Starting phenix.real_space_refine on Tue Jun 24 02:11:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y8d_39042/06_2025/8y8d_39042.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y8d_39042/06_2025/8y8d_39042.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y8d_39042/06_2025/8y8d_39042.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y8d_39042/06_2025/8y8d_39042.map" model { file = "/net/cci-nas-00/data/ceres_data/8y8d_39042/06_2025/8y8d_39042.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y8d_39042/06_2025/8y8d_39042.cif" } resolution = 3.41 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= 0.060 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 163 5.16 5 C 17757 2.51 5 N 4519 2.21 5 O 5428 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 27867 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 9117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1172, 9117 Classifications: {'peptide': 1172} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 3, 'PTRANS': 53, 'TRANS': 1115} Chain breaks: 4 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "A" Number of atoms: 9100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1172, 9100 Classifications: {'peptide': 1172} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 3, 'PTRANS': 53, 'TRANS': 1115} Chain breaks: 5 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "B" Number of atoms: 9219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1185, 9219 Classifications: {'peptide': 1185} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 3, 'PTRANS': 53, 'TRANS': 1128} Chain breaks: 3 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'PHE:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 17.88, per 1000 atoms: 0.64 Number of scatterers: 27867 At special positions: 0 Unit cell: (145.96, 147.6, 218.12, 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 163 16.00 O 5428 8.00 N 4519 7.00 C 17757 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=67, symmetry=0 Simple disulfide: pdb=" SG CYS C 20 " - pdb=" SG CYS C 156 " distance=2.03 Simple disulfide: pdb=" SG CYS C 151 " - pdb=" SG CYS C 183 " distance=2.03 Simple disulfide: pdb=" SG CYS C 163 " - pdb=" SG CYS C 242 " distance=2.03 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 292 " distance=2.03 Simple disulfide: pdb=" SG CYS C 327 " - pdb=" SG CYS C 352 " distance=2.03 Simple disulfide: pdb=" SG CYS C 370 " - pdb=" SG CYS C 423 " distance=2.03 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 603 " distance=2.03 Simple disulfide: pdb=" SG CYS C 466 " - pdb=" SG CYS C 546 " distance=2.03 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 495 " distance=2.03 Simple disulfide: pdb=" SG CYS C 476 " - pdb=" SG CYS C 565 " distance=2.03 Simple disulfide: pdb=" SG CYS C 520 " - pdb=" SG CYS C 533 " distance=2.03 Simple disulfide: pdb=" SG CYS C 556 " - pdb=" SG CYS C 567 " distance=2.03 Simple disulfide: pdb=" SG CYS C 580 " - pdb=" SG CYS C 586 " distance=2.03 Simple disulfide: pdb=" SG CYS C 619 " - pdb=" SG CYS C 672 " distance=2.03 Simple disulfide: pdb=" SG CYS C 697 " - pdb=" SG CYS C 719 " distance=2.03 Simple disulfide: pdb=" SG CYS C 734 " - pdb=" SG CYS C 743 " distance=2.03 Simple disulfide: pdb=" SG CYS C 814 " - pdb=" SG CYS C 836 " distance=2.03 Simple disulfide: pdb=" SG CYS C 819 " - pdb=" SG CYS C 825 " distance=2.03 Simple disulfide: pdb=" SG CYS C 890 " - pdb=" SG CYS C 895 " distance=2.03 Simple disulfide: pdb=" SG CYS C 925 " - pdb=" SG CYS C 936 " distance=2.03 Simple disulfide: pdb=" SG CYS C1113 " - pdb=" SG CYS C1124 " distance=2.03 Simple disulfide: pdb=" SG CYS C1163 " - pdb=" SG CYS C1208 " distance=2.03 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS A 156 " distance=2.03 Simple disulfide: pdb=" SG CYS A 151 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 163 " - pdb=" SG CYS A 242 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 292 " distance=2.03 Simple disulfide: pdb=" SG CYS A 327 " - pdb=" SG CYS A 352 " distance=2.03 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 423 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 603 " distance=2.03 Simple disulfide: pdb=" SG CYS A 466 " - pdb=" SG CYS A 546 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 495 " distance=2.03 Simple disulfide: pdb=" SG CYS A 476 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 520 " - pdb=" SG CYS A 533 " distance=2.03 Simple disulfide: pdb=" SG CYS A 556 " - pdb=" SG CYS A 567 " distance=2.03 Simple disulfide: pdb=" SG CYS A 580 " - pdb=" SG CYS A 586 " distance=2.03 Simple disulfide: pdb=" SG CYS A 619 " - pdb=" SG CYS A 672 " distance=2.03 Simple disulfide: pdb=" SG CYS A 697 " - pdb=" SG CYS A 719 " distance=2.03 Simple disulfide: pdb=" SG CYS A 734 " - pdb=" SG CYS A 743 " distance=2.03 Simple disulfide: pdb=" SG CYS A 814 " - pdb=" SG CYS A 836 " distance=2.03 Simple disulfide: pdb=" SG CYS A 819 " - pdb=" SG CYS A 825 " distance=2.03 Simple disulfide: pdb=" SG CYS A 890 " - pdb=" SG CYS A 895 " distance=2.03 Simple disulfide: pdb=" SG CYS A 925 " - pdb=" SG CYS A 936 " distance=2.03 Simple disulfide: pdb=" SG CYS A1113 " - pdb=" SG CYS A1124 " distance=2.03 Simple disulfide: pdb=" SG CYS A1163 " - pdb=" SG CYS A1208 " distance=2.03 Simple disulfide: pdb=" SG CYS B 20 " - pdb=" SG CYS B 156 " distance=2.03 Simple disulfide: pdb=" SG CYS B 151 " - pdb=" SG CYS B 183 " distance=2.03 Simple disulfide: pdb=" SG CYS B 163 " - pdb=" SG CYS B 242 " distance=2.03 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 292 " distance=2.03 Simple disulfide: pdb=" SG CYS B 327 " - pdb=" SG CYS B 352 " distance=2.03 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS B 423 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 603 " distance=2.03 Simple disulfide: pdb=" SG CYS B 466 " - pdb=" SG CYS B 546 " distance=2.03 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 495 " distance=2.03 Simple disulfide: pdb=" SG CYS B 476 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 485 " - pdb=" SG CYS B 516 " distance=2.03 Simple disulfide: pdb=" SG CYS B 504 " - pdb=" SG CYS B 518 " distance=2.03 Simple disulfide: pdb=" SG CYS B 520 " - pdb=" SG CYS B 533 " distance=2.03 Simple disulfide: pdb=" SG CYS B 556 " - pdb=" SG CYS B 567 " distance=2.03 Simple disulfide: pdb=" SG CYS B 619 " - pdb=" SG CYS B 672 " distance=2.03 Simple disulfide: pdb=" SG CYS B 697 " - pdb=" SG CYS B 719 " distance=2.03 Simple disulfide: pdb=" SG CYS B 734 " - pdb=" SG CYS B 743 " distance=2.03 Simple disulfide: pdb=" SG CYS B 814 " - pdb=" SG CYS B 836 " distance=2.03 Simple disulfide: pdb=" SG CYS B 819 " - pdb=" SG CYS B 825 " distance=2.03 Simple disulfide: pdb=" SG CYS B 890 " - pdb=" SG CYS B 895 " distance=2.03 Simple disulfide: pdb=" SG CYS B 925 " - pdb=" SG CYS B 936 " distance=2.03 Simple disulfide: pdb=" SG CYS B1113 " - pdb=" SG CYS B1124 " distance=2.03 Simple disulfide: pdb=" SG CYS B1163 " - pdb=" SG CYS B1208 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A1301 " - " ASN A 188 " " NAG A1302 " - " ASN A 192 " " NAG A1303 " - " ASN A 335 " " NAG A1304 " - " ASN A 664 " " NAG A1305 " - " ASN A 703 " " NAG A1306 " - " ASN A 793 " " NAG A1307 " - " ASN A 355 " " NAG A1308 " - " ASN A1211 " " NAG A1309 " - " ASN A 58 " " NAG B1301 " - " ASN B 192 " " NAG B1302 " - " ASN B 664 " " NAG B1303 " - " ASN B 703 " " NAG B1304 " - " ASN B 725 " " NAG B1305 " - " ASN B 793 " " NAG B1306 " - " ASN B1211 " " NAG C1301 " - " ASN C 188 " " NAG C1302 " - " ASN C 192 " " NAG C1303 " - " ASN C 335 " " NAG C1304 " - " ASN C 664 " " NAG C1305 " - " ASN C 703 " " NAG C1306 " - " ASN C 725 " " NAG C1307 " - " ASN C 793 " " NAG C1308 " - " ASN C 355 " " NAG C1309 " - " ASN C1211 " " NAG C1310 " - " ASN C 19 " " NAG C1311 " - " ASN C 924 " " NAG E 1 " - " ASN A 725 " Time building additional restraints: 6.88 Conformation dependent library (CDL) restraints added in 3.6 seconds 6998 Ramachandran restraints generated. 3499 Oldfield, 0 Emsley, 3499 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6650 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 59 sheets defined 24.6% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.78 Creating SS restraints... Processing helix chain 'C' and resid 88 through 91 Processing helix chain 'C' and resid 285 through 295 removed outlier: 3.516A pdb=" N GLN C 291 " --> pdb=" O LEU C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 334 Processing helix chain 'C' and resid 340 through 344 removed outlier: 4.055A pdb=" N TRP C 344 " --> pdb=" O PRO C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 362 Processing helix chain 'C' and resid 374 through 378 removed outlier: 3.661A pdb=" N ILE C 378 " --> pdb=" O LYS C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 401 removed outlier: 3.861A pdb=" N LEU C 401 " --> pdb=" O ARG C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 413 Processing helix chain 'C' and resid 442 through 447 removed outlier: 3.877A pdb=" N ARG C 447 " --> pdb=" O SER C 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 482 removed outlier: 3.580A pdb=" N VAL C 481 " --> pdb=" O ASP C 478 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL C 482 " --> pdb=" O PRO C 479 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 478 through 482' Processing helix chain 'C' and resid 568 through 572 removed outlier: 4.117A pdb=" N PHE C 572 " --> pdb=" O PRO C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 623 through 627 removed outlier: 3.713A pdb=" N GLY C 626 " --> pdb=" O ASP C 623 " (cutoff:3.500A) Processing helix chain 'C' and resid 696 through 704 removed outlier: 3.788A pdb=" N ASN C 702 " --> pdb=" O SER C 698 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 818 removed outlier: 3.938A pdb=" N PHE C 817 " --> pdb=" O ASP C 813 " (cutoff:3.500A) Processing helix chain 'C' and resid 822 through 830 removed outlier: 4.072A pdb=" N LEU C 828 " --> pdb=" O ALA C 824 " (cutoff:3.500A) Processing helix chain 'C' and resid 833 through 862 removed outlier: 3.580A pdb=" N ASP C 837 " --> pdb=" O GLY C 833 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ILE C 839 " --> pdb=" O PHE C 835 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN C 840 " --> pdb=" O CYS C 836 " (cutoff:3.500A) Processing helix chain 'C' and resid 904 through 909 Processing helix chain 'C' and resid 914 through 924 removed outlier: 3.915A