Starting phenix.real_space_refine on Sat Jul 27 00:39:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zr7_14885/07_2024/7zr7_14885.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zr7_14885/07_2024/7zr7_14885.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zr7_14885/07_2024/7zr7_14885.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zr7_14885/07_2024/7zr7_14885.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zr7_14885/07_2024/7zr7_14885.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zr7_14885/07_2024/7zr7_14885.cif" } resolution = 3.7 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= -0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5153 atoms to isotropic. 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 132 5.16 5 C 19566 2.51 5 N 5048 2.21 5 O 6018 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 30764 Number of models: 1 Model: "" Number of chains: 24 Chain: "B" Number of atoms: 8281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1060, 8281 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 54, 'TRANS': 1005} Chain breaks: 6 Chain: "A" Number of atoms: 8287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8287 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 54, 'TRANS': 1006} Chain breaks: 6 Chain: "C" Number of atoms: 8287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8287 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 54, 'TRANS': 1006} Chain breaks: 6 Chain: "H" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 940 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 120} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "L" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 783 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "D" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 927 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 783 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "F" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 937 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 120} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "G" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 783 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "I" 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: "J" 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: "K" 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: "M" 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: "N" 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: "O" 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: "P" 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: "Q" 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: "R" 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: "S" 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: "T" 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: "U" 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: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 15.97, per 1000 atoms: 0.52 Number of scatterers: 30764 At special positions: 0 Unit cell: (161.02, 157.7, 209.16, 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 132 16.00 O 6018 8.00 N 5048 7.00 C 19566 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.03 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " distance=2.03 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 587 " distance=2.03 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.03 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.03 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.03 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 587 " distance=2.04 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 646 " distance=2.03 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS C 376 " - pdb=" SG CYS C 429 " distance=2.03 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 522 " distance=2.03 Simple disulfide: pdb=" SG CYS C 477 " - pdb=" SG CYS C 485 " distance=2.03 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 587 " distance=2.03 Simple disulfide: pdb=" SG CYS C 614 " - pdb=" SG CYS C 646 " distance=2.03 Simple disulfide: pdb=" SG CYS C 659 " - pdb=" SG CYS C 668 " distance=2.03 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 757 " distance=2.03 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.03 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 90 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 90 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 279 " " NAG A1303 " - " ASN A 328 " " NAG A1304 " - " ASN A 600 " " NAG A1305 " - " ASN A 613 " " NAG A1306 " - " ASN A 654 " " NAG A1307 " - " ASN A 706 " " NAG A1308 " - " ASN A1071 " " NAG A1309 " - " ASN A 165 " " NAG A1310 " - " ASN A 340 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 279 " " NAG B1303 " - " ASN B 328 " " NAG B1304 " - " ASN B 600 " " NAG B1305 " - " ASN B 613 " " NAG B1306 " - " ASN B 654 " " NAG B1307 " - " ASN B 706 " " NAG B1308 " - " ASN B1071 " " NAG B1309 " - " ASN B 165 " " NAG B1310 " - " ASN B 340 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 279 " " NAG C1303 " - " ASN C 328 " " NAG C1304 " - " ASN C 600 " " NAG C1305 " - " ASN C 613 " " NAG C1306 " - " ASN C 654 " " NAG C1307 " - " ASN C 706 " " NAG C1308 " - " ASN C1071 " " NAG C1309 " - " ASN C 165 " " NAG C1310 " - " ASN C 340 " " NAG I 1 " - " ASN B 714 " " NAG J 1 " - " ASN B 798 " " NAG K 1 " - " ASN B1095 " " NAG M 1 " - " ASN B1131 " " NAG N 1 " - " ASN A 714 " " NAG O 1 " - " ASN A 798 " " NAG P 1 " - " ASN A1095 " " NAG Q 1 " - " ASN A1131 " " NAG R 1 " - " ASN C 714 " " NAG S 1 " - " ASN C 798 " " NAG T 1 " - " ASN C1095 " " NAG U 1 " - " ASN C1131 " Time building additional restraints: 12.36 Conformation dependent library (CDL) restraints added in 5.3 seconds 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7158 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 72 sheets defined 21.7% alpha, 34.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.95 Creating SS restraints... Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 335 through 340 Processing helix chain 'B' and resid 361 through 367 Processing helix chain 'B' and resid 382 through 387 removed outlier: 3.803A pdb=" N ASN B 385 " --> pdb=" O THR B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 407 Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 435 through 440 Processing helix chain 'B' and resid 734 through 740 Processing helix chain 'B' and resid 743 through 752 removed outlier: 3.936A pdb=" N GLN B 752 " --> pdb=" O ASN B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 780 Processing helix chain 'B' and resid 813 through 823 Processing helix chain 'B' and resid 863 through 882 Processing helix chain 'B' and resid 883 through 888 removed outlier: 3.836A pdb=" N ALA B 887 " --> pdb=" O TRP B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 906 removed outlier: 3.603A pdb=" N ILE B 906 " --> pdb=" O ARG B 902 " (cutoff:3.500A) Processing helix chain 'B' and resid 909 through 916 removed outlier: 4.224A pdb=" N LEU B 913 " --> pdb=" O THR B 909 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 938 Processing helix chain 'B' and resid 942 through 962 Processing helix chain 'B' and resid 963 through 965 No H-bonds generated for 'chain 'B' and resid 963 through 965' Processing helix chain 'B' and resid 973 through 981 Processing helix chain 'B' and resid 982 through 1029 removed outlier: 4.467A pdb=" N VAL B 988 " --> pdb=" O PRO B 984 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLN B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG B 992 " --> pdb=" O VAL B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1137 through 1144 removed outlier: 3.955A pdb=" N GLU B1141 " --> pdb=" O PRO B1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 361 through 367 Processing helix chain 'A' and resid 380 through 387 removed outlier: 3.652A pdb=" N LEU A 384 " --> pdb=" O PRO A 381 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASN A 385 " --> pdb=" O THR A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 435 through 440 Processing helix