 HIS cc_start: 0.7010 (p90) cc_final: 0.6753 (p90) REVERT: A 237 ARG cc_start: 0.7543 (mtt90) cc_final: 0.7048 (ttm-80) REVERT: A 239 GLN cc_start: 0.8413 (tt0) cc_final: 0.7852 (tm-30) REVERT: A 284 THR cc_start: 0.8597 (OUTLIER) cc_final: 0.8174 (p) REVERT: A 954 GLN cc_start: 0.7762 (mt0) cc_final: 0.7558 (mt0) REVERT: A 994 ASP cc_start: 0.7535 (OUTLIER) cc_final: 0.7262 (m-30) REVERT: B 52 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.7658 (tt0) REVERT: B 202 LYS cc_start: 0.7207 (mttm) cc_final: 0.6765 (mttp) REVERT: B 239 GLN cc_start: 0.7429 (tt0) cc_final: 0.7164 (tt0) REVERT: B 436 TRP cc_start: 0.7385 (p90) cc_final: 0.6986 (p-90) REVERT: B 462 LYS cc_start: 0.7450 (mptp) cc_final: 0.6700 (pptt) REVERT: B 529 LYS cc_start: 0.8111 (mttt) cc_final: 0.7806 (ttpp) REVERT: B 740 MET cc_start: 0.8209 (OUTLIER) cc_final: 0.7934 (ttp) REVERT: B 773 GLU cc_start: 0.8135 (tt0) cc_final: 0.7882 (tt0) REVERT: C 41 LYS cc_start: 0.8124 (mttt) cc_final: 0.7837 (mttp) REVERT: C 102 ARG cc_start: 0.5818 (OUTLIER) cc_final: 0.5494 (ttm170) REVERT: C 205 SER cc_start: 0.9120 (p) cc_final: 0.8731 (t) REVERT: C 231 ILE cc_start: 0.8305 (OUTLIER) cc_final: 0.8072 (pt) REVERT: C 321 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7766 (mp10) REVERT: C 424 LYS cc_start: 0.7102 (tppt) cc_final: 0.6750 (tttm) REVERT: C 675 GLN cc_start: 0.7134 (mt0) cc_final: 0.6794 (pt0) outliers start: 78 outliers final: 37 residues processed: 250 average time/residue: 1.0458 time to fit residues: 312.5525 Evaluate side-chains 228 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 183 time to evaluate : 2.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1142 GLN Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 97 optimal weight: 0.9990 chunk 261 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 170 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 290 optimal weight: 2.9990 chunk 240 optimal weight: 10.0000 chunk 134 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 96 optimal weight: 2.9990 chunk 152 optimal weight: 5.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN A1106 GLN B 207 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN C 901 GLN C1002 GLN C1010 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 24366 Z= 0.284 Angle : 0.567 11.256 33144 Z= 0.295 Chirality : 0.047 0.328 3876 Planarity : 0.004 0.041 4251 Dihedral : 5.158 54.168 3831 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.78 % Allowed : 10.83 % Favored : 85.39 % 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: 0.60 (0.15), residues: 2955 helix: 1.65 (0.21), residues: 666 sheet: 0.51 (0.19), residues: 642 loop : -0.11 (0.15), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.005 0.001 HIS C1064 PHE 0.014 0.002 PHE B 823 TYR 0.023 0.002 TYR B 170 ARG 0.005 0.001 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 192 time to evaluate : 2.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7412 (t0) cc_final: 0.7038 (t70) REVERT: A 190 ARG cc_start: 0.7226 (OUTLIER) cc_final: 0.6826 (mmt-90) REVERT: A 237 ARG cc_start: 0.7618 (mtt90) cc_final: 0.7026 (ttm-80) REVERT: A 239 GLN cc_start: 0.8414 (tt0) cc_final: 0.8128 (tm-30) REVERT: A 284 THR cc_start: 0.8562 (OUTLIER) cc_final: 0.8141 (p) REVERT: A 309 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7367 (mm-30) REVERT: A 651 ILE cc_start: 0.9305 (OUTLIER) cc_final: 0.9039 (mm) REVERT: A 994 ASP cc_start: 0.7612 (OUTLIER) cc_final: 0.7326 (m-30) REVERT: A 1106 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.8600 (pt0) REVERT: B 52 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7590 (tt0) REVERT: B 202 LYS cc_start: 0.7327 (mttm) cc_final: 0.6770 (mttp) REVERT: B 239 GLN cc_start: 0.7384 (tt0) cc_final: 0.7152 (tt0) REVERT: B 436 TRP cc_start: 0.7393 (p90) cc_final: 0.7011 (p-90) REVERT: B 462 LYS cc_start: 0.7533 (OUTLIER) cc_final: 0.6743 (pptt) REVERT: B 529 LYS cc_start: 0.8142 (mttt) cc_final: 0.7808 (ttpp) REVERT: B 560 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7439 (mp) REVERT: B 740 MET cc_start: 0.8296 (OUTLIER) cc_final: 0.7885 (ttt) REVERT: C 41 LYS cc_start: 0.8260 (mttt) cc_final: 0.7884 (mttp) REVERT: C 121 ASN cc_start: 0.6642 (m-40) cc_final: 0.6350 (m110) REVERT: C 170 TYR cc_start: 0.5486 (t80) cc_final: 0.5220 (t80) REVERT: C 231 ILE cc_start: 0.8338 (OUTLIER) cc_final: 0.8111 (pt) REVERT: C 424 LYS cc_start: 0.7296 (tppt) cc_final: 0.6920 (tttm) outliers start: 99 outliers final: 46 residues processed: 261 average time/residue: 1.0930 time to fit residues: 341.9651 Evaluate side-chains 230 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 173 time to evaluate : 2.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1142 GLN Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1123 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 279 optimal weight: 3.9990 chunk 32 optimal weight: 0.0570 chunk 165 optimal weight: 1.9990 chunk 211 optimal weight: 20.0000 chunk 164 optimal weight: 0.8980 chunk 244 optimal weight: 0.9990 chunk 162 optimal weight: 1.9990 chunk 289 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 chunk 176 optimal weight: 0.5980 chunk 133 optimal weight: 4.9990 overall best weight: 0.9102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 935 GLN A 954 GLN ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN C 207 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN C1002 GLN C1010 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 24366 Z= 0.166 Angle : 0.512 8.790 33144 Z= 0.267 Chirality : 0.044 0.320 3876 Planarity : 0.003 0.036 4251 Dihedral : 4.788 46.930 3831 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.56 % Allowed : 11.82 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.76 (0.15), residues: 2955 helix: 2.10 (0.21), residues: 648 sheet: 0.52 (0.19), residues: 642 loop : -0.10 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 436 HIS 0.010 0.001 HIS A 207 PHE 0.020 0.001 PHE C 855 TYR 0.025 0.001 TYR B 170 ARG 0.006 0.000 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 197 time to evaluate : 2.804 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7386 (t0) cc_final: 0.7021 (t70) REVERT: A 118 LEU cc_start: 0.7539 (tp) cc_final: 0.7328 (tm) REVERT: A 190 ARG cc_start: 0.7147 (OUTLIER) cc_final: 0.6905 (mmt-90) REVERT: A 237 ARG cc_start: 0.7593 (mtt90) cc_final: 0.7027 (ttm-80) REVERT: A 239 GLN cc_start: 0.8431 (tt0) cc_final: 0.8028 (tm-30) REVERT: A 284 THR cc_start: 0.8572 (OUTLIER) cc_final: 0.8213 (p) REVERT: A 994 ASP cc_start: 0.7559 (OUTLIER) cc_final: 0.7269 (m-30) REVERT: B 52 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7541 (tt0) REVERT: B 202 LYS cc_start: 0.7144 (mttm) cc_final: 0.6595 (mttp) REVERT: B 239 GLN cc_start: 0.7434 (tt0) cc_final: 0.7223 (tt0) REVERT: B 436 TRP cc_start: 0.7362 (p90) cc_final: 0.6998 (p-90) REVERT: B 462 LYS cc_start: 0.7405 (mptp) cc_final: 0.6608 (pptt) REVERT: B 529 LYS cc_start: 0.8167 (mttt) cc_final: 0.7853 (ttpp) REVERT: B 560 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.7295 (mt) REVERT: B 773 GLU cc_start: 0.8189 (tt0) cc_final: 