pdb=" N VAL C 919 " --> pdb=" O ASP C 915 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN C 924 " --> pdb=" O GLU C 920 " (cutoff:3.500A) Processing helix chain 'C' and resid 933 through 941 removed outlier: 3.521A pdb=" N VAL C 937 " --> pdb=" O ASP C 933 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N PHE C 940 " --> pdb=" O CYS C 936 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN C 941 " --> pdb=" O VAL C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 951 through 965 removed outlier: 3.522A pdb=" N ALA C 961 " --> pdb=" O GLY C 957 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA C 962 " --> pdb=" O TYR C 958 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR C 963 " --> pdb=" O THR C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 991 removed outlier: 3.951A pdb=" N LEU C 990 " --> pdb=" O ARG C 986 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY C 991 " --> pdb=" O ILE C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 1000 removed outlier: 3.700A pdb=" N LEU C 997 " --> pdb=" O THR C 993 " (cutoff:3.500A) Processing helix chain 'C' and resid 1000 through 1018 removed outlier: 3.666A pdb=" N ASN C1009 " --> pdb=" O ALA C1005 " (cutoff:3.500A) Processing helix chain 'C' and resid 1023 through 1046 removed outlier: 3.652A pdb=" N ALA C1027 " --> pdb=" O PRO C1023 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS C1028 " --> pdb=" O SER C1024 " (cutoff:3.500A) Processing helix chain 'C' and resid 1047 through 1049 No H-bonds generated for 'chain 'C' and resid 1047 through 1049' Processing helix chain 'C' and resid 1066 through 1113 removed outlier: 5.105A pdb=" N VAL C1072 " --> pdb=" O PRO C1068 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN C1073 " --> pdb=" O GLU C1069 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ARG C1076 " --> pdb=" O VAL C1072 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU C1077 " --> pdb=" O GLN C1073 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER C1090 " --> pdb=" O ASN C1086 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER C1094 " --> pdb=" O SER C1090 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU C1098 " --> pdb=" O SER C1094 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG C1105 " --> pdb=" O ALA C1101 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 91 Processing helix chain 'A' and resid 285 through 295 removed outlier: 3.555A pdb=" N ILE A 290 " --> pdb=" O PHE A 286 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN A 291 " --> pdb=" O LEU A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 334 removed outlier: 3.559A pdb=" N TRP A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU A 333 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN A 334 " --> pdb=" O ASP A 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 328 through 334' Processing helix chain 'A' and resid 355 through 363 removed outlier: 3.607A pdb=" N VAL A 363 " --> pdb=" O LEU A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 401 removed outlier: 3.752A pdb=" N LEU A 401 " --> pdb=" O ARG A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 413 removed outlier: 3.681A pdb=" N SER A 412 " --> pdb=" O PHE A 408 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN A 413 " --> pdb=" O LEU A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 482 removed outlier: 3.542A pdb=" N VAL A 481 " --> pdb=" O ASP A 478 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL A 482 " --> pdb=" O PRO A 479 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 478 through 482' Processing helix chain 'A' and resid 568 through 570 No H-bonds generated for 'chain 'A' and resid 568 through 570' Processing helix chain 'A' and resid 696 through 704 removed outlier: 3.668A pdb=" N ASN A 702 " --> pdb=" O SER A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 819 removed outlier: 3.655A pdb=" N PHE A 817 " --> pdb=" O ASP A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 830 removed outlier: 3.768A pdb=" N HIS A 826 " --> pdb=" O TYR A 822 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP A 827 " --> pdb=" O ALA A 823 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU A 828 " --> pdb=" O ALA A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 862 Processing helix chain 'A' and resid 870 through 872 No H-bonds generated for 'chain 'A' and resid 870 through 872' Processing helix chain 'A' and resid 878 through 882 removed outlier: 4.175A pdb=" N ASN A 881 " --> pdb=" O ASP A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 888 removed outlier: 3.546A pdb=" N LEU A 888 " --> pdb=" O LYS A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 909 removed outlier: 3.904A pdb=" N LEU A 906 " --> pdb=" O PRO A 902 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LEU A 907 " --> pdb=" O LEU A 903 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A 908 " --> pdb=" O GLU A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 924 removed outlier: 3.908A pdb=" N VAL A 919 " --> pdb=" O ASP A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 941 removed outlier: 3.677A pdb=" N VAL A 937 " --> pdb=" O ASP A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 951 through 965 Processing helix chain 'A' and resid 978 through 990 removed outlier: 3.544A pdb=" N GLN A 984 " --> pdb=" O PRO A 980 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU A 990 " --> pdb=" O ARG A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1000 removed outlier: 3.893A pdb=" N LEU A 997 " --> pdb=" O THR A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1019 removed outlier: 3.700A pdb=" N ASN A1009 " --> pdb=" O ALA A1005 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY A1018 " --> pdb=" O SER A1014 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE A1019 " --> pdb=" O ILE A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1023 through 1045 removed outlier: 3.615A pdb=" N VAL A1032 " --> pdb=" O LYS A1028 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL A1033 " --> pdb=" O ILE A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1049 removed outlier: 3.581A pdb=" N ASN A1049 " --> pdb=" O GLN A1046 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1046 through 1049' Processing helix chain 'A' and resid 1060 through 1065 Processing helix chain 'A' and resid 1066 through 1114 removed outlier: 3.572A pdb=" N GLN A1071 " --> pdb=" O PRO A1067 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N VAL A1072 " --> pdb=" O PRO A1068 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLN A1073 " --> pdb=" O GLU A1069 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA A1084 " --> pdb=" O GLY A1080 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU A1093 " --> pdb=" O VAL A1089 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER A1094 " --> pdb=" O SER A1090 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR A1097 " --> pdb=" O LEU A1093 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU A1098 " --> pdb=" O SER A1094 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 46 removed outlier: 3.660A pdb=" N GLY B 45 " --> pdb=" O VAL B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.855A pdb=" N GLU B 289 " --> pdb=" O SER B 285 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE B 290 " --> pdb=" O PHE B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 334 removed outlier: 3.590A pdb=" N TRP B 332 " --> pdb=" O ASP B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 362 Processing helix chain 'B' and resid 375 through 379 removed outlier: 3.528A pdb=" N PHE B 379 " --> pdb=" O SER B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 402 removed outlier: 3.502A pdb=" N ASP B 400 " --> pdb=" O ARG B 397 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU B 401 " --> pdb=" O ARG B 398 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN B 402 " --> pdb=" O ASP B 399 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 397 through 402' Processing helix chain 'B' and resid 408 through 413 Processing helix chain 'B' and resid 443 through 448 removed outlier: 3.973A pdb=" N TYR B 448 " --> pdb=" O TRP B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 483 Processing helix chain 'B' and resid 553 through 556 removed outlier: 3.632A pdb=" N CYS B 556 " --> pdb=" O GLU B 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 553 through 556' Processing helix chain 'B' and resid 568 through 570 No H-bonds generated for 'chain 'B' and resid 568 through 570' Processing helix chain 'B' and resid 696 through 701 removed outlier: 3.729A pdb=" N LEU B 701 " --> pdb=" O CYS B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 819 Processing helix chain 'B' and resid 822 through 830 removed outlier: 3.576A pdb=" N HIS B 826 " --> pdb=" O TYR B 822 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP B 827 " --> pdb=" O ALA B 823 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU B 828 " --> pdb=" O ALA B 824 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 862 removed outlier: 3.853A pdb=" N ILE B 839 " --> pdb=" O PHE B 835 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU B 861 " --> pdb=" O VAL B 857 " (cutoff:3.500A) Processing helix chain 'B' and resid 878 through 882 removed outlier: 4.012A pdb=" N ASN B 881 " --> pdb=" O ASP B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 888 Processing helix chain 'B' and resid 901 through 909 removed outlier: 3.829A pdb=" N LEU B 906 " --> pdb=" O PRO B 902 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU B 907 " --> pdb=" O LEU B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 924 removed outlier: 3.808A pdb=" N VAL B 919 " --> pdb=" O ASP B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 933 through 941 removed outlier: 4.254A pdb=" N VAL B 937 " --> pdb=" O ASP B 933 " (cutoff:3.500A) Processing helix chain 'B' and resid 951 through 965 Processing helix chain 'B' and resid 978 through 989 removed outlier: 3.554A pdb=" N GLN B 984 " --> pdb=" O PRO B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 993 through 1000 removed outlier: 3.863A pdb=" N LEU B 997 " --> pdb=" O THR B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1000 through 1019 removed outlier: 3.661A pdb=" N ILE B1004 " --> pdb=" O ASN B1000 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN B1009 " --> pdb=" O ALA B1005 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE B1019 " --> pdb=" O ILE B1015 " (cutoff:3.500A) Processing helix chain 'B' and resid 1023 through 1045 Processing helix chain 'B' and resid 1046 through 1049 removed outlier: 3.614A pdb=" N ASN B1049 " --> pdb=" O GLN B1046 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1046 through 1049' Processing helix chain 'B' and resid 1057 through 1062 removed outlier: 3.680A pdb=" N ILE B1061 " --> pdb=" O SER B1057 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU B1062 " --> pdb=" O LEU B1058 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1057 through 1062' Processing helix chain 'B' and resid 1066 through 1114 removed outlier: 3.508A pdb=" N GLN B1071 " --> pdb=" O PRO B1067 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N VAL B1072 " --> pdb=" O PRO B1068 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLN B1073 " --> pdb=" O GLU B1069 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU B1077 " --> pdb=" O GLN B1073 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY B1080 " --> pdb=" O ARG B1076 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA B1084 " --> pdb=" O GLY B1080 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER B1094 " --> pdb=" O SER B1090 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR B1097 " --> pdb=" O LEU B1093 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU B1098 " --> pdb=" O SER B1094 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE B1099 " --> pdb=" O ASP B1095 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU B1112 " --> pdb=" O GLU B1108 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL B1114 " --> pdb=" O VAL B1110 " (cutoff:3.500A) Processing helix chain 'B' and resid 1198 through 1200 No H-bonds generated for 'chain 'B' and resid 1198 through 1200' Processing sheet with id=AA1, first strand: chain 'C' and resid 25 through 26 removed outlier: 3.578A pdb=" N ASN C 26 " --> pdb=" O LEU C 85 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 34 through 37 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 34 through 37 current: chain 'C' and resid 197 through 205 removed outlier: 3.733A pdb=" N TYR C 199 " --> pdb=" O ALA C 214 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA C 214 " --> pdb=" O TYR C 199 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR C 203 " --> pdb=" O TYR C 210 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE C 224 " --> pdb=" O ALA C 211 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N TYR C 213 " --> pdb=" O PHE C 222 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N PHE C 222 " --> pdb=" O TYR C 213 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 221 through 227 current: chain 'C' and resid 276 through 278 Processing sheet with id=AA3, first strand: chain 'C' and resid 109 through 112 removed outlier: 3.765A pdb=" N THR C 109 " --> pdb=" O GLU C 120 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU C 120 " --> pdb=" O THR C 109 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU C 111 " --> pdb=" O TYR C 118 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 183 through 190 removed outlier: 3.765A pdb=" N PHE C 185 " --> pdb=" O ALA C 150 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N CYS C 151 " --> pdb=" O THR C 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 161 through 162 removed outlier: 6.001A pdb=" N THR C 161 " --> pdb=" O THR C 241 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 302 through 305 Processing sheet with id=AA7, first strand: chain 'C' and resid 337 through 338 Processing sheet with id=AA8, first strand: chain 'C' and resid 347 through 349 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 347 through 349 current: chain 'C' and resid 585 through 595 No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 353 through 354 removed outlier: 3.649A pdb=" N PHE C 354 " --> pdb=" O CYS C 603 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 620 through 621 removed outlier: 4.219A pdb=" N VAL C 620 " --> pdb=" O GLY C 631 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLY C 631 " --> pdb=" O VAL C 620 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS C 634 " --> pdb=" O THR C 668 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL C 636 " --> pdb=" O THR C 666 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N THR C 666 " --> pdb=" O VAL C 636 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ILE C 656 " --> pdb=" O ILE C 669 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU C 648 " --> pdb=" O ILE C 656 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU C 647 " --> pdb=" O VAL B 55 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 724 through 725 removed outlier: 6.832A pdb=" N VAL C 724 " --> pdb=" O PHE C 764 " (cutoff:3.500A) removed outlier: 9.052A pdb=" N THR C 766 " --> pdb=" O VAL C 724 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU C 736 " --> pdb=" O ILE C 744 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 773 through 775 removed outlier: 6.000A pdb=" N SER C 773 " --> pdb=" O LEU B 867 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 786 through 789 removed outlier: 3.685A pdb=" N VAL C1158 " --> pdb=" O PHE C 786 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE C 788 " --> pdb=" O VAL C1156 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL C1156 " --> pdb=" O ILE C 788 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 794 through 796 removed outlier: 3.572A pdb=" N LYS C1149 " --> pdb=" O THR C 795 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 799 through 803 removed outlier: 3.866A pdb=" N LEU C1131 " --> pdb=" O PHE C1146 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 809 through 811 removed outlier: 4.383A pdb=" N LYS C 809 " --> pdb=" O LEU C 946 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS C 944 " --> pdb=" O THR C 811 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 866 through 868 Processing sheet with id=AB9, first strand: chain 'C' and resid 1202 through 1203 removed outlier: 3.650A pdb=" N ARG C1168 " --> pdb=" O LEU C1164 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 1175 through 1179 Processing sheet with id=AC2, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AC3, first strand: chain 'A' and resid 60 through 68 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 60 through 68 current: chain 'A' and resid 197 through 204 removed outlier: 3.636A pdb=" N TYR A 203 " --> pdb=" O TYR A 210 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA A 211 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE A 224 " --> pdb=" O ALA A 211 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N TYR A 213 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N PHE A 222 " --> pdb=" O TYR A 213 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 221 through 227 current: chain 'A' and resid 276 through 281 Processing sheet with id=AC4, first strand: chain 'A' and resid 80 through 81 removed outlier: 3.720A pdb=" N GLY A 81 " --> pdb=" O LEU A 240 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'A' and resid 110 through 112 removed outlier: 3.638A pdb=" N TYR A 118 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 124 through 127 removed outlier: 4.264A pdb=" N ILE A 124 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL A 139 " --> pdb=" O ILE A 124 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N CYS A 151 " --> pdb=" O THR A 136 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR A 149 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN A 140 " --> pdb=" O GLU A 147 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N PHE A 185 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 302 through 305 removed outlier: 3.512A pdb=" N PHE A 681 " --> pdb=" O GLY A 302 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 316 through 319 removed outlier: 3.780A pdb=" N VAL A 620 " --> pdb=" O GLY A 631 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLY A 631 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY A 629 " --> pdb=" O TYR A 622 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N ILE A 656 " --> pdb=" O ILE A 669 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY A 657 " --> pdb=" O LEU A 648 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 337 through 339 removed outlier: 7.104A pdb=" N VAL A 338 " --> pdb=" O ASN A 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'A' and resid 345 through 349 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 345 through 349 current: chain 'A' and resid 585 through 595 No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'A' and resid 353 through 354 removed outlier: 3.829A pdb=" N PHE A 354 " --> pdb=" O CYS A 603 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'A' and resid 460 through 463 removed outlier: 3.842A pdb=" N TYR A 462 " --> pdb=" O SER A 576 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 467 through 468 removed outlier: 3.615A pdb=" N LYS A 536 " --> pdb=" O SER A 468 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 550 through 551 removed outlier: 3.528A pdb=" N LEU A 573 " --> pdb=" O GLY A 550 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 712 through 713 removed outlier: 4.000A pdb=" N PHE A 713 " --> pdb=" O VAL A 720 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 724 through 725 removed outlier: 6.599A pdb=" N VAL A 724 " --> pdb=" O PHE A 764 " (cutoff:3.500A) removed outlier: 8.879A pdb=" N THR A 766 " --> pdb=" O VAL A 724 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 786 through 790 removed outlier: 7.180A pdb=" N LEU A1157 " --> pdb=" O LYS A1179 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LYS A1179 " --> pdb=" O LEU A1157 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE A1177 " --> pdb=" O SER A1159 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 794 through 803 removed outlier: 3.732A pdb=" N SER A1147 " --> pdb=" O ALA A 797 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY A1140 " --> pdb=" O ALA A1137 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A1137 " --> pdb=" O GLY A1140 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU A1131 " --> pdb=" O PHE A1146 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N TYR A1148 " --> pdb=" O HIS A1129 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N HIS A1129 " --> pdb=" O TYR