chain 'A' and resid 734 through 740 Processing helix chain 'A' and resid 743 through 752 removed outlier: 3.802A pdb=" N GLN A 752 " --> pdb=" O ASN A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 780 Processing helix chain 'A' and resid 813 through 823 Processing helix chain 'A' and resid 863 through 882 Processing helix chain 'A' and resid 883 through 888 removed outlier: 3.632A pdb=" N ALA A 887 " --> pdb=" O TRP A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 907 Processing helix chain 'A' and resid 910 through 938 removed outlier: 3.507A pdb=" N TYR A 914 " --> pdb=" O GLN A 910 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N LYS A 918 " --> pdb=" O TYR A 914 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU A 919 " --> pdb=" O GLU A 915 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR A 938 " --> pdb=" O SER A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 941 No H-bonds generated for 'chain 'A' and resid 939 through 941' Processing helix chain 'A' and resid 942 through 962 removed outlier: 3.533A pdb=" N VAL A 948 " --> pdb=" O LYS A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 965 No H-bonds generated for 'chain 'A' and resid 963 through 965' Processing helix chain 'A' and resid 973 through 981 removed outlier: 3.612A pdb=" N ILE A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 1029 removed outlier: 4.874A pdb=" N VAL A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLN A 989 " --> pdb=" O GLU A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1144 removed outlier: 3.673A pdb=" N GLU A1141 " --> pdb=" O PRO A1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 335 through 340 Processing helix chain 'C' and resid 361 through 367 Processing helix chain 'C' and resid 380 through 387 removed outlier: 3.652A pdb=" N LEU C 384 " --> pdb=" O PRO C 381 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASN C 385 " --> pdb=" O THR C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 407 Processing helix chain 'C' and resid 413 through 419 Processing helix chain 'C' and resid 435 through 440 Processing helix chain 'C' and resid 734 through 740 Processing helix chain 'C' and resid 743 through 752 removed outlier: 3.802A pdb=" N GLN C 752 " --> pdb=" O ASN C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 780 Processing helix chain 'C' and resid 813 through 823 Processing helix chain 'C' and resid 863 through 882 Processing helix chain 'C' and resid 883 through 888 removed outlier: 3.631A pdb=" N ALA C 887 " --> pdb=" O TRP C 883 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 907 Processing helix chain 'C' and resid 909 through 938 removed outlier: 4.224A pdb=" N LEU C 913 " --> pdb=" O THR C 909 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR C 914 " --> pdb=" O GLN C 910 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LYS C 918 " --> pdb=" O TYR C 914 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LEU C 919 " --> pdb=" O GLU C 915 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR C 938 " --> pdb=" O SER C 934 " (cutoff:3.500A) Processing helix chain 'C' and resid 939 through 941 No H-bonds generated for 'chain 'C' and resid 939 through 941' Processing helix chain 'C' and resid 942 through 962 removed outlier: 3.533A pdb=" N VAL C 948 " --> pdb=" O LYS C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 963 through 965 No H-bonds generated for 'chain 'C' and resid 963 through 965' Processing helix chain 'C' and resid 973 through 981 removed outlier: 3.612A pdb=" N ILE C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 1029 removed outlier: 4.874A pdb=" N VAL C 988 " --> pdb=" O PRO C 984 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLN C 989 " --> pdb=" O GLU C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1144 removed outlier: 3.673A pdb=" N GLU C1141 " --> pdb=" O PRO C1137 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 105 through 111 Processing helix chain 'L' and resid 81 through 85 Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'D' and resid 105 through 111 Processing helix chain 'E' and resid 81 through 85 Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'F' and resid 105 through 111 Processing helix chain 'G' and resid 81 through 85 Processing sheet with id=AA1, first strand: chain 'B' and resid 21 through 22 Processing sheet with id=AA2, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.626A pdb=" N ASN B 61 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N TYR B 266 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.982A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.005A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 11.277A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 9.876A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.359A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.655A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.412A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 9.548A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 10.862A pdb=" N PHE B 140 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N SER B 155 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N GLY B 142 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N MET B 153 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N TYR B 144 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N SER B 151 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.005A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N SER B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU B 141 " --> pdb=" O SER B 244 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL B 143 " --> pdb=" O LEU B 246 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 308 through 316 removed outlier: 5.416A pdb=" N ILE B 309 " --> pdb=" O THR B 596 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N THR B 596 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N GLN B 311 " --> pdb=" O VAL B 594 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL B 594 " --> pdb=" O GLN B 311 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLY B 591 " --> pdb=" O GLN B 610 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 322 through 325 removed outlier: 6.976A pdb=" N PHE B 562 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 351 through 355 Processing sheet with id=AB1, first strand: chain 'B' and resid 358 through 359 removed outlier: 7.090A pdb=" N CYS B 358 " --> pdb=" O CYS B 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AB3, first strand: chain 'B' and resid 470 through 471 Processing sheet with id=AB4, first strand: chain 'B' and resid 661 through 664 removed outlier: 6.509A pdb=" N ALA B 669 " --> pdb=" O PRO B 662 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 699 through 700 Processing sheet with id=AB6, first strand: chain 'B' and resid 709 through 712 Processing sheet with id=AB7, first strand: chain 'B' and resid 715 through 725 removed outlier: 6.936A pdb=" N GLY B1056 " --> pdb=" O SER B1052 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N SER B1052 " --> pdb=" O GLY B1056 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL B1058 " --> pdb=" O PRO B1050 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU B1060 " --> pdb=" O SER B1048 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N SER B1048 " --> pdb=" O LEU B1060 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL B1062 " --> pdb=" O LEU B1046 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 730 through 733 removed outlier: 4.371A pdb=" N LYS B 730 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 785 through 786 removed outlier: 5.727A pdb=" N ILE B 785 " --> pdb=" O ASN A 700 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 1117 through 1122 removed outlier: 4.862A pdb=" N ALA B1084 " --> pdb=" O SER B1120 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 21 through 22 Processing sheet with id=AC3, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.726A pdb=" N ASN A 61 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N TYR A 266 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA A 260 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AC5, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.866A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.551A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 11.291A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.787A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.210A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.327A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 9.414A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 10.818A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 8.674A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N GLY A 142 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N MET A 153 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N TYR A 144 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N SER A 151 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.551A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N SER A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU A 141 " --> pdb=" O SER A 244 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N VAL A 143 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 308 through 316 removed outlier: 5.492A pdb=" N ILE A 309 " --> pdb=" O THR A 596 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N THR A 596 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N GLN A 311 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL A 594 " --> pdb=" O GLN A 311 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY A 591 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 322 through 325 Processing sheet with id=AD1, first strand: chain 'A' and resid 351 through 355 Processing sheet with id=AD2, first strand: chain 'A' and resid 358 through 359 removed outlier: 6.846A pdb=" N CYS A 358 " --> pdb=" O CYS A 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AD4, first strand: chain 'A' and resid 470 through 471 Processing sheet with id=AD5, first strand: chain 'A' and resid 651 through 652 removed outlier: 6.427A pdb=" N ALA A 669 " --> pdb=" O PRO A 662 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 708 through 712 Processing sheet with id=AD7, first strand: chain 'A' and resid 715 through 725 removed outlier: 7.070A pdb=" N GLY A1056 " --> pdb=" O SER A1052 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N SER A1052 " --> pdb=" O GLY A1056 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL A1058 " --> pdb=" O PRO A1050 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU A1060 " --> pdb=" O SER A1048 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N SER A1048 " --> pdb=" O LEU A1060 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL A1062 " --> pdb=" O LEU A1046 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 730 through 733 removed outlier: 4.589A pdb=" N LYS A 730 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 1117 through 1122 removed outlier: 4.520A pdb=" N ALA A1084 " --> pdb=" O SER A1120 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 1091 through 1094 Processing sheet with id=AE2, first strand: chain 'C' and resid 21 through 22 Processing sheet with id=AE3, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.726A pdb=" N ASN C 61 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N TYR C 266 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA C 260 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.866A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.551A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 11.292A pdb=" N VAL C 126 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 9.787A pdb=" N GLU C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 11.210A pdb=" N ILE C 128 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N THR C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N VAL C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ASN C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 11.327A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 9.412A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 10.818A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 8.674A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N GLY C 142 " --> pdb=" O MET C 153 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N MET C 153 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N TYR C 144 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N SER C 151 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.551A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N SER C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU C 141 " --> pdb=" O SER C 244 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL C 143 " --> pdb=" O LEU C 246 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 308 through 316 removed outlier: 5.492A pdb=" N ILE C 309 " --> pdb=" O THR C 596 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N THR C 596 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N GLN C 311 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL C 594 " --> pdb=" O GLN C 311 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY C 591 " --> pdb=" O GLN C 610 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 322 through 325 Processing sheet with id=AE9, first strand: chain 'C' and resid 351 through 355 Processing sheet with id=AF1, first strand: chain 'C' and resid 358 through 359 removed outlier: 6.846A pdb=" N CYS C 358 " --> pdb=" O CYS C 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'C' and resid 449 through 451 Processing sheet with id=AF3, first strand: chain 'C' and resid 470 through 471 Processing sheet with id=AF4, first strand: chain 'C' and resid 651 through 652 removed outlier: 6.426A pdb=" N ALA C 669 " --> pdb=" O PRO C 662 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 708 through 712 Processing sheet with id=AF6, first strand: chain 'C' and resid 715 through 725 removed outlier: 7.070A pdb=" N GLY C1056 " --> pdb=" O SER C1052 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N SER C1052 " --> pdb=" O GLY C1056 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL C1058 " --> pdb=" O PRO C1050 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU C1060 " --> pdb=" O SER C1048 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N SER C1048 " --> pdb=" O LEU C1060 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL C1062 " --> pdb=" O LEU C1046 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 730 through 733 removed outlier: 4.589A pdb=" N LYS C 730 " --> pdb=" O LEU C 858 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 1117 through 1122 removed outlier: 4.520A pdb=" N ALA C1084 " --> pdb=" O SER C1120 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 1091 through 1094 Processing sheet with id=AG1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AG2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.301A pdb=" N GLY H 10 " --> pdb=" O THR H 122 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ILE H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N SER H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.301A pdb=" N GLY H 10 " --> pdb=" O THR H 122 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL H 114 " --> pdb=" O LYS H 98 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.259A pdb=" N TRP L 37 " --> pdb=" O MET L 49 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 9 through 13 Processing sheet with id=AG6, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AG7, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AG8, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.302A pdb=" N GLY D 10 " --> pdb=" O THR D 122 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ILE D 34 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N SER D 50 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.302A pdb=" N GLY D 10 " --> pdb=" O THR D 122 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL D 114 " --> pdb=" O LYS D 98 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'E' and resid 9 through 13 removed outlier: 6.259A pdb=" N TRP E 37 " --> pdb=" O MET E 49 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'E' and resid 9 through 13 Processing sheet with id=AH3, first strand: chain 'E' and resid 18 through 23 Processing sheet with id=AH4, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AH5, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.302A pdb=" N GLY F 10 " --> pdb=" O THR F 122 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ILE F 34 " --> pdb=" O SER F 50 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N SER F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.302A pdb=" N GLY F 10 " --> pdb=" O THR F 122 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL F 114 " --> pdb=" O LYS F 98 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'G' and resid 9 through 13 removed outlier: 6.258A pdb=" N TRP G 37 " --> pdb=" O MET G 49 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'G' and resid 9 through 13 Processing sheet with id=AH9, first strand: chain 'G' and resid 18 through 23 1348 hydrogen bonds defined for protein. 