0.7917 (tt0) REVERT: C 41 LYS cc_start: 0.8248 (mttt) cc_final: 0.7862 (mttp) REVERT: C 121 ASN cc_start: 0.6642 (m-40) cc_final: 0.6380 (m-40) REVERT: C 170 TYR cc_start: 0.5630 (t80) cc_final: 0.5285 (t80) REVERT: C 231 ILE cc_start: 0.8257 (OUTLIER) cc_final: 0.8019 (pt) REVERT: C 424 LYS cc_start: 0.7298 (tppt) cc_final: 0.6945 (tttm) REVERT: C 453 PHE cc_start: 0.6221 (p90) cc_final: 0.5818 (p90) outliers start: 67 outliers final: 36 residues processed: 241 average time/residue: 0.9843 time to fit residues: 286.6265 Evaluate side-chains 223 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 181 time to evaluate : 2.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 178 optimal weight: 2.9990 chunk 115 optimal weight: 0.4980 chunk 172 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 chunk 196 optimal weight: 1.9990 chunk 142 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 227 optimal weight: 10.0000 chunk 263 optimal weight: 3.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A1106 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN C 207 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN C1010 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 24366 Z= 0.277 Angle : 0.565 9.630 33144 Z= 0.293 Chirality : 0.047 0.444 3876 Planarity : 0.004 0.037 4251 Dihedral : 5.069 47.353 3831 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.94 % Allowed : 11.98 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.61 (0.15), residues: 2955 helix: 1.89 (0.21), residues: 648 sheet: 0.48 (0.19), residues: 651 loop : -0.18 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.017 0.002 HIS A 207 PHE 0.024 0.002 PHE A 855 TYR 0.026 0.002 TYR B 170 ARG 0.004 0.000 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 183 time to evaluate : 2.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.7584 (tp) cc_final: 0.7369 (tm) REVERT: A 125 ASN cc_start: 0.6236 (p0) cc_final: 0.6020 (p0) REVERT: A 190 ARG cc_start: 0.7186 (OUTLIER) cc_final: 0.6937 (mmt-90) REVERT: A 239 GLN cc_start: 0.8427 (tt0) cc_final: 0.8069 (tm-30) REVERT: A 284 THR cc_start: 0.8561 (OUTLIER) cc_final: 0.8174 (p) REVERT: A 651 ILE cc_start: 0.9304 (OUTLIER) cc_final: 0.9042 (mm) REVERT: A 994 ASP cc_start: 0.7577 (OUTLIER) cc_final: 0.7296 (m-30) REVERT: A 1106 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.8373 (pt0) REVERT: B 52 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.7570 (tt0) REVERT: B 202 LYS cc_start: 0.7270 (mttm) cc_final: 0.6702 (mttp) REVERT: B 436 TRP cc_start: 0.7338 (p90) cc_final: 0.7013 (p-90) REVERT: B 462 LYS cc_start: 0.7361 (OUTLIER) cc_final: 0.6580 (pptt) REVERT: B 529 LYS cc_start: 0.8179 (mttt) cc_final: 0.7836 (ttpp) REVERT: B 560 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7354 (mt) REVERT: C 41 LYS cc_start: 0.8286 (mttt) cc_final: 0.7847 (mttp) REVERT: C 121 ASN cc_start: 0.6830 (m-40) cc_final: 0.6487 (m-40) REVERT: C 130 VAL cc_start: 0.6511 (t) cc_final: 0.6196 (m) REVERT: C 170 TYR cc_start: 0.5637 (t80) cc_final: 0.5321 (t80) REVERT: C 231 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.8127 (pt) REVERT: C 424 LYS cc_start: 0.7321 (tppt) cc_final: 0.6976 (tttm) REVERT: C 453 PHE cc_start: 0.6206 (p90) cc_final: 0.5776 (p90) outliers start: 77 outliers final: 47 residues processed: 233 average time/residue: 0.9479 time to fit residues: 267.8707 Evaluate side-chains 231 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 175 time to evaluate : 2.