A1148 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 809 through 812 removed outlier: 4.347A pdb=" N LYS A 809 " --> pdb=" O LEU A 946 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 866 through 868 Processing sheet with id=AE3, first strand: chain 'A' and resid 1162 through 1163 removed outlier: 4.163A pdb=" N CYS A1163 " --> pdb=" O THR A1213 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'A' and resid 1169 through 1172 removed outlier: 3.716A pdb=" N GLY A1169 " --> pdb=" O MET A1205 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA A1171 " --> pdb=" O VAL A1203 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 60 through 61 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 60 through 61 current: chain 'B' and resid 197 through 205 removed outlier: 3.731A pdb=" N TYR B 199 " --> pdb=" O ALA B 214 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR B 203 " --> pdb=" O TYR B 210 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N PHE B 209 " --> pdb=" O SER B 225 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N SER B 225 " --> pdb=" O PHE B 209 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ALA B 211 " --> pdb=" O LEU B 223 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 221 through 227 current: chain 'B' and resid 280 through 281 Processing sheet with id=AE6, first strand: chain 'B' and resid 80 through 81 removed outlier: 3.911A pdb=" N GLY B 81 " --> pdb=" O LEU B 240 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'B' and resid 109 through 111 removed outlier: 4.109A pdb=" N THR B 109 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLU B 120 " --> pdb=" O THR B 109 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 183 through 190 removed outlier: 4.116A pdb=" N PHE B 185 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE B 189 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR B 149 " --> pdb=" O VAL B 138 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N CYS B 151 " --> pdb=" O THR B 136 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL B 139 " --> pdb=" O ILE B 124 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE B 124 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N THR B 123 " --> pdb=" O MET B 238 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 302 through 306 Processing sheet with id=AF1, first strand: chain 'B' and resid 337 through 339 Processing sheet with id=AF2, first strand: chain 'B' and resid 346 through 350 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 346 through 350 current: chain 'B' and resid 585 through 597 No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'B' and resid 459 through 463 Processing sheet with id=AF4, first strand: chain 'B' and resid 467 through 468 removed outlier: 3.738A pdb=" N LYS B 536 " --> pdb=" O SER B 468 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 504 through 506 Processing sheet with id=AF6, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AF7, first strand: chain 'B' and resid 634 through 635 removed outlier: 3.807A pdb=" N TYR B 667 " --> pdb=" O PHE B 658 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N PHE B 658 " --> pdb=" O TYR B 667 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLY B 657 " --> pdb=" O LEU B 648 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'B' and resid 712 through 713 removed outlier: 3.703A pdb=" N PHE B 713 " --> pdb=" O VAL B 720 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'B' and resid 724 through 725 removed outlier: 6.770A pdb=" N VAL B 724 " --> pdb=" O PHE B 764 " (cutoff:3.500A) removed outlier: 8.931A pdb=" N THR B 766 " --> pdb=" O VAL B 724 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE B 742 " --> pdb=" O MET B 738 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET B 738 " --> pdb=" O PHE B 742 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'B' and resid 786 through 791 removed outlier: 7.009A pdb=" N LEU B1157 " --> pdb=" O LYS B1179 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LYS B1179 " --> pdb=" O LEU B1157 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE B1177 " --> pdb=" O SER B1159 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'B' and resid 794 through 803 removed outlier: 3.530A pdb=" N ALA B1137 " --> pdb=" O GLY B1140 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU B1131 " --> pdb=" O PHE B1146 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'B' and resid 809 through 812 removed outlier: 4.332A pdb=" N LYS B 809 " --> pdb=" O LEU B 946 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS B 944 " --> pdb=" O THR B 811 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'B' and resid 1162 through 1163 removed outlier: 3.521A pdb=" N CYS B1163 " --> pdb=" O THR B1213 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'B' and resid 1169 through 1172 706 hydrogen bonds defined for protein. 1959 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: 11.68 Time building geometry restraints manager: 8.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8843 1.34 - 1.46: 7011 1.46 - 1.58: 12493 1.58 - 1.70: 0 1.70 - 1.81: 190 Bond restraints: 28537 Sorted by residual: bond pdb=" C1 NAG C1308 " pdb=" O5 NAG C1308 " ideal model delta sigma weight residual 1.406 1.482 -0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" C1 NAG B1306 " pdb=" O5 NAG B1306 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.32e+00 bond pdb=" C1 BMA D 3 " pdb=" C2 BMA D 3 " ideal model delta sigma weight residual 1.519 1.549 -0.030 2.00e-02 2.50e+03 2.28e+00 bond pdb=" C1 NAG C1305 " pdb=" O5 NAG C1305 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.28e+00 bond pdb=" C1 NAG A1307 " pdb=" O5 NAG A1307 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.27e+00 ... (remaining 28532 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 38124 1.39 - 2.78: 666 2.78 - 4.17: 70 4.17 - 5.56: 14 5.56 - 6.95: 6 Bond angle restraints: 38880 Sorted by residual: angle pdb=" N SER A1055 " pdb=" CA SER A1055 " pdb=" C SER A1055 " ideal model delta sigma weight residual 107.73 111.43 -3.70 1.34e+00 5.57e-01 7.60e+00 angle pdb=" C THR B 873 " pdb=" N ASN B 874 " pdb=" CA ASN B 874 " ideal model delta sigma weight residual 121.54 126.50 -4.96 1.91e+00 2.74e-01 6.73e+00 angle pdb=" N ASP A 464 " pdb=" CA ASP A 464 " pdb=" C ASP A 464 " ideal model delta sigma weight residual 114.56 111.42 3.14 1.27e+00 6.20e-01 6.10e+00 angle pdb=" C PHE B 130 " pdb=" N VAL B 131 " pdb=" CA VAL B 131 " ideal model delta sigma weight residual 121.97 118.05 3.92 1.80e+00 3.09e-01 4.74e+00 angle pdb=" N CYS B 925 " pdb=" CA CYS B 925 " pdb=" C CYS B 925 " ideal model delta sigma weight residual 113.18 110.40 2.78 1.33e+00 5.65e-01 4.35e+00 ... (remaining 38875 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.56: 17100 24.56 - 49.12: 265 49.12 - 73.67: 28 73.67 - 98.23: 9 98.23 - 122.79: 6 Dihedral angle restraints: 17408 sinusoidal: 7059 harmonic: 10349 Sorted by residual: dihedral pdb=" CB CYS C 819 " pdb=" SG CYS C 819 " pdb=" SG CYS C 825 " pdb=" CB CYS C 825 " ideal model delta sinusoidal sigma weight residual -86.00 -140.71 54.71 1 1.00e+01 1.00e-02 4.05e+01 dihedral pdb=" CB CYS B 925 " pdb=" SG CYS B 925 " pdb=" SG CYS B 936 " pdb=" CB CYS B 936 " ideal model delta sinusoidal sigma weight residual 93.00 133.49 -40.49 1 1.00e+01 1.00e-02 2.30e+01 dihedral pdb=" C2 NAG C1308 " pdb=" C1 NAG C1308 " pdb=" O5 NAG C1308 " pdb=" C5 NAG C1308 " ideal model delta sinusoidal sigma weight residual -62.96 59.83 -122.79 1 3.00e+01 1.11e-03 1.64e+01 ... (remaining 17405 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 3796 0.054 - 0.109: 590 0.109 - 0.163: 86 0.163 - 0.217: 0 0.217 - 0.272: 1 Chirality restraints: 4473 Sorted by residual: chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" C1 NAG A1308 " pdb=" ND2 ASN A1211 " pdb=" C2 NAG A1308 " pdb=" O5 NAG A1308 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 5.62e-01 chirality pdb=" CA PRO B 313 " pdb=" N PRO B 313 " pdb=" C PRO B 313 " pdb=" CB PRO B 313 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.48e-01 ... (remaining 4470 not shown) Planarity restraints: 5004 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B1066 " -0.030 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO B1067 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO B1067 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B1067 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A1066 " -0.027 5.00e-02 4.00e+02 4.07e-02 2.65e+00 pdb=" N PRO A1067 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A1067 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A1067 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C1066 " -0.021 5.00e-02 4.00e+02 3.16e-02 1.60e+00 pdb=" N PRO C1067 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO C1067 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C1067 " -0.017 5.00e-02 4.00e+02 ... (remaining 5001 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 4312 2.76 - 3.30: 25939 3.30 - 3.83: 43551 3.83 - 4.37: 50198 4.37 - 4.90: 88534 Nonbonded interactions: 212534 Sorted by model distance: nonbonded pdb=" O VAL A 113 " pdb=" OG1 THR A 116 " model vdw 2.230 3.040 nonbonded pdb=" OD2 ASP A 478 " pdb=" OG SER A 480 " model vdw 2.236 3.040 nonbonded pdb=" OH TYR A 448 " pdb=" O PHE A 473 " model vdw 2.242 3.040 nonbonded pdb=" O PRO B 68 " pdb=" OH TYR B 266 " model vdw 2.248 3.040 nonbonded pdb=" O GLY A 864 " pdb=" OG SER A 972 " model vdw 2.251 3.040 ... (remaining 212529 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 163 or (resid 164 and (name N or name CA or nam \ e C or name O or name CB )) or resid 165 or (resid 166 and (name N or name CA or \ name C or name O or name CB )) or resid 167 through 244 or resid 254 through 45 \ 4 or (resid 455 and (name N or name CA or name C or name O or name CB )) or resi \ d 456 through 491 or (resid 492 through 493 and (name N or name CA or name C or \ name O or name CB )) or resid 494 through 553 or (resid 554 and (name N or name \ CA or name C or name O or name CB )) or resid 555 through 557 or resid 563 throu \ gh 607 or (resid 608 through 609 and (name N or name CA or name C or name O or n \ ame CB )) or resid 610 through 660 or (resid 661 and (name N or name CA or name \ C or name O or name CB )) or resid 662 through 1221 or resid 1301 through 1306)) \ selection = (chain 