3612 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: 15.04 Time building geometry restraints manager: 13.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9770 1.34 - 1.46: 7907 1.46 - 1.58: 13625 1.58 - 1.70: 3 1.70 - 1.82: 168 Bond restraints: 31473 Sorted by residual: bond pdb=" CA VAL A 317 " pdb=" C VAL A 317 " ideal model delta sigma weight residual 1.523 1.618 -0.095 1.14e-02 7.69e+03 6.91e+01 bond pdb=" N THR B 304 " pdb=" CA THR B 304 " ideal model delta sigma weight residual 1.457 1.544 -0.087 1.23e-02 6.61e+03 4.97e+01 bond pdb=" CA PHE B 303 " pdb=" C PHE B 303 " ideal model delta sigma weight residual 1.521 1.616 -0.095 1.36e-02 5.41e+03 4.89e+01 bond pdb=" N GLN A 318 " pdb=" CA GLN A 318 " ideal model delta sigma weight residual 1.453 1.548 -0.095 1.64e-02 3.72e+03 3.35e+01 bond pdb=" CA GLN A 318 " pdb=" C GLN A 318 " ideal model delta sigma weight residual 1.524 1.581 -0.057 1.28e-02 6.10e+03 1.99e+01 ... (remaining 31468 not shown) Histogram of bond angle deviations from ideal: 100.41 - 107.14: 1020 107.14 - 113.86: 17685 113.86 - 120.59: 11673 120.59 - 127.31: 12133 127.31 - 134.03: 311 Bond angle restraints: 42822 Sorted by residual: angle pdb=" N ASN C 328 " pdb=" CA ASN C 328 " pdb=" C ASN C 328 " ideal model delta sigma weight residual 112.38 123.59 -11.21 1.22e+00 6.72e-01 8.44e+01 angle pdb=" N GLN A 318 " pdb=" CA GLN A 318 " pdb=" C GLN A 318 " ideal model delta sigma weight residual 110.39 117.76 -7.37 1.30e+00 5.92e-01 3.21e+01 angle pdb=" N ASN C 328 " pdb=" CA ASN C 328 " pdb=" CB ASN C 328 " ideal model delta sigma weight residual 110.32 101.08 9.24 1.70e+00 3.46e-01 2.96e+01 angle pdb=" N SER B 588 " pdb=" CA SER B 588 " pdb=" C SER B 588 " ideal model delta sigma weight residual 110.35 117.72 -7.37 1.40e+00 5.10e-01 2.77e+01 angle pdb=" CA VAL A 317 " pdb=" C VAL A 317 " pdb=" N GLN A 318 " ideal model delta sigma weight residual 116.30 122.11 -5.81 1.13e+00 7.83e-01 2.64e+01 ... (remaining 42817 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 18419 17.73 - 35.46: 674 35.46 - 53.19: 170 53.19 - 70.92: 39 70.92 - 88.65: 16 Dihedral angle restraints: 19318 sinusoidal: 8124 harmonic: 11194 Sorted by residual: dihedral pdb=" CA THR C 596 " pdb=" C THR C 596 " pdb=" N PRO C 597 " pdb=" CA PRO C 597 " ideal model delta harmonic sigma weight residual 180.00 161.54 18.46 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA THR A 596 " pdb=" C THR A 596 " pdb=" N PRO A 597 " pdb=" CA PRO A 597 " ideal model delta harmonic sigma weight residual 180.00 161.56 18.44 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA THR B 596 " pdb=" C THR B 596 " pdb=" N PRO B 597 " pdb=" CA PRO B 597 " ideal model delta harmonic sigma weight residual 180.00 162.84 17.16 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 19315 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 4504 0.085 - 0.170: 452 0.170 - 0.255: 5 0.255 - 0.340: 2 0.340 - 0.425: 2 Chirality restraints: 4965 Sorted by residual: chirality pdb=" C1 NAG C1308 " pdb=" ND2 ASN C1071 " pdb=" C2 NAG C1308 " pdb=" O5 NAG C1308 " both_signs ideal model delta sigma weight residual False -2.40 -2.83 0.43 2.00e-01 2.50e+01 4.52e+00 chirality pdb=" CA VAL A 317 " pdb=" N VAL A 317 " pdb=" C VAL A 317 " pdb=" CB VAL A 317 " both_signs ideal model delta sigma weight residual False 2.44 2.79 -0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" CA ASN C 328 " pdb=" N ASN C 328 " pdb=" C ASN C 328 " pdb=" CB ASN C 328 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.87e+00 ... (remaining 4962 not shown) Planarity restraints: 5507 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 340 " -0.147 2.00e-02 2.50e+03 1.56e-01 3.03e+02 pdb=" CG ASN A 340 " 0.059 2.00e-02 2.50e+03 pdb=" OD1 ASN A 340 " 0.068 2.00e-02 2.50e+03 pdb=" ND2 ASN A 340 " 0.224 2.00e-02 2.50e+03 pdb=" C1 NAG A1310 " -0.203 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C1071 " -0.130 2.00e-02 2.50e+03 1.43e-01 2.56e+02 pdb=" CG ASN C1071 " 0.049 2.00e-02 2.50e+03 pdb=" OD1 ASN C1071 " 0.032 2.00e-02 2.50e+03 pdb=" ND2 ASN C1071 " 0.225 2.00e-02 2.50e+03 pdb=" C1 NAG C1308 " -0.177 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 340 " -0.122 2.00e-02 2.50e+03 1.27e-01 2.01e+02 pdb=" CG ASN C 340 " 0.047 2.00e-02 2.50e+03 pdb=" OD1 ASN C 340 " 0.053 2.00e-02 2.50e+03 pdb=" ND2 ASN C 340 " 0.184 2.00e-02 2.50e+03 pdb=" C1 NAG C1310 " -0.163 2.00e-02 2.50e+03 ... (remaining 5504 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 338 2.61 - 3.18: 27050 3.18 - 3.75: 46131 3.75 - 4.33: 67856 4.33 - 4.90: 112975 Nonbonded interactions: 254350 Sorted by model distance: nonbonded pdb=" OD1 ASN A 537 " pdb=" OG1 THR A 546 " model vdw 2.034 2.440 nonbonded pdb=" OD1 ASN C 537 " pdb=" OG1 THR C 546 " model vdw 2.035 2.440 nonbonded pdb=" OD2 ASP B 575 " pdb=" OG1 THR B 578 " model vdw 2.040 2.440 nonbonded pdb=" OG1 THR B 109 " pdb=" OD1 ASP B 111 " model vdw 2.044 2.440 nonbonded pdb=" O ASN B 436 " pdb=" OG SER B 440 " model vdw 2.069 2.440 ... (remaining 254345 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 13 through 619 or resid 638 through 1144 or resid 1301 thr \ ough 1310)) selection = chain 'B' selection = (chain 'C' and (resid 13 through 619 or resid 638 through 1144 or resid 1301 thr \ ough 1310)) } ncs_group { reference = (chain 'D' and (resid 1 through 18 or (resid 19 and (name N or name CA or name C \ or name O or name CB )) or resid 20 through 86 or (resid 87 through 88 and (nam \ e N or name CA or name C or name O or name CB )) or resid 89 through 125)) selection = (chain 'F' and (resid 1 through 13 or resid 17 through 18 or (resid 19 and (name \ N or name CA or name C or name O or name CB )) or resid 20 through 125)) selection = (chain 'H' and (resid 1 through 13 or resid 17 through 72 or (resid 73 and (name \ N or name CA or name C or name O or name CB )) or resid 74 through 86 or (resid \ 87 through 88 and (name N or name CA or name C or name O or name CB )) or resid \ 89 through 125)) } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 15.910 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: 1.090 Check model and map are aligned: 0.200 Set scattering table: 0.260 Process input model: 86.480 Find NCS groups from input model: 3.750 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 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 : 0.004 0.095 31473 Z= 0.231 Angle : 0.538 11.210 42822 Z= 0.294 Chirality : 0.045 0.425 4965 Planarity : 0.003 0.034 5465 Dihedral : 10.305 88.654 12016 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.69 % Favored : 96.28 % Rotamer: Outliers : 0.75 % Allowed : 4.09 % Favored : 95.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.13), residues: 3822 helix: 0.33 (0.20), residues: 721 sheet: -0.20 (0.15), residues: 1042 loop : -0.75 (0.13), residues: 2059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 883 HIS 0.004 0.001 HIS C1061 PHE 0.012 0.001 PHE B 65 TYR 0.013 0.001 TYR B1064 ARG 0.003 0.000 ARG B1016 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 339 time to evaluate : 3.