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1142 GLN Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1123 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 277 optimal weight: 0.8980 chunk 252 optimal weight: 2.9990 chunk 269 optimal weight: 0.9980 chunk 276 optimal weight: 0.5980 chunk 162 optimal weight: 3.9990 chunk 117 optimal weight: 7.9990 chunk 211 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 chunk 243 optimal weight: 0.0010 chunk 254 optimal weight: 5.9990 chunk 268 optimal weight: 0.0270 overall best weight: 0.5044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN B 762 GLN C 207 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 ASN C1002 GLN C1010 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 24366 Z= 0.131 Angle : 0.502 10.835 33144 Z= 0.259 Chirality : 0.044 0.313 3876 Planarity : 0.003 0.043 4251 Dihedral : 5.408 103.505 3831 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.06 % Allowed : 12.93 % Favored : 85.01 % 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: 0.78 (0.15), residues: 2955 helix: 2.35 (0.21), residues: 630 sheet: 0.41 (0.19), residues: 681 loop : -0.11 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 436 HIS 0.016 0.001 HIS A 207 PHE 0.021 0.001 PHE C 855 TYR 0.025 0.001 TYR B 170 ARG 0.003 0.000 ARG C 567 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 196 time to evaluate : 3.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.7564 (tp) cc_final: 0.7352 (tm) REVERT: A 125 ASN cc_start: 0.6078 (p0) cc_final: 0.5853 (p0) REVERT: A 190 ARG cc_start: 0.7089 (OUTLIER) cc_final: 0.6857 (mmt-90) REVERT: A 239 GLN cc_start: 0.8437 (tt0) cc_final: 0.8091 (tm-30) REVERT: A 790 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8236 (ptmm) REVERT: A 994 ASP cc_start: 0.7503 (OUTLIER) cc_final: 0.7239 (m-30) REVERT: B 202 LYS cc_start: 0.7148 (mttm) cc_final: 0.6614 (mttp) REVERT: B 436 TRP cc_start: 0.7331 (p90) cc_final: 0.7019 (p-90) REVERT: B 516 GLU cc_start: 0.5918 (OUTLIER) cc_final: 0.5594 (mt-10) REVERT: B 529 LYS cc_start: 0.8148 (mttt) cc_final: 0.7856 (ttpp) REVERT: B 560 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.7352 (mt) REVERT: B 773 GLU cc_start: 0.8056 (tt0) cc_final: 0.7823 (tt0) REVERT: C 41 LYS cc_start: 0.8235 (mttt) cc_final: 0.7810 (mttp) REVERT: C 121 ASN cc_start: 0.6840 (m-40) cc_final: 0.6514 (m-40) REVERT: C 170 TYR cc_start: 0.5754 (t80) cc_final: 0.5440 (t80) REVERT: C 231 ILE cc_start: 0.8252 (OUTLIER) cc_final: 0.7986 (pt) REVERT: C 424 LYS cc_start: 0.7327 (tppt) cc_final: 0.6996 (tttm) REVERT: C 453 PHE cc_start: 0.6176 (p90) cc_final: 0.5763 (p90) outliers start: 54 outliers final: 30 residues processed: 230 average time/residue: 1.0163 time to fit residues: 281.4787 Evaluate side-chains 218 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 182 time to evaluate : 2.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 608 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 176 optimal weight: 0.5980 chunk 284 optimal weight: 1.9990 chunk 173 optimal weight: 3.9990 chunk 135 optimal weight: 20.0000 chunk 198 optimal weight: 2.9990 chunk 298 optimal weight: 3.9990 chunk 275 optimal weight: 0.6980 chunk 237 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 ASN A 914 ASN A1106 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN C 207 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN C1010 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 24366 Z= 0.273 Angle : 0.565 11.002 33144 Z= 0.295 Chirality : 0.047 0.327 3876 Planarity : 0.004 0.042 4251 Dihedral : 5.442 97.439 3831 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.06 % Allowed : 13.20 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.62 (0.15), residues: 2955 helix: 2.13 (0.21), residues: 630 sheet: 0.32 (0.19), residues: 690 loop : -0.18 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.016 0.002 HIS A 207 PHE 0.024 0.001 PHE A 855 TYR 0.019 0.001 TYR B 380 ARG 0.004 0.000 ARG A 905 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 182 time to evaluate : 2.