'B' and (resid 14 through 163 or (resid 164 and (name N or name CA or nam \ e C or name O or name CB )) or resid 165 or (resid 166 and (name N or name CA or \ name C or name O or name CB )) or resid 167 through 185 or (resid 186 and (name \ N or name CA or name C or name O or name CB )) or resid 187 through 205 or (res \ id 206 and (name N or name CA or name C or name O or name CB )) or resid 207 thr \ ough 235 or resid 237 through 239 or (resid 240 and (name N or name CA or name C \ or name O or name CB )) or resid 241 through 454 or (resid 455 and (name N or n \ ame CA or name C or name O or name CB )) or resid 456 through 483 or resid 490 t \ hrough 501 or (resid 502 and (name N or name CA or name C or name O or name CB ) \ ) or resid 519 through 520 or (resid 521 and (name N or name CA or name C or nam \ e O or name CB )) or resid 522 through 779 or (resid 780 and (name N or name CA \ or name C or name O or name CB )) or resid 781 through 1221 or resid 1301 throug \ h 1306)) selection = (chain 'C' and (resid 14 through 185 or (resid 186 and (name N or name CA or nam \ e C or name O or name CB )) or resid 187 through 205 or (resid 206 and (name N o \ r name CA or name C or name O or name CB )) or resid 207 through 235 or resid 23 \ 7 through 239 or (resid 240 and (name N or name CA or name C or name O or name C \ B )) or resid 241 through 244 or resid 254 through 311 or (resid 312 and (name N \ or name CA or name C or name O or name CB )) or resid 313 through 491 or (resid \ 492 through 493 and (name N or name CA or name C or name O or name CB )) or res \ id 494 through 553 or (resid 554 and (name N or name CA or name C or name O or n \ ame CB )) or resid 555 through 607 or (resid 608 through 609 and (name N or name \ CA or name C or name O or name CB )) or resid 610 through 660 or (resid 661 and \ (name N or name CA or name C or name O or name CB )) or resid 662 through 779 o \ r (resid 780 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 81 through 931 or (resid 932 and (name N or name CA or name C or name O or name \ CB )) or resid 933 through 1221 or resid 1301 through 1306)) } 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: 3.640 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: 1.310 Check model and map are aligned: 0.220 Set scattering table: 0.280 Process input model: 65.930 Find NCS groups from input model: 1.760 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.076 28634 Z= 0.113 Angle : 0.439 6.953 39104 Z= 0.227 Chirality : 0.041 0.272 4473 Planarity : 0.003 0.045 4977 Dihedral : 8.483 122.789 10557 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.41 % Allowed : 5.27 % Favored : 93.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.42 % 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: -3.34 (0.12), residues: 3499 helix: -3.15 (0.11), residues: 674 sheet: -1.01 (0.19), residues: 702 loop : -2.42 (0.12), residues: 2123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 344 HIS 0.001 0.000 HIS C 876 PHE 0.012 0.001 PHE B 130 TYR 0.006 0.001 TYR B 625 ARG 0.002 0.000 ARG A 446 Details of bonding type rmsd link_NAG-ASN : bond 0.00259 ( 27) link_NAG-ASN : angle 1.00792 ( 81) link_BETA1-4 : bond 0.00382 ( 3) link_BETA1-4 : angle 0.99564 ( 9) hydrogen bonds : bond 0.31270 ( 706) hydrogen bonds : angle 8.45151 ( 1959) SS BOND : bond 0.00085 ( 67) SS BOND : angle 0.41673 ( 134) covalent geometry : bond 0.00221 (28537) covalent geometry : angle 0.43672 (38880) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6998 Ramachandran restraints generated. 3499 Oldfield, 0 Emsley, 3499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6998 Ramachandran restraints generated. 3499 Oldfield, 0 Emsley, 3499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 475 time to evaluate : 3.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 236 TYR cc_start: 0.7627 (t80) cc_final: 0.7356 (t80) REVERT: C 453 PHE cc_start: 0.7610 (m-80) cc_final: 0.7306 (m-80) REVERT: A 191 TYR cc_start: 0.6990 (p90) cc_final: 0.6614 (p90) REVERT: A 851 ASP cc_start: 0.7988 (m-30) cc_final: 0.7766 (m-30) REVERT: A 883 ASP cc_start: 0.7519 (t0) cc_final: 0.6713 (p0) REVERT: A 1079 ASN cc_start: 0.8701 (t0) cc_final: 0.8499 (t0) REVERT: A 1214 LYS cc_start: 0.8684 (mmmt) cc_final: 0.8398 (mmmt) REVERT: B 34 ARG cc_start: 0.7263 (mpt180) cc_final: 0.6902 (mmt-90) REVERT: B 220 THR cc_start: 0.8711 (p) cc_final: 0.8507 (t) REVERT: B 662 LEU cc_start: 0.8205 (pt) cc_final: 0.7957 (mp) REVERT: B 666 THR cc_start: 0.7633 (p) cc_final: 0.7312 (p) REVERT: B 1204 PHE cc_start: 0.7986 (m-80) cc_final: 0.7700 (m-80) outliers start: 44 outliers final: 15 residues processed: 506 average time/residue: 0.3892 time to fit residues: 320.0971 Evaluate side-chains 256 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 241 time to evaluate : 5.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 836 CYS Chi-restraints excluded: chain C residue 926 THR Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 601 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 297 optimal weight: 1.9990 chunk 266 optimal weight: 20.0000 chunk 148 optimal weight: 1.9990 chunk 91 optimal weight: 0.0010 chunk 179 optimal weight: 9.9990 chunk 142 optimal weight: 9.9990 chunk 275 optimal weight: 0.7980 chunk 106 optimal weight: 0.7980 chunk 167 optimal weight: 8.9990 chunk 205 optimal weight: 10.0000 chunk 319 optimal weight: 0.9990 overall best weight: 0.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 440 ASN C 583 ASN C 847 ASN A 99 ASN A 248 ASN A 265 GLN A 291 GLN A 372 ASN A 413 ASN A 445 ASN A 587 ASN A 605 ASN A 709 GLN A 872 ASN A1046 GLN A1180 GLN A1181 ASN B 19 ASN B 654 ASN B 683 GLN B 804 GLN B1059 GLN B1126 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.126658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.095124 restraints weight = 70061.616| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 3.52 r_work: 0.3363 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 28634 Z= 0.129 Angle : 0.528 8.961 39104 Z= 0.273 Chirality : 0.044 0.250 4473 Planarity : 0.004 0.043 4977 Dihedral : 6.250 109.388 4456 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.46 % Allowed : 8.34 % Favored : 89.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.13), residues: 3499 helix: -0.06 (0.19), residues: 715 sheet: -0.66 (0.19), residues: 710 loop : -2.10 (0.12), residues: 2074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 174 HIS 0.004 0.001 HIS C 201 PHE 0.016 0.001 PHE B 835 TYR 0.015 0.001 TYR B 622 ARG 0.006 0.000 ARG B1076 Details of bonding type rmsd link_NAG-ASN : bond 0.00318 ( 27) link_NAG-ASN : angle 1.51927 ( 81) link_BETA1-4 : bond 0.00792 ( 3) link_BETA1-4 : angle 1.87735 ( 9) hydrogen bonds : bond 0.06947 ( 706) hydrogen bonds : angle 5.50608 ( 1959) SS BOND : bond 0.00254 ( 67) SS BOND : angle 1.25014 ( 134) covalent geometry : bond 0.00275 (28537) covalent geometry : angle 0.51917 (38880) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6998 Ramachandran restraints generated. 3499 Oldfield, 0 Emsley, 3499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6998 Ramachandran restraints generated. 3499 Oldfield, 0 Emsley, 3499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 256 time to evaluate : 3.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 462 TYR cc_start: 0.6385 (p90) cc_final: 0.5832 (p90) REVERT: C 994 MET cc_start: 0.9036 (mtp) cc_final: 0.8809 (ttt) REVERT: A 801 GLU cc_start: 0.8063 (tt0) cc_final: 0.7830 (tt0) REVERT: A 883 ASP cc_start: 0.8261 (t0) cc_final: 0.7097 (p0) REVERT: B 34 ARG cc_start: 0.7754 (mpt180) cc_final: 0.7192 (mmt-90) REVERT: B 63 PHE cc_start: 0.8638 (t80) cc_final: 0.8436 (t80) REVERT: B 1205 MET cc_start: 0.7554 (ttm) cc_final: 0.7279 (ttm) outliers start: 77 outliers final: 53 residues processed: 316 average time/residue: 0.3686 time to fit residues: 199.1548 Evaluate side-chains 262 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 209 time to evaluate : 3.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 470 ASN Chi-restraints excluded: chain C residue 566 PHE Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 787 GLU Chi-restraints excluded: chain C residue 836 CYS Chi-restraints excluded: chain C residue 926 THR Chi-restraints excluded: chain C residue 1047 LEU Chi-restraints excluded: chain C residue 1208 CYS Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 453 PHE Chi-restraints excluded: chain A residue 621 ASN Chi-restraints excluded: chain A residue 654 ASN Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1041 ASN Chi-restraints excluded: chain A residue 1058 LEU Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 690 LEU Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 830 SER Chi-restraints excluded: chain B residue 1013 LEU Chi-restraints excluded: chain B residue 1128 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 150 optimal weight: 3.9990 chunk 314 optimal weight: 1.9990 chunk 245 optimal weight: 5.9990 chunk 186 optimal weight: 5.9990 chunk 261 optimal weight: 5.9990 chunk 285 optimal weight: 30.0000 chunk 317 optimal weight: 9.9990 chunk 205 optimal weight: 9.9990 chunk 77 optimal weight: 6.9990 chunk 263 optimal weight: 1.9990 chunk 174 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 132 ASN C 142 HIS C 160 HIS C 278 ASN C 683 GLN C 870 ASN ** C 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 984 GLN C1049 ASN A 108 ASN A 140 GLN ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 ASN ** A 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 ASN B 465 HIS B 854 GLN B 998 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.116926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.084296 restraints weight = 69907.504| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 3.41 r_work: 0.3162 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 28634 Z= 0.271 Angle : 0.703 11.614 39104 Z= 0.360 Chirality : 0.050 0.517 4473 Planarity : 0.005 0.050 4977 Dihedral : 6.362 102.350 4454 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.89 % Favored : 93.08 % Rotamer: Outliers : 3.16 % Allowed : 9.08 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.13), residues: 3499 helix: 0.44 (0.20), residues: 735 sheet: -0.88 (0.18), residues: 782 loop : -2.09 (0.13), residues: 1982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP A 644 HIS 0.013 0.002 HIS B1145 PHE 0.025 0.002 PHE A 592 TYR 0.026 0.002 TYR A 153 ARG 0.005 0.001 ARG C 361 Details of bonding type rmsd link_NAG-ASN : bond 0.00296 ( 27) link_NAG-ASN : angle 2.32210 ( 81) link_BETA1-4 : bond 0.00522 ( 3) link_BETA1-4 : angle 1.67257 ( 9) hydrogen bonds : bond 0.06405 ( 706) hydrogen bonds : angle 5.25249 ( 1959) SS BOND : bond 0.00427 ( 67) SS BOND : angle 1.55926 ( 134) covalent geometry : bond 0.00635 (28537) covalent geometry : angle 0.69088 (38880) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6998 Ramachandran restraints generated. 