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 PHE cc_start: 0.8220 (m-80) cc_final: 0.7326 (m-80) REVERT: B 88 ASP cc_start: 0.8772 (m-30) cc_final: 0.8166 (p0) REVERT: B 191 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8007 (pm20) REVERT: B 275 LYS cc_start: 0.9232 (tmtt) cc_final: 0.9018 (ptmt) REVERT: B 529 ASN cc_start: 0.8813 (t0) cc_final: 0.8612 (t0) REVERT: B 555 LYS cc_start: 0.9384 (tptt) cc_final: 0.8680 (ttpp) REVERT: B 778 VAL cc_start: 0.9587 (t) cc_final: 0.9180 (m) REVERT: B 866 MET cc_start: 0.9117 (mtt) cc_final: 0.8806 (mmt) REVERT: B 910 GLN cc_start: 0.7718 (pt0) cc_final: 0.7389 (pm20) REVERT: B 1034 SER cc_start: 0.8274 (t) cc_final: 0.7301 (p) REVERT: A 760 LEU cc_start: 0.9354 (mt) cc_final: 0.8413 (mt) REVERT: C 229 LEU cc_start: 0.8389 (mt) cc_final: 0.7933 (mp) REVERT: C 998 LEU cc_start: 0.8974 (tp) cc_final: 0.8749 (pp) REVERT: H 80 TYR cc_start: 0.8833 (m-80) cc_final: 0.8546 (m-10) REVERT: L 47 LYS cc_start: 0.8474 (tttt) cc_final: 0.7840 (mptt) REVERT: D 48 VAL cc_start: 0.6382 (t) cc_final: 0.5063 (t) REVERT: F 95 TYR cc_start: 0.8316 (m-80) cc_final: 0.8099 (m-80) outliers start: 25 outliers final: 6 residues processed: 361 average time/residue: 0.4590 time to fit residues: 256.8876 Evaluate side-chains 160 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 154 time to evaluate : 3.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain C residue 65 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 324 optimal weight: 6.9990 chunk 291 optimal weight: 1.9990 chunk 161 optimal weight: 0.2980 chunk 99 optimal weight: 1.9990 chunk 196 optimal weight: 0.5980 chunk 155 optimal weight: 5.9990 chunk 300 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 chunk 183 optimal weight: 0.0570 chunk 224 optimal weight: 9.9990 chunk 348 optimal weight: 8.9990 overall best weight: 0.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 311 GLN B 331 ASN B 603 ASN B 975 ASN B1008 GLN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 490 GLN ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 999 GLN ** A1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 318 GLN C 962 GLN ** C1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 31473 Z= 0.256 Angle : 0.574 10.813 42822 Z= 0.297 Chirality : 0.043 0.209 4965 Planarity : 0.004 0.076 5465 Dihedral : 6.600 58.118 5303 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.01 % Favored : 96.96 % Rotamer: Outliers : 1.62 % Allowed : 8.24 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.13), residues: 3822 helix: 1.27 (0.19), residues: 733 sheet: 0.10 (0.15), residues: 1036 loop : -0.58 (0.13), residues: 2053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 36 HIS 0.006 0.001 HIS A1061 PHE 0.022 0.002 PHE B 135 TYR 0.025 0.001 TYR A1064 ARG 0.015 0.001 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 148 time to evaluate : 3.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8864 (tp) REVERT: B 55 PHE cc_start: 0.8215 (m-80) cc_final: 0.7621 (m-80) REVERT: B 88 ASP cc_start: 0.8858 (OUTLIER) cc_final: 0.7691 (p0) REVERT: B 191 GLU cc_start: 0.8401 (mt-10) cc_final: 0.7761 (pm20) REVERT: B 275 LYS cc_start: 0.9015 (tttt) cc_final: 0.8801 (ptmt) REVERT: B 510 LEU cc_start: 0.9795 (mm) cc_final: 0.9550 (mp) REVERT: B 529 ASN cc_start: 0.8878 (t0) cc_final: 0.8670 (t0) REVERT: B 555 LYS cc_start: 0.9384 (tptt) cc_final: 0.8629 (ttpp) REVERT: B 866 MET cc_start: 0.9056 (mtt) cc_final: 0.8821 (mmt) REVERT: B 945 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.9125 (mt) REVERT: A 159 VAL cc_start: 0.9554 (t) cc_final: 0.9335 (m) REVERT: A 737 MET cc_start: 0.9072 (tpp) cc_final: 0.8195 (tpp) REVERT: A 759 GLN cc_start: 0.8657 (pp30) cc_final: 0.8168 (pp30) REVERT: A 897 MET cc_start: 0.9179 (mtm) cc_final: 0.8968 (mtm) REVERT: C 339 PHE cc_start: 0.8322 (m-80) cc_final: 0.8116 (t80) REVERT: C 375 LYS cc_start: 0.9612 (mttt) cc_final: 0.9388 (mmtt) REVERT: C 944 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8555 (mtmm) REVERT: D 38 ARG cc_start: 0.6837 (ptt-90) cc_final: 0.6446 (ptt-90) outliers start: 54 outliers final: 29 residues processed: 191 average time/residue: 0.4208 time to fit residues: 132.1152 Evaluate side-chains 147 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 114 time to evaluate : 3.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 750 LEU Chi-restraints excluded: chain C residue 944 LYS Chi-restraints excluded: chain C residue 965 SER Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain F residue 69 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 193 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 290 optimal weight: 0.5980 chunk 237 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 349 optimal weight: 0.9980 chunk 377 optimal weight: 2.9990 chunk 311 optimal weight: 0.2980 chunk 346 optimal weight: 10.0000 chunk 119 optimal weight: 7.9990 chunk 280 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 447 ASN ** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 ASN ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 447 ASN C 962 GLN ** C1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 31473 Z= 0.240 Angle : 0.521 12.956 42822 Z= 0.271 Chirality : 0.042 0.174 4965 Planarity : 0.004 0.071 5465 Dihedral : 5.915 59.379 5301 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.38 % Favored : 97.59 % Rotamer: Outliers : 1.90 % Allowed : 9.30 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.13), residues: 3822 helix: 1.72 (0.20), residues: 737 sheet: 0.38 (0.15), residues: 1033 loop : -0.46 (0.14), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 36 HIS 0.006 0.001 HIS A1061 PHE 0.015 0.001 PHE B 135 TYR 0.016 0.001 TYR A1064 ARG 0.009 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 133 time to evaluate : 3.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 PHE cc_start: 0.8506 (m-80) cc_final: 0.7757 (m-80) REVERT: B 88 ASP cc_start: 0.8960 (m-30) cc_final: 0.8130 (p0) REVERT: B 177 MET cc_start: -0.2171 (OUTLIER) cc_final: -0.3609 (ttp) REVERT: B 191 GLU cc_start: 0.8488 (mt-10) cc_final: 0.7726 (pm20) REVERT: B 275 LYS cc_start: 0.9014 (tttt) cc_final: 0.8741 (ptmt) REVERT: B 909 THR cc_start: 0.8756 (OUTLIER) cc_final: 0.8551 (p) REVERT: A 737 MET cc_start: 0.9227 (tpp) cc_final: 0.8412 (tpp) REVERT: A 760 LEU cc_start: 0.9417 (mt) cc_final: 0.8940 (mt) REVERT: A 897 MET cc_start: 0.9181 (OUTLIER) cc_final: 0.8667 (mtm) REVERT: A 999 GLN cc_start: 0.8987 (tt0) cc_final: 0.8275 (tm-30) REVERT: A 1047 MET cc_start: 0.8759 (ptp) cc_final: 0.8277 (mtm) REVERT: C 339 PHE cc_start: 0.8327 (m-80) cc_final: 0.8102 (t80) REVERT: C 375 LYS cc_start: 0.9625 (mttt) cc_final: 0.9410 (mmtt) REVERT: C 694 MET cc_start: 0.8666 (pmm) cc_final: 0.7813 (pmm) REVERT: L 18 VAL cc_start: 0.7131 (OUTLIER) cc_final: 0.6770 (m) REVERT: D 83 MET cc_start: 0.0860 (ptp) cc_final: 0.0543 (ptp) REVERT: G 71 ASN cc_start: 0.8303 (m-40) cc_final: 0.8093 (m-40) outliers start: 63 outliers final: 39 residues processed: 180 average time/residue: 0.4460 time to fit residues: 133.4546 Evaluate side-chains 161 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 118 time to evaluate : 3.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 909 THR Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 935 LEU Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 728 MET Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 965 SER Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain F residue 69 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 345 optimal weight: 0.3980 chunk 262 optimal weight: 1.9990 chunk 181 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 166 optimal weight: 0.6980 chunk 234 optimal weight: 3.9990 chunk 350 optimal weight: 0.9980 chunk 371 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 332 optimal weight: 10.0000 chunk 100 optimal weight: 0.0870 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 999 GLN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** C1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31473 Z= 0.166 Angle : 0.476 7.788 42822 Z= 0.249 Chirality : 0.042 0.168 4965 Planarity : 0.003 0.041 5465 Dihedral : 5.398 57.982 5301 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.09 % Favored : 97.88 % Rotamer: Outliers : 1.99 % Allowed : 9.78 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.13), residues: 3822 helix: 2.14 (0.20), residues: 719 sheet: 0.50 (0.15), residues: 1035 loop : -0.39 (0.14), residues: 2068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 115 HIS 0.004 0.001 HIS A1085 PHE 0.013 0.001 PHE G 64 TYR 0.022 0.001 TYR B 446 ARG 0.006 0.000 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 126 time to evaluate : 3.