Starting phenix.real_space_refine on Thu Mar 21 16:03:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q9p_13875/03_2024/7q9p_13875.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q9p_13875/03_2024/7q9p_13875.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q9p_13875/03_2024/7q9p_13875.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q9p_13875/03_2024/7q9p_13875.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q9p_13875/03_2024/7q9p_13875.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q9p_13875/03_2024/7q9p_13875.pdb" } resolution = 4.5 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= 0.003 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 132 5.16 5 C 19400 2.51 5 N 5010 2.21 5 O 5952 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 30494 Number of models: 1 Model: "" Number of chains: 24 Chain: "B" Number of atoms: 8148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8148 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 52, 'TRANS': 987} Chain breaks: 6 Chain: "C" Number of atoms: 8118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1036, 8118 Classifications: {'peptide': 1036} Link IDs: {'PTRANS': 51, 'TRANS': 984} Chain breaks: 6 Chain: "A" Number of atoms: 8154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8154 Classifications: {'peptide': 1041} Link IDs: {'PTRANS': 52, 'TRANS': 988} Chain breaks: 6 Chain: "H" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 946 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 6, 'TRANS': 115} Chain: "L" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 836 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 99} Chain: "E" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 946 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 6, 'TRANS': 115} Chain: "F" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 836 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 99} Chain: "J" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 946 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 6, 'TRANS': 115} Chain: "K" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 836 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 99} Chain: "D" 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: "G" 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: "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: "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: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 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 Time building chain proxies: 15.48, per 1000 atoms: 0.51 Number of scatterers: 30494 At special positions: 0 Unit cell: (160.19, 184.26, 221.61, 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 5952 8.00 N 5010 7.00 C 19400 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=2.02 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=2.02 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=2.02 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=2.03 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=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 97 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 97 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " 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 D 1 " - " NAG D 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 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 600 " " NAG C1304 " - " ASN C 613 " " NAG C1305 " - " ASN C 654 " " NAG C1306 " - " ASN C 706 " " NAG C1307 " - " ASN C1071 " " NAG C1308 " - " ASN C 340 " " NAG D 1 " - " ASN B 714 " " NAG G 1 " - " ASN B 798 " " NAG I 1 " - " ASN B1095 " " NAG M 1 " - " ASN B1131 " " NAG N 1 " - " ASN C 714 " " NAG O 1 " - " ASN C 798 " " NAG P 1 " - " ASN C1095 " " NAG Q 1 " - " ASN C1131 " " NAG R 1 " - " ASN A 714 " " NAG S 1 " - " ASN A 798 " " NAG T 1 " - " ASN A1095 " " NAG U 1 " - " ASN A1131 " Time building additional restraints: 12.24 Conformation dependent library (CDL) restraints added in 5.9 seconds 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7116 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 69 sheets defined 21.7% alpha, 32.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.26 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 386 removed outlier: 3.507A pdb=" N ASN B 385 " --> pdb=" O THR B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 407 removed outlier: 3.918A pdb=" N ARG B 405 " --> pdb=" O ASP B 402 " (cutoff:3.500A) 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 741 Processing helix chain 'B' and resid 743 through 752 removed outlier: 3.771A 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: 3.887A pdb=" N ALA B 887 " --> pdb=" O TRP B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 906 Processing helix chain 'B' and resid 909 through 916 removed outlier: 4.068A 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 939 through 941 No H-bonds generated for 'chain 'B' and resid 939 through 941' Processing helix chain 'B' and resid 942 through 963 removed outlier: 3.653A pdb=" N LEU B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 973 through 981 Processing helix chain 'B' and resid 982 through 1029 removed outlier: 4.330A pdb=" N VAL B 988 " --> pdb=" O PRO B 984 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLN B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG B 992 " --> pdb=" O VAL B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1137 through 1144 removed outlier: 3.952A pdb=" N GLU B1141 " --> pdb=" O PRO B1137 " (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 362 through 367 Processing helix chain 'C' and resid 381 through 386 removed outlier: 3.720A pdb=" N LEU C 384 " --> pdb=" O PRO C 381 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASN C 385 " --> pdb=" O THR C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 407 removed outlier: 3.894A pdb=" N ARG C 405 " --> pdb=" O ASP C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 419 Processing helix chain 'C' and resid 435 through 440 Processing helix chain 'C' and resid 499 through 502 Processing helix chain 'C' and resid 734 through 741 Processing helix chain 'C' and resid 743 through 752 removed outlier: 3.883A 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 814 through 823 Processing helix chain 'C' and resid 863 through 882 Processing helix chain 'C' and resid 883 through 888 removed outlier: 4.011A pdb=" N ALA C 887 " --> pdb=" O TRP C 883 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 906 Processing helix chain 'C' and resid 909 through 916 removed outlier: 4.318A pdb=" N LEU C 913 " --> pdb=" O THR C 909 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 938 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 963 