3499 Oldfield, 0 Emsley, 3499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6998 Ramachandran restraints generated. 3499 Oldfield, 0 Emsley, 3499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 208 time to evaluate : 3.342 Fit side-chains revert: symmetry clash REVERT: C 41 ASP cc_start: 0.8375 (t0) cc_final: 0.8065 (t70) REVERT: C 220 THR cc_start: 0.8938 (OUTLIER) cc_final: 0.8732 (p) REVERT: C 453 PHE cc_start: 0.7786 (m-80) cc_final: 0.7564 (m-80) REVERT: A 1026 LEU cc_start: 0.8907 (tp) cc_final: 0.8659 (mt) REVERT: B 218 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.8467 (mmp) REVERT: B 815 SER cc_start: 0.8618 (m) cc_final: 0.8192 (p) outliers start: 99 outliers final: 66 residues processed: 287 average time/residue: 0.3445 time to fit residues: 167.7840 Evaluate side-chains 233 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 165 time to evaluate : 3.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 132 ASN Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 566 PHE Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 676 ARG Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 787 GLU Chi-restraints excluded: chain C residue 834 THR Chi-restraints excluded: chain C residue 926 THR Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1208 CYS Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 453 PHE Chi-restraints excluded: chain A residue 654 ASN Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 884 PHE Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1041 ASN Chi-restraints excluded: chain A residue 1058 LEU Chi-restraints excluded: chain A residue 1076 ARG Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 255 GLU Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 690 LEU Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 830 SER Chi-restraints excluded: chain B residue 1013 LEU Chi-restraints excluded: chain B residue 1054 ILE Chi-restraints excluded: chain B residue 1128 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 254 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 324 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 187 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 161 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 306 optimal weight: 0.5980 chunk 213 optimal weight: 4.9990 chunk 303 optimal weight: 0.8980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 142 HIS ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1071 GLN B1086 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.118004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.085601 restraints weight = 70359.518| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 3.44 r_work: 0.3177 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28634 Z= 0.149 Angle : 0.553 10.791 39104 Z= 0.282 Chirality : 0.045 0.400 4473 Planarity : 0.004 0.050 4977 Dihedral : 5.838 101.977 4452 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.72 % Favored : 94.26 % Rotamer: Outliers : 2.88 % Allowed : 10.00 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.14), residues: 3499 helix: 0.97 (0.20), residues: 733 sheet: -0.80 (0.18), residues: 783 loop : -1.95 (0.13), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 174 HIS 0.006 0.001 HIS C 201 PHE 0.018 0.001 PHE B 130 TYR 0.020 0.001 TYR C 462 ARG 0.007 0.000 ARG A 264 Details of bonding type rmsd link_NAG-ASN : bond 0.00235 ( 27) link_NAG-ASN : angle 2.06641 ( 81) link_BETA1-4 : bond 0.00418 ( 3) link_BETA1-4 : angle 1.54310 ( 9) hydrogen bonds : bond 0.05170 ( 706) hydrogen bonds : angle 4.86740 ( 1959) SS BOND : bond 0.00280 ( 67) SS BOND : angle 1.19932 ( 134) covalent geometry : bond 0.00348 (28537) covalent geometry : angle 0.54096 (38880) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6998 Ramachandran restraints generated. 3499 Oldfield, 0 Emsley, 3499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6998 Ramachandran restraints generated. 3499 Oldfield, 0 Emsley, 3499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 182 time to evaluate : 3.054 Fit side-chains revert: symmetry clash REVERT: C 238 MET cc_start: 0.8774 (mmm) cc_final: 0.8568 (mmt) REVERT: C 453 PHE cc_start: 0.7696 (m-80) cc_final: 0.7487 (m-80) REVERT: C 1185 MET cc_start: 0.9337 (tpt) cc_final: 0.9107 (mmm) REVERT: C 1195 GLU cc_start: 0.8350 (pt0) cc_final: 0.8046 (pt0) REVERT: A 934 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7690 (mt) REVERT: B 218 MET cc_start: 0.8678 (OUTLIER) cc_final: 0.8176 (mmp) REVERT: B 815 SER cc_start: 0.8641 (m) cc_final: 0.8308 (p) outliers start: 90 outliers final: 65 residues processed: 252 average time/residue: 0.3393 time to fit residues: 146.4674 Evaluate side-chains 228 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 161 time to evaluate : 3.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 566 PHE Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 787 GLU Chi-restraints excluded: chain C residue 926 THR Chi-restraints excluded: chain C residue 972 SER Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1047 LEU Chi-restraints excluded: chain C residue 1074 ILE Chi-restraints excluded: chain C residue 1208 CYS Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 453 PHE Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 654 ASN Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1041 ASN Chi-restraints excluded: chain A residue 1076 ARG Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 690 LEU Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 830 SER Chi-restraints excluded: chain B residue 1013 LEU Chi-restraints excluded: chain B residue 1054 ILE Chi-restraints excluded: chain B residue 1128 ASN Chi-restraints excluded: chain B residue 1203 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 65 optimal weight: 1.9990 chunk 240 optimal weight: 0.0470 chunk 47 optimal weight: 7.9990 chunk 132 optimal weight: 8.9990 chunk 170 optimal weight: 10.0000 chunk 104 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 241 optimal weight: 7.9990 chunk 220 optimal weight: 4.9990 chunk 298 optimal weight: 7.9990 chunk 278 optimal weight: 30.0000 overall best weight: 3.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 132 ASN C 142 HIS C 874 ASN ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 372 ASN A 847 ASN ** A 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 ASN B 108 ASN B 587 ASN B1122 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.114528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.081526 restraints weight = 70498.012| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 3.46 r_work: 0.3075 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 28634 Z= 0.242 Angle : 0.645 15.657 39104 Z= 0.326 Chirality : 0.047 0.310 4473 Planarity : 0.004 0.059 4977 Dihedral : 6.058 98.262 4452 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.66 % Favored : 92.31 % Rotamer: Outliers : 3.29 % Allowed : 10.35 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.14), residues: 3499 helix: 0.86 (0.20), residues: 749 sheet: -0.87 (0.18), residues: 772 loop : -2.03 (0.13), residues: 1978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 644 HIS 0.008 0.002 HIS B1145 PHE 0.020 0.002 PHE A 592 TYR 0.023 0.002 TYR B 49 ARG 0.006 0.001 ARG A 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00524 ( 27) link_NAG-ASN : angle 2.85317 ( 81) link_BETA1-4 : bond 0.00285 ( 3) link_BETA1-4 : angle 1.47111 ( 9) hydrogen bonds : bond 0.05684 ( 706) hydrogen bonds : angle 5.03325 ( 1959) SS BOND : bond 0.00402 ( 67) SS BOND : angle 1.42259 ( 134) covalent geometry : bond 0.00569 (28537) covalent geometry : angle 0.62751 (38880) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6998 Ramachandran restraints generated. 3499 Oldfield, 0 Emsley, 3499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6998 Ramachandran restraints generated. 3499 Oldfield, 0 Emsley, 3499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 174 time to evaluate : 3.219 Fit side-chains revert: symmetry clash REVERT: C 34 ARG cc_start: 0.7319 (mmm160) cc_final: 0.6782 (mmt180) REVERT: C 238 MET cc_start: 0.9017 (mmm) cc_final: 0.8713 (mmt) REVERT: C 453 PHE cc_start: 0.7718 (m-80) cc_final: 0.7451 (m-80) REVERT: C 1185 MET cc_start: 0.9387 (tpt) cc_final: 0.8900 (mmm) REVERT: C 1195 GLU cc_start: 0.8412 (pt0) cc_final: 0.7955 (pt0) REVERT: A 41 ASP cc_start: 0.8056 (m-30) cc_final: 0.7755 (p0) REVERT: A 402 GLN cc_start: 0.7789 (OUTLIER) cc_final: 0.7474 (mm-40) REVERT: A 934 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7731 (mt) REVERT: B 34 ARG cc_start: 0.7980 (mpt180) cc_final: 0.7305 (mmt180) REVERT: B 625 TYR cc_start: 0.5238 (m-80) cc_final: 0.4682 (m-80) REVERT: B 780 GLU cc_start: 0.8515 (tp30) cc_final: 0.8197 (tp30) REVERT: B 815 SER cc_start: 0.8769 (m) cc_final: 0.8370 (p) REVERT: B 1065 LEU cc_start: 0.8784 (mp) cc_final: 0.8526 (mp) REVERT: B 1204 PHE cc_start: 0.8247 (m-80) cc_final: 0.7999 (m-80) outliers start: 103 outliers final: 77 residues processed: 261 average time/residue: 0.3428 time to fit residues: 151.7842 Evaluate side-chains 233 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 154 time to evaluate : 3.