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 PHE cc_start: 0.8657 (m-80) cc_final: 0.7926 (m-80) REVERT: B 88 ASP cc_start: 0.8973 (OUTLIER) cc_final: 0.8078 (p0) REVERT: B 191 GLU cc_start: 0.8496 (mt-10) cc_final: 0.7719 (pm20) REVERT: B 200 TYR cc_start: 0.8727 (OUTLIER) cc_final: 0.8146 (t80) REVERT: B 228 ASP cc_start: 0.8458 (p0) cc_final: 0.7163 (p0) REVERT: B 275 LYS cc_start: 0.8969 (tttt) cc_final: 0.8761 (ptmt) REVERT: B 510 LEU cc_start: 0.9786 (mm) cc_final: 0.9531 (mp) REVERT: A 737 MET cc_start: 0.9257 (tpp) cc_final: 0.8362 (tpp) REVERT: A 897 MET cc_start: 0.9161 (OUTLIER) cc_final: 0.8575 (mtm) REVERT: A 999 GLN cc_start: 0.8961 (tt0) cc_final: 0.8367 (tm-30) REVERT: C 375 LYS cc_start: 0.9625 (mttt) cc_final: 0.9405 (mmtt) REVERT: C 694 MET cc_start: 0.8755 (pmm) cc_final: 0.7930 (pmm) REVERT: D 38 ARG cc_start: 0.7024 (ptt-90) cc_final: 0.6773 (ptt-90) REVERT: D 83 MET cc_start: 0.0427 (ptp) cc_final: 0.0036 (ptp) REVERT: G 49 MET cc_start: 0.8703 (ptt) cc_final: 0.8478 (ptt) outliers start: 66 outliers final: 39 residues processed: 170 average time/residue: 0.4081 time to fit residues: 115.3772 Evaluate side-chains 153 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 111 time to evaluate : 3.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 935 LEU Chi-restraints excluded: chain B residue 936 SER Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 115 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 309 optimal weight: 0.9990 chunk 210 optimal weight: 0.6980 chunk 5 optimal weight: 8.9990 chunk 276 optimal weight: 2.9990 chunk 153 optimal weight: 8.9990 chunk 316 optimal weight: 0.3980 chunk 256 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 189 optimal weight: 1.9990 chunk 333 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 610 GLN ** B 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 999 GLN B1116 ASN A 66 HIS ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 ASN A 447 ASN ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 759 GLN A 932 GLN C1002 GLN C1132 ASN G 40 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 31473 Z= 0.283 Angle : 0.537 12.227 42822 Z= 0.278 Chirality : 0.042 0.178 4965 Planarity : 0.003 0.050 5465 Dihedral : 5.111 50.472 5300 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.83 % Favored : 97.15 % Rotamer: Outliers : 2.35 % Allowed : 9.81 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.13), residues: 3822 helix: 1.97 (0.20), residues: 715 sheet: 0.47 (0.15), residues: 1051 loop : -0.38 (0.14), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 115 HIS 0.007 0.001 HIS A1061 PHE 0.014 0.002 PHE F 68 TYR 0.030 0.001 TYR F 104 ARG 0.005 0.000 ARG F 72 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 110 time to evaluate : 3.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 36 VAL cc_start: 0.9324 (OUTLIER) cc_final: 0.9022 (m) REVERT: B 54 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8993 (tp) REVERT: B 55 PHE cc_start: 0.8777 (m-80) cc_final: 0.7889 (m-80) REVERT: B 88 ASP cc_start: 0.8809 (OUTLIER) cc_final: 0.7580 (p0) REVERT: B 191 GLU cc_start: 0.8440 (mt-10) cc_final: 0.7804 (pm20) REVERT: B 200 TYR cc_start: 0.8842 (OUTLIER) cc_final: 0.8410 (t80) REVERT: B 502 TYR cc_start: 0.9595 (OUTLIER) cc_final: 0.9164 (t80) REVERT: A 737 MET cc_start: 0.9316 (tpp) cc_final: 0.8514 (tpp) REVERT: A 759 GLN cc_start: 0.9317 (OUTLIER) cc_final: 0.8878 (pp30) REVERT: A 897 MET cc_start: 0.9270 (OUTLIER) cc_final: 0.8611 (mtm) REVERT: A 999 GLN cc_start: 0.9060 (tt0) cc_final: 0.8426 (tm-30) REVERT: A 1047 MET cc_start: 0.8879 (ptp) cc_final: 0.8564 (mtm) REVERT: C 694 MET cc_start: 0.8822 (pmm) cc_final: 0.8286 (pmm) REVERT: C 866 MET cc_start: 0.9054 (mtm) cc_final: 0.8485 (ptp) REVERT: G 49 MET cc_start: 0.8751 (ptt) cc_final: 0.8457 (ptt) outliers start: 78 outliers final: 53 residues processed: 169 average time/residue: 0.4026 time to fit residues: 114.0958 Evaluate side-chains 159 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 99 time to evaluate : 3.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 502 TYR Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 935 LEU Chi-restraints excluded: chain B residue 936 SER Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1115 ASP Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 759 GLN Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 1093 VAL Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 728 MET Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 750 LEU Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1132 ASN Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 49 MET Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 115 TRP Chi-restraints excluded: chain G residue 76 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 124 optimal weight: 0.9980 chunk 334 optimal weight: 10.0000 chunk 73 optimal weight: 1.9990 chunk 217 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 371 optimal weight: 6.9990 chunk 308 optimal weight: 0.6980 chunk 172 optimal weight: 0.8980 chunk 30 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 195 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 999 GLN A 164 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 759 GLN A 962 GLN C 66 HIS C1002 GLN ** L 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 31473 Z= 0.289 Angle : 0.537 9.873 42822 Z= 0.278 Chirality : 0.042 0.244 4965 Planarity : 0.003 0.055 5465 Dihedral : 4.959 41.049 5300 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.83 % Favored : 97.15 % Rotamer: Outliers : 2.35 % Allowed : 10.56 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.13), residues: 3822 helix: 2.20 (0.20), residues: 688 sheet: 0.42 (0.15), residues: 1068 loop : -0.40 (0.14), residues: 2066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C1099 HIS 0.005 0.001 HIS A1061 PHE 0.018 0.001 PHE F 68 TYR 0.015 0.001 TYR A 263 ARG 0.003 0.000 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 104 time to evaluate : 3.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 ASP cc_start: 0.8794 (OUTLIER) cc_final: 0.8358 (p0) REVERT: B 200 TYR cc_start: 0.8868 (OUTLIER) cc_final: 0.8483 (t80) REVERT: B 510 LEU cc_start: 0.9550 (OUTLIER) cc_final: 0.9313 (pp) REVERT: B 759 GLN cc_start: 0.9155 (OUTLIER) cc_final: 0.8895 (pp30) REVERT: A 104 TRP cc_start: 0.7796 (m-90) cc_final: 0.7302 (m-90) REVERT: A 737 MET cc_start: 0.9373 (tpp) cc_final: 0.8534 (tpp) REVERT: A 759 GLN cc_start: 0.9421 (OUTLIER) cc_final: 0.9070 (pp30) REVERT: A 897 MET cc_start: 0.9292 (OUTLIER) cc_final: 0.8655 (mtm) REVERT: A 999 GLN cc_start: 0.9054 (tt0) cc_final: 0.8452 (tm-30) REVERT: C 694 MET cc_start: 0.8863 (pmm) cc_final: 0.8330 (pmm) REVERT: C 866 MET cc_start: 0.8953 (mtm) cc_final: 0.8750 (mtm) REVERT: C 1047 MET cc_start: 0.8899 (ptp) cc_final: 0.8602 (ptp) REVERT: C 1132 ASN cc_start: 0.9464 (OUTLIER) cc_final: 0.8966 (m-40) REVERT: L 105 LYS cc_start: 0.9106 (tptt) cc_final: 0.8880 (tptp) REVERT: D 38 ARG cc_start: 0.7264 (ptt-90) cc_final: 0.7013 (ptt-90) REVERT: E 97 LYS cc_start: 0.9110 (pttt) cc_final: 0.8764 (tmtt) REVERT: G 49 MET cc_start: 0.8773 (ptt) cc_final: 0.8484 (ptt) REVERT: G 96 ASN cc_start: 0.8863 (OUTLIER) cc_final: 0.8653 (t0) outliers start: 78 outliers final: 62 residues processed: 162 average time/residue: 0.4120 time to fit residues: 112.0756 Evaluate side-chains 169 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 99 time to evaluate : 3.