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.7577 (tp) cc_final: 0.7361 (tm) REVERT: A 125 ASN cc_start: 0.6123 (p0) cc_final: 0.5890 (p0) REVERT: A 190 ARG cc_start: 0.7159 (OUTLIER) cc_final: 0.6923 (mmt-90) REVERT: A 239 GLN cc_start: 0.8425 (tt0) cc_final: 0.8055 (tm-30) REVERT: A 914 ASN cc_start: 0.9157 (OUTLIER) cc_final: 0.8938 (p0) REVERT: A 994 ASP cc_start: 0.7564 (OUTLIER) cc_final: 0.7294 (m-30) REVERT: A 1106 GLN cc_start: 0.8755 (OUTLIER) cc_final: 0.8280 (pt0) REVERT: B 202 LYS cc_start: 0.7232 (mttm) cc_final: 0.6683 (mttp) REVERT: B 436 TRP cc_start: 0.7355 (p90) cc_final: 0.7065 (p-90) REVERT: B 462 LYS cc_start: 0.7338 (mptp) cc_final: 0.6590 (pptt) REVERT: B 529 LYS cc_start: 0.8198 (mttt) cc_final: 0.7871 (ttpp) REVERT: B 560 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7360 (mt) REVERT: B 786 LYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7655 (pttt) REVERT: C 41 LYS cc_start: 0.8276 (mttt) cc_final: 0.7843 (mttp) REVERT: C 120 VAL cc_start: 0.8531 (p) cc_final: 0.8276 (t) REVERT: C 121 ASN cc_start: 0.6897 (m-40) cc_final: 0.6426 (m-40) REVERT: C 170 TYR cc_start: 0.5626 (t80) cc_final: 0.5290 (t80) REVERT: C 231 ILE cc_start: 0.8447 (OUTLIER) cc_final: 0.8193 (pt) REVERT: C 424 LYS cc_start: 0.7351 (tppt) cc_final: 0.7040 (tttm) REVERT: C 453 PHE cc_start: 0.6163 (p90) cc_final: 0.5731 (p90) outliers start: 54 outliers final: 38 residues processed: 220 average time/residue: 1.0139 time to fit residues: 268.0530 Evaluate side-chains 217 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 172 time to evaluate : 2.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 615 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 189 optimal weight: 0.9980 chunk 253 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 219 optimal weight: 1.9990 chunk 35 optimal weight: 40.0000 chunk 66 optimal weight: 2.9990 chunk 238 optimal weight: 4.9990 chunk 99 optimal weight: 0.6980 chunk 244 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 43 optimal weight: 8.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN C 207 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN C1010 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.185095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.118595 restraints weight = 28763.221| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.32 r_work: 0.3134 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.461 24366 Z= 0.427 Angle : 0.814 65.899 33144 Z= 0.505 Chirality : 0.049 0.644 3876 Planarity : 0.006 0.277 4251 Dihedral : 5.460 97.443 3831 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.14 % Allowed : 13.08 % Favored : 84.78 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.60 (0.15), residues: 2955 helix: 2.11 (0.21), residues: 630 sheet: 0.32 (0.18), residues: 690 loop : -0.19 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.013 0.001 HIS A 207 PHE 0.018 0.001 PHE C 643 TYR 0.019 0.001 TYR A1067 ARG 0.004 0.000 ARG A 905 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6861.11 seconds wall clock time: 123 minutes 6.59 seconds (7386.59 seconds total)