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 132 ASN Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 410 GLN Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 566 PHE Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 676 ARG Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 787 GLU Chi-restraints excluded: chain C residue 834 THR Chi-restraints excluded: chain C residue 926 THR Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1047 LEU Chi-restraints excluded: chain C residue 1074 ILE Chi-restraints excluded: chain C residue 1208 CYS Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 175 HIS Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 402 GLN Chi-restraints excluded: chain A residue 453 PHE Chi-restraints excluded: chain A residue 654 ASN Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1041 ASN Chi-restraints excluded: chain A residue 1121 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 690 LEU Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 830 SER Chi-restraints excluded: chain B residue 1054 ILE Chi-restraints excluded: chain B residue 1128 ASN Chi-restraints excluded: chain B residue 1203 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 125 optimal weight: 10.0000 chunk 12 optimal weight: 0.7980 chunk 312 optimal weight: 0.6980 chunk 244 optimal weight: 10.0000 chunk 285 optimal weight: 0.9990 chunk 265 optimal weight: 5.9990 chunk 338 optimal weight: 0.7980 chunk 345 optimal weight: 3.9990 chunk 235 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 137 optimal weight: 5.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 132 ASN C 142 HIS C 583 ASN A1045 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.118367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.086087 restraints weight = 69924.292| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 3.46 r_work: 0.3179 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 28634 Z= 0.103 Angle : 0.532 13.770 39104 Z= 0.268 Chirality : 0.044 0.369 4473 Planarity : 0.004 0.065 4977 Dihedral : 5.511 96.286 4451 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.27 % Allowed : 11.63 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.14), residues: 3499 helix: 1.38 (0.21), residues: 745 sheet: -0.72 (0.18), residues: 764 loop : -1.82 (0.13), residues: 1990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 644 HIS 0.005 0.001 HIS B 876 PHE 0.020 0.001 PHE C 18 TYR 0.021 0.001 TYR C 462 ARG 0.004 0.000 ARG A1076 Details of bonding type rmsd link_NAG-ASN : bond 0.00616 ( 27) link_NAG-ASN : angle 2.39909 ( 81) link_BETA1-4 : bond 0.00258 ( 3) link_BETA1-4 : angle 1.39033 ( 9) hydrogen bonds : bond 0.04444 ( 706) hydrogen bonds : angle 4.55449 ( 1959) SS BOND : bond 0.00229 ( 67) SS BOND : angle 1.06992 ( 134) covalent geometry : bond 0.00229 (28537) covalent geometry : angle 0.51764 (38880) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6998 Ramachandran restraints generated. 3499 Oldfield, 0 Emsley, 3499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6998 Ramachandran restraints generated. 3499 Oldfield, 0 Emsley, 3499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 181 time to evaluate : 3.672 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 34 ARG cc_start: 0.7313 (mmm160) cc_final: 0.6886 (mmt180) REVERT: C 575 TRP cc_start: 0.8160 (p-90) cc_final: 0.7886 (p90) REVERT: C 746 TYR cc_start: 0.8774 (t80) cc_final: 0.8500 (t80) REVERT: C 1185 MET cc_start: 0.9249 (tpt) cc_final: 0.8946 (mmm) REVERT: C 1195 GLU cc_start: 0.8322 (pt0) cc_final: 0.7886 (pt0) REVERT: A 41 ASP cc_start: 0.7947 (m-30) cc_final: 0.7685 (p0) REVERT: A 402 GLN cc_start: 0.7797 (OUTLIER) cc_final: 0.7488 (mm-40) REVERT: A 934 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7557 (mt) REVERT: B 780 GLU cc_start: 0.8358 (tp30) cc_final: 0.8119 (tp30) REVERT: B 815 SER cc_start: 0.8551 (m) cc_final: 0.8241 (p) outliers start: 71 outliers final: 55 residues processed: 239 average time/residue: 0.4219 time to fit residues: 174.0032 Evaluate side-chains 215 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 158 time to evaluate : 3.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 132 ASN Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 566 PHE Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 676 ARG Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 787 GLU Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 926 THR Chi-restraints excluded: chain C residue 972 SER Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1047 LEU Chi-restraints excluded: chain C residue 1208 CYS Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 402 GLN Chi-restraints excluded: chain A residue 453 PHE Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 654 ASN Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1041 ASN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 830 SER Chi-restraints excluded: chain B residue 1128 ASN Chi-restraints excluded: chain B residue 1203 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 124 optimal weight: 6.9990 chunk 339 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 327 optimal weight: 0.0970 chunk 148 optimal weight: 0.9980 chunk 9 optimal weight: 6.9990 chunk 325 optimal weight: 0.0870 chunk 204 optimal weight: 0.4980 chunk 205 optimal weight: 0.1980 chunk 171 optimal weight: 0.0980 overall best weight: 0.1956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 583 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.120140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.088404 restraints weight = 69962.856| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 3.41 r_work: 0.3227 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 28634 Z= 0.091 Angle : 0.508 9.627 39104 Z= 0.255 Chirality : 0.043 0.357 4473 Planarity : 0.004 0.054 4977 Dihedral : 5.143 91.409 4451 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.27 % Allowed : 12.11 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.14), residues: 3499 helix: 1.61 (0.21), residues: 747 sheet: -0.54 (0.19), residues: 733 loop : -1.71 (0.13), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 644 HIS 0.004 0.001 HIS B 876 PHE 0.042 0.001 PHE A 222 TYR 0.023 0.001 TYR C 462 ARG 0.003 0.000 ARG A 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00381 ( 27) link_NAG-ASN : angle 1.87384 ( 81) link_BETA1-4 : bond 0.00291 ( 3) link_BETA1-4 : angle 1.39396 ( 9) hydrogen bonds : bond 0.03838 ( 706) hydrogen bonds : angle 4.29154 ( 1959) SS BOND : bond 0.00189 ( 67) SS BOND : angle 0.84952 ( 134) covalent geometry : bond 0.00194 (28537) covalent geometry : angle 0.49929 (38880) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6998 Ramachandran restraints generated. 3499 Oldfield, 0 Emsley, 3499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6998 Ramachandran restraints generated. 3499 Oldfield, 0 Emsley, 3499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 178 time to evaluate : 3.160 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 575 TRP cc_start: 0.8109 (p-90) cc_final: 0.7845 (p90) REVERT: C 1195 GLU cc_start: 0.8217 (pt0) cc_final: 0.7825 (pt0) REVERT: C 1205 MET cc_start: 0.7511 (OUTLIER) cc_final: 0.7300 (ppp) REVERT: A 41 ASP cc_start: 0.7921 (m-30) cc_final: 0.7668 (p0) REVERT: A 402 GLN cc_start: 0.7801 (OUTLIER) cc_final: 0.7467 (mm-40) REVERT: B 815 SER cc_start: 0.8374 (m) cc_final: 0.7990 (p) outliers start: 71 outliers final: 51 residues processed: 236 average time/residue: 0.3487 time to fit residues: 139.9162 Evaluate side-chains 217 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 164 time to evaluate : 3.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 470 ASN Chi-restraints excluded: chain C residue 566 PHE Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 676 ARG Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 926 THR Chi-restraints excluded: chain C residue 972 SER Chi-restraints excluded: chain C residue 1205 MET Chi-restraints excluded: chain C residue 1208 CYS Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 402 GLN Chi-restraints excluded: chain A residue 453 PHE Chi-restraints excluded: chain A residue 546 CYS Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 654 ASN Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 255 GLU Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 690 LEU Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 830 SER Chi-restraints excluded: chain B residue 1128 ASN Chi-restraints excluded: chain B residue 1203 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 72 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 120 optimal weight: 0.7980 chunk 178 optimal weight: 0.3980 chunk 343 optimal weight: 0.7980 chunk 223 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 319 optimal weight: 6.9990 chunk 237 optimal weight: 5.9990 chunk 182 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 583 ASN B 874 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.119986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.087951 restraints weight = 69753.223| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 3.46 r_work: 0.3221 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 28634 Z= 0.092 Angle : 0.514 13.450 39104 Z= 0.256 Chirality : 0.044 0.499 4473 Planarity : 0.004 0.050 4977 Dihedral : 4.998 86.265 4450 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.17 % Allowed : 12.37 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.42 % 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: -0.88 (0.14), residues: 3499 helix: 1.83 (0.21), residues: 739 sheet: -0.53 (0.19), residues: 768 loop : -1.62 (0.13), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 644 HIS 0.004 0.001 HIS C 201 PHE 0.032 0.001 PHE B 968 TYR 0.020 0.001 TYR B 49 ARG 0.004 0.000 ARG A1076 Details of bonding type rmsd link_NAG-ASN : bond 0.00454 ( 27) link_NAG-ASN : angle 2.39396 ( 81) link_BETA1-4 : bond 0.00348 ( 3) link_BETA1-4 : angle 1.34340 ( 9) hydrogen bonds : bond 0.03726 ( 706) hydrogen bonds : angle 4.22351 ( 1959) SS BOND : bond 0.00184 ( 67) SS BOND : angle 0.83183 ( 134) covalent geometry : bond 0.00208 (28537) covalent geometry : angle 0.50143 (38880) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6998 Ramachandran restraints generated. 3499 Oldfield, 0 Emsley, 3499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6998 Ramachandran restraints generated. 3499 Oldfield, 0 Emsley, 3499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 174 time to evaluate : 3.217 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 327 CYS cc_start: 0.7664 (OUTLIER) cc_final: 0.7100 (m) REVERT: C 575 TRP cc_start: 0.8132 (p-90) cc_final: 0.7891 (p90) REVERT: C 1185 MET cc_start: 0.9251 (mmm) cc_final: 0.8836 (mmm) REVERT: C 1195 GLU cc_start: 0.8283 (pt0) cc_final: 0.7980 (pt0) REVERT: A 41 ASP cc_start: 0.7946 (m-30) cc_final: 0.7685 (p0) REVERT: A 402 GLN cc_start: 0.7780 (OUTLIER) cc_final: 0.7427 (mm-40) REVERT: B 815 SER cc_start: 0.8346 (m) cc_final: 0.7948 (p) outliers start: 68 outliers final: 52 residues processed: 228 average time/residue: 0.3697 time to fit residues: 143.3305 Evaluate side-chains 210 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 156 time to evaluate : 3.