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 516 HIS Chi-restraints excluded: chain B residue 541 ASN Chi-restraints excluded: chain B residue 574 ARG Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 759 GLN Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 935 LEU Chi-restraints excluded: chain B residue 936 SER Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1115 ASP Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 759 GLN Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 985 GLU Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1093 VAL Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 711 ILE Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 750 LEU Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 912 VAL Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1132 ASN Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 49 MET Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain G residue 96 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 358 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 211 optimal weight: 2.9990 chunk 271 optimal weight: 2.9990 chunk 210 optimal weight: 1.9990 chunk 312 optimal weight: 0.8980 chunk 207 optimal weight: 0.9990 chunk 370 optimal weight: 9.9990 chunk 231 optimal weight: 0.0770 chunk 225 optimal weight: 7.9990 chunk 170 optimal weight: 2.9990 overall best weight: 1.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 533 ASN ** B 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 759 GLN C 610 GLN C 853 ASN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 31473 Z= 0.307 Angle : 0.546 9.310 42822 Z= 0.281 Chirality : 0.042 0.187 4965 Planarity : 0.003 0.051 5465 Dihedral : 4.893 41.882 5300 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.14 % Favored : 96.83 % Rotamer: Outliers : 2.59 % Allowed : 10.71 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.14), residues: 3822 helix: 2.00 (0.20), residues: 704 sheet: 0.36 (0.15), residues: 1077 loop : -0.42 (0.14), residues: 2041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 64 HIS 0.005 0.001 HIS A1061 PHE 0.038 0.002 PHE F 68 TYR 0.019 0.001 TYR B 502 ARG 0.014 0.000 ARG A 992 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 102 time to evaluate : 3.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 36 VAL cc_start: 0.9470 (OUTLIER) cc_final: 0.9179 (m) REVERT: B 200 TYR cc_start: 0.8883 (OUTLIER) cc_final: 0.8517 (t80) REVERT: B 329 ILE cc_start: 0.7660 (OUTLIER) cc_final: 0.7265 (tp) REVERT: B 510 LEU cc_start: 0.9622 (tp) cc_final: 0.9318 (pp) REVERT: B 574 ARG cc_start: 0.9441 (OUTLIER) cc_final: 0.9111 (ttm-80) REVERT: B 999 GLN cc_start: 0.9044 (tt0) cc_final: 0.8359 (tp40) REVERT: A 104 TRP cc_start: 0.7500 (m-90) cc_final: 0.6948 (m-90) REVERT: A 737 MET cc_start: 0.9401 (tpp) cc_final: 0.8634 (tpp) REVERT: A 759 GLN cc_start: 0.9406 (OUTLIER) cc_final: 0.8642 (pp30) REVERT: A 897 MET cc_start: 0.9308 (OUTLIER) cc_final: 0.8664 (mtm) REVERT: A 966 ASN cc_start: 0.9158 (m-40) cc_final: 0.8804 (m-40) REVERT: A 999 GLN cc_start: 0.9089 (tt0) cc_final: 0.8527 (tm-30) REVERT: C 694 MET cc_start: 0.8869 (pmm) cc_final: 0.8378 (pmm) REVERT: E 97 LYS cc_start: 0.9194 (pttt) cc_final: 0.8848 (tmtt) REVERT: G 49 MET cc_start: 0.8770 (ptt) cc_final: 0.8463 (ptt) outliers start: 86 outliers final: 64 residues processed: 171 average time/residue: 0.4094 time to fit residues: 118.4534 Evaluate side-chains 167 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 97 time to evaluate : 3.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 574 ARG Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 893 ILE Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 935 LEU Chi-restraints excluded: chain B residue 936 SER Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1115 ASP Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 759 GLN Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1093 VAL Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 711 ILE Chi-restraints excluded: chain C residue 750 LEU Chi-restraints excluded: chain C residue 802 ILE Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 912 VAL Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1115 ASP Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 49 MET Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain G residue 76 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 228 optimal weight: 2.9990 chunk 147 optimal weight: 0.6980 chunk 221 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 235 optimal weight: 6.9990 chunk 252 optimal weight: 10.0000 chunk 182 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 290 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 999 GLN A 125 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 759 GLN C1002 GLN ** C1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.4326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 31473 Z= 0.221 Angle : 0.509 9.726 42822 Z= 0.261 Chirality : 0.042 0.177 4965 Planarity : 0.003 0.049 5465 Dihedral : 4.666 42.111 5300 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.83 % Favored : 97.15 % Rotamer: Outliers : 2.14 % Allowed : 11.40 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.14), residues: 3822 helix: 2.43 (0.20), residues: 676 sheet: 0.30 (0.15), residues: 1066 loop : -0.39 (0.14), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 36 HIS 0.004 0.001 HIS F 35 PHE 0.022 0.001 PHE F 68 TYR 0.014 0.001 TYR A1064 ARG 0.006 0.000 ARG A 992 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 104 time to evaluate : 3.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 200 TYR cc_start: 0.8847 (OUTLIER) cc_final: 0.8485 (t80) REVERT: B 510 LEU cc_start: 0.9632 (tp) cc_final: 0.9415 (pp) REVERT: B 574 ARG cc_start: 0.9376 (OUTLIER) cc_final: 0.8922 (ttm-80) REVERT: A 104 TRP cc_start: 0.7473 (m-90) cc_final: 0.6948 (m-90) REVERT: A 737 MET cc_start: 0.9403 (tpp) cc_final: 0.8638 (tpp) REVERT: A 759 GLN cc_start: 0.9414 (OUTLIER) cc_final: 0.9000 (pp30) REVERT: A 897 MET cc_start: 0.9271 (OUTLIER) cc_final: 0.8594 (mtm) REVERT: A 966 ASN cc_start: 0.9210 (m-40) cc_final: 0.8861 (t0) REVERT: A 999 GLN cc_start: 0.9080 (tt0) cc_final: 0.8564 (tm-30) REVERT: A 1026 MET cc_start: 0.9400 (mmm) cc_final: 0.9043 (tpp) REVERT: A 1047 MET cc_start: 0.8877 (ptp) cc_final: 0.8354 (mtm) REVERT: C 694 MET cc_start: 0.8839 (pmm) cc_final: 0.8219 (pmm) REVERT: D 38 ARG cc_start: 0.7795 (ptt-90) cc_final: 0.7581 (ptt-90) REVERT: E 97 LYS cc_start: 0.9293 (pttt) cc_final: 0.9076 (tmtt) REVERT: G 49 MET cc_start: 0.8727 (ptt) cc_final: 0.8396 (ptt) outliers start: 71 outliers final: 60 residues processed: 160 average time/residue: 0.4051 time to fit residues: 108.8708 Evaluate side-chains 163 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 99 time to evaluate : 3.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 516 HIS Chi-restraints excluded: chain B residue 574 ARG Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 893 ILE Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 935 LEU Chi-restraints excluded: chain B residue 936 SER Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1115 ASP Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 759 GLN Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 711 ILE Chi-restraints excluded: chain C residue 750 LEU Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 802 ILE Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 912 VAL Chi-restraints excluded: chain C residue 1115 ASP Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 49 MET Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain G residue 76 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 336 optimal weight: 9.9990 chunk 354 optimal weight: 0.0570 chunk 323 optimal weight: 0.5980 chunk 344 optimal weight: 7.9990 chunk 207 optimal weight: 1.9990 chunk 150 optimal weight: 6.9990 chunk 270 optimal weight: 2.9990 chunk 105 optimal weight: 0.0470 chunk 311 optimal weight: 0.8980 chunk 326 optimal weight: 8.9990 chunk 343 optimal weight: 6.