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 470 ASN Chi-restraints excluded: chain C residue 566 PHE Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 676 ARG Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 834 THR Chi-restraints excluded: chain C residue 926 THR Chi-restraints excluded: chain C residue 972 SER Chi-restraints excluded: chain C residue 1208 CYS Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 402 GLN Chi-restraints excluded: chain A residue 453 PHE Chi-restraints excluded: chain A residue 546 CYS Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 1041 ASN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 690 LEU Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 719 CYS Chi-restraints excluded: chain B residue 1128 ASN Chi-restraints excluded: chain B residue 1203 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 337 optimal weight: 0.6980 chunk 232 optimal weight: 5.9990 chunk 158 optimal weight: 0.9980 chunk 331 optimal weight: 4.9990 chunk 91 optimal weight: 9.9990 chunk 275 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 chunk 162 optimal weight: 9.9990 chunk 104 optimal weight: 2.9990 chunk 149 optimal weight: 0.6980 chunk 1 optimal weight: 0.0060 overall best weight: 1.0798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 583 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.120207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.088391 restraints weight = 70756.897| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 3.40 r_work: 0.3211 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 28634 Z= 0.103 Angle : 0.518 12.099 39104 Z= 0.259 Chirality : 0.044 0.544 4473 Planarity : 0.004 0.050 4977 Dihedral : 4.894 79.601 4450 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.11 % Allowed : 12.75 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.42 % 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: -0.84 (0.14), residues: 3499 helix: 1.90 (0.21), residues: 736 sheet: -0.46 (0.19), residues: 746 loop : -1.62 (0.13), residues: 2017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 644 HIS 0.004 0.001 HIS C 201 PHE 0.037 0.001 PHE B 968 TYR 0.019 0.001 TYR B 49 ARG 0.002 0.000 ARG C 676 Details of bonding type rmsd link_NAG-ASN : bond 0.00407 ( 27) link_NAG-ASN : angle 2.25010 ( 81) link_BETA1-4 : bond 0.00338 ( 3) link_BETA1-4 : angle 1.33688 ( 9) hydrogen bonds : bond 0.03797 ( 706) hydrogen bonds : angle 4.24276 ( 1959) SS BOND : bond 0.00195 ( 67) SS BOND : angle 1.08461 ( 134) covalent geometry : bond 0.00239 (28537) covalent geometry : angle 0.50482 (38880) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6998 Ramachandran restraints generated. 3499 Oldfield, 0 Emsley, 3499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6998 Ramachandran restraints generated. 3499 Oldfield, 0 Emsley, 3499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 173 time to evaluate : 4.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 145 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.8255 (tp) REVERT: C 575 TRP cc_start: 0.8153 (p-90) cc_final: 0.7907 (p90) REVERT: C 1185 MET cc_start: 0.9247 (mmm) cc_final: 0.8729 (mmm) REVERT: C 1195 GLU cc_start: 0.8328 (pt0) cc_final: 0.7952 (pt0) REVERT: A 41 ASP cc_start: 0.7954 (m-30) cc_final: 0.7711 (p0) REVERT: A 654 ASN cc_start: 0.8769 (OUTLIER) cc_final: 0.8287 (p0) REVERT: B 815 SER cc_start: 0.8365 (m) cc_final: 0.7961 (p) outliers start: 66 outliers final: 55 residues processed: 225 average time/residue: 0.4632 time to fit residues: 182.5854 Evaluate side-chains 215 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 158 time to evaluate : 3.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 470 ASN Chi-restraints excluded: chain C residue 566 PHE Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 676 ARG Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 926 THR Chi-restraints excluded: chain C residue 972 SER Chi-restraints excluded: chain C residue 1208 CYS Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 402 GLN Chi-restraints excluded: chain A residue 453 PHE Chi-restraints excluded: chain A residue 465 HIS Chi-restraints excluded: chain A residue 546 CYS Chi-restraints excluded: chain A residue 654 ASN Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 1041 ASN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 255 GLU Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 690 LEU Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 719 CYS Chi-restraints excluded: chain B residue 830 SER Chi-restraints excluded: chain B residue 1128 ASN Chi-restraints excluded: chain B residue 1203 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 247 optimal weight: 9.9990 chunk 346 optimal weight: 0.1980 chunk 161 optimal weight: 0.9990 chunk 318 optimal weight: 3.9990 chunk 149 optimal weight: 0.0010 chunk 210 optimal weight: 0.9980 chunk 267 optimal weight: 6.9990 chunk 245 optimal weight: 7.9990 chunk 307 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 147 optimal weight: 0.0980 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 583 ASN C 621 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.120585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.088835 restraints weight = 69813.657| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 3.43 r_work: 0.3241 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 28634 Z= 0.089 Angle : 0.508 10.236 39104 Z= 0.253 Chirality : 0.043 0.485 4473 Planarity : 0.004 0.050 4977 Dihedral : 4.709 71.848 4450 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.82 % Allowed : 13.14 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.42 % 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 (0.14), residues: 3499 helix: 1.95 (0.21), residues: 738 sheet: -0.37 (0.19), residues: 744 loop : -1.57 (0.13), residues: 2017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 644 HIS 0.004 0.001 HIS C 201 PHE 0.030 0.001 PHE B 884 TYR 0.028 0.001 TYR A 729 ARG 0.004 0.000 ARG C 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00386 ( 27) link_NAG-ASN : angle 2.02865 ( 81) link_BETA1-4 : bond 0.00379 ( 3) link_BETA1-4 : angle 1.30233 ( 9) hydrogen bonds : bond 0.03460 ( 706) hydrogen bonds : angle 4.11358 ( 1959) SS BOND : bond 0.00196 ( 67) SS BOND : angle 0.95765 ( 134) covalent geometry : bond 0.00197 (28537) covalent geometry : angle 0.49712 (38880) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6998 Ramachandran restraints generated. 3499 Oldfield, 0 Emsley, 3499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6998 Ramachandran restraints generated. 3499 Oldfield, 0 Emsley, 3499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 179 time to evaluate : 3.079 Fit side-chains revert: symmetry clash REVERT: C 145 ILE cc_start: 0.8588 (OUTLIER) cc_final: 0.8249 (tp) REVERT: C 327 CYS cc_start: 0.7553 (OUTLIER) cc_final: 0.6994 (m) REVERT: C 1185 MET cc_start: 0.9252 (mmm) cc_final: 0.8754 (mmm) REVERT: C 1195 GLU cc_start: 0.8291 (pt0) cc_final: 0.7928 (pt0) REVERT: A 41 ASP cc_start: 0.7942 (m-30) cc_final: 0.7729 (p0) REVERT: A 714 ASP cc_start: 0.8023 (m-30) cc_final: 0.7493 (t70) REVERT: B 815 SER cc_start: 0.8270 (m) cc_final: 0.7891 (p) outliers start: 57 outliers final: 50 residues processed: 226 average time/residue: 0.3519 time to fit residues: 135.2226 Evaluate side-chains 216 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 164 time to evaluate : 3.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 470 ASN Chi-restraints excluded: chain C residue 566 PHE Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 676 ARG Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 926 THR Chi-restraints excluded: chain C residue 972 SER Chi-restraints excluded: chain C residue 1208 CYS Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 402 GLN Chi-restraints excluded: chain A residue 453 PHE Chi-restraints excluded: chain A residue 465 HIS Chi-restraints excluded: chain A residue 546 CYS Chi-restraints excluded: chain A residue 654 ASN Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 690 LEU Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 719 CYS Chi-restraints excluded: chain B residue 830 SER Chi-restraints excluded: chain B residue 1128 ASN Chi-restraints excluded: chain B residue 1203 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 203 optimal weight: 0.0370 chunk 233 optimal weight: 5.9990 chunk 300 optimal weight: 3.9990 chunk 318 optimal weight: 0.2980 chunk 103 optimal weight: 0.7980 chunk 42 optimal weight: 20.0000 chunk 180 optimal weight: 6.9990 chunk 304 optimal weight: 10.0000 chunk 334 optimal weight: 0.8980 chunk 313 optimal weight: 8.9990 chunk 4 optimal weight: 0.6980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 587 ASN C1049 ASN A 100 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.121596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.089958 restraints weight = 70501.264| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 3.40 r_work: 0.3252 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 28634 Z= 0.088 Angle : 0.502 9.901 39104 Z= 0.250 Chirality : 0.043 0.468 4473 Planarity : 0.003 0.050 4977 Dihedral : 4.575 62.982 4449 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.79 % Allowed : 13.23 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.42 % 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: -0.69 (0.14), residues: 3499 helix: 2.01 (0.21), residues: 736 sheet: -0.32 (0.19), residues: 746 loop : -1.53 (0.13), residues: 2017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 644 HIS 0.004 0.001 HIS C 201 PHE 0.028 0.001 PHE B 884 TYR 0.019 0.001 TYR C 462 ARG 0.003 0.000 ARG C 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00359 ( 27) link_NAG-ASN : angle 1.98585 ( 81) link_BETA1-4 : bond 0.00351 ( 3) link_BETA1-4 : angle 1.31738 ( 9) hydrogen bonds : bond 0.03415 ( 706) hydrogen bonds : angle 4.07513 ( 1959) SS BOND : bond 0.00164 ( 67) SS BOND : angle 0.92791 ( 134) covalent geometry : bond 0.00199 (28537) covalent geometry : angle 0.49199 (38880) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16070.95 seconds wall clock time: 283 minutes 28.93 seconds (17008.93 seconds total)