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 999 GLN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 759 GLN ** C 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** C1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 31473 Z= 0.187 Angle : 0.500 12.071 42822 Z= 0.256 Chirality : 0.042 0.185 4965 Planarity : 0.003 0.047 5465 Dihedral : 4.485 42.298 5299 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.88 % Favored : 97.10 % Rotamer: Outliers : 2.11 % Allowed : 11.46 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.14), residues: 3822 helix: 2.51 (0.20), residues: 676 sheet: 0.34 (0.15), residues: 1074 loop : -0.37 (0.14), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 36 HIS 0.004 0.001 HIS F 35 PHE 0.030 0.001 PHE B 389 TYR 0.015 0.001 TYR A1064 ARG 0.004 0.000 ARG A 992 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 102 time to evaluate : 3.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 200 TYR cc_start: 0.8818 (OUTLIER) cc_final: 0.8451 (t80) REVERT: B 502 TYR cc_start: 0.9664 (OUTLIER) cc_final: 0.9344 (t80) REVERT: B 510 LEU cc_start: 0.9728 (tp) cc_final: 0.9405 (pp) REVERT: B 574 ARG cc_start: 0.9322 (OUTLIER) cc_final: 0.8852 (ttm-80) REVERT: B 999 GLN cc_start: 0.9046 (tt0) cc_final: 0.8467 (tp-100) REVERT: A 104 TRP cc_start: 0.7474 (m-90) cc_final: 0.6971 (m-90) REVERT: A 737 MET cc_start: 0.9406 (tpp) cc_final: 0.8642 (tpp) REVERT: A 759 GLN cc_start: 0.9430 (OUTLIER) cc_final: 0.8716 (pp30) REVERT: A 897 MET cc_start: 0.9239 (OUTLIER) cc_final: 0.8531 (mtm) REVERT: A 999 GLN cc_start: 0.9047 (tt0) cc_final: 0.8562 (tm-30) REVERT: A 1026 MET cc_start: 0.9389 (mmm) cc_final: 0.8731 (tpp) REVERT: A 1047 MET cc_start: 0.8857 (OUTLIER) cc_final: 0.8335 (mtm) REVERT: C 694 MET cc_start: 0.8864 (pmm) cc_final: 0.8149 (pmm) REVERT: D 38 ARG cc_start: 0.7830 (ptt-90) cc_final: 0.7609 (ptt-90) REVERT: E 97 LYS cc_start: 0.9309 (pttt) cc_final: 0.9089 (tmtt) REVERT: G 49 MET cc_start: 0.8704 (ptt) cc_final: 0.8360 (ptt) outliers start: 70 outliers final: 56 residues processed: 157 average time/residue: 0.4184 time to fit residues: 110.1890 Evaluate side-chains 161 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 99 time to evaluate : 3.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 502 TYR Chi-restraints excluded: chain B residue 574 ARG Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 893 ILE Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 935 LEU Chi-restraints excluded: chain B residue 936 SER Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1115 ASP Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 759 GLN Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 1047 MET Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 711 ILE Chi-restraints excluded: chain C residue 728 MET Chi-restraints excluded: chain C residue 750 LEU Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1115 ASP Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 49 MET Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain G residue 76 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 226 optimal weight: 0.7980 chunk 364 optimal weight: 5.9990 chunk 222 optimal weight: 6.9990 chunk 173 optimal weight: 2.9990 chunk 253 optimal weight: 9.9990 chunk 382 optimal weight: 30.0000 chunk 352 optimal weight: 2.9990 chunk 304 optimal weight: 0.9980 chunk 31 optimal weight: 7.9990 chunk 235 optimal weight: 5.9990 chunk 186 optimal weight: 0.8980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 687 GLN ** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 638 ASN A 687 GLN A 759 GLN A 853 ASN C 314 ASN ** C 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.4803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 31473 Z= 0.370 Angle : 0.605 8.764 42822 Z= 0.310 Chirality : 0.043 0.184 4965 Planarity : 0.004 0.048 5465 Dihedral : 4.919 44.233 5299 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.64 % Favored : 96.34 % Rotamer: Outliers : 2.14 % Allowed : 11.49 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.14), residues: 3822 helix: 1.97 (0.20), residues: 697 sheet: 0.25 (0.15), residues: 1085 loop : -0.44 (0.14), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP F 36 HIS 0.005 0.001 HIS A1061 PHE 0.027 0.002 PHE B 389 TYR 0.018 0.002 TYR A 263 ARG 0.007 0.001 ARG L 56 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 102 time to evaluate : 3.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 200 TYR cc_start: 0.8892 (OUTLIER) cc_final: 0.8396 (t80) REVERT: B 502 TYR cc_start: 0.9660 (OUTLIER) cc_final: 0.9377 (t80) REVERT: B 510 LEU cc_start: 0.9750 (tp) cc_final: 0.9449 (pp) REVERT: B 574 ARG cc_start: 0.9396 (OUTLIER) cc_final: 0.8864 (ttm-80) REVERT: B 999 GLN cc_start: 0.9071 (tt0) cc_final: 0.8403 (tp40) REVERT: A 737 MET cc_start: 0.9441 (tpp) cc_final: 0.8702 (tpp) REVERT: A 759 GLN cc_start: 0.9487 (OUTLIER) cc_final: 0.9096 (pp30) REVERT: A 897 MET cc_start: 0.9329 (OUTLIER) cc_final: 0.8649 (mtm) REVERT: A 999 GLN cc_start: 0.9098 (tt0) cc_final: 0.8562 (tm-30) REVERT: C 153 MET cc_start: 0.4913 (mmm) cc_final: 0.4687 (tpp) REVERT: C 694 MET cc_start: 0.8896 (pmm) cc_final: 0.8400 (pmm) REVERT: D 38 ARG cc_start: 0.7856 (ptt-90) cc_final: 0.7595 (ptt-90) REVERT: E 71 ASN cc_start: 0.7750 (m-40) cc_final: 0.7529 (t0) REVERT: E 97 LYS cc_start: 0.9423 (pttt) cc_final: 0.9180 (tmtt) REVERT: G 49 MET cc_start: 0.8787 (ptt) cc_final: 0.8485 (ptt) outliers start: 71 outliers final: 58 residues processed: 155 average time/residue: 0.4045 time to fit residues: 105.9042 Evaluate side-chains 161 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 98 time to evaluate : 3.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 502 TYR Chi-restraints excluded: chain B residue 516 HIS Chi-restraints excluded: chain B residue 574 ARG Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 893 ILE Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 935 LEU Chi-restraints excluded: chain B residue 936 SER Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1115 ASP Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 759 GLN Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 1047 MET Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 711 ILE Chi-restraints excluded: chain C residue 750 LEU Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 802 ILE Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 912 VAL Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1115 ASP Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 49 MET Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain G residue 76 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 241 optimal weight: 1.9990 chunk 324 optimal weight: 6.9990 chunk 93 optimal weight: 0.5980 chunk 280 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 305 optimal weight: 0.5980 chunk 127 optimal weight: 0.7980 chunk 313 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 687 GLN ** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 391 ASN A 759 GLN ** C 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.078068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.048099 restraints weight = 169998.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.049752 restraints weight = 76559.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.050783 restraints weight = 47290.191| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.4823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 31473 Z= 0.190 Angle : 0.519 9.909 42822 Z= 0.265 Chirality : 0.042 0.198 4965 Planarity : 0.003 0.046 5465 Dihedral : 4.652 43.757 5299 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.69 % Favored : 97.28 % Rotamer: Outliers : 1.93 % Allowed : 11.79 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.14), residues: 3822 helix: 2.12 (0.20), residues: 712 sheet: 0.26 (0.15), residues: 1091 loop : -0.34 (0.14), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP F 36 HIS 0.004 0.001 HIS F 35 PHE 0.020 0.001 PHE F 68 TYR 0.015 0.001 TYR A1064 ARG 0.004 0.000 ARG A 992 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5112.57 seconds wall clock time: 95 minutes 14.38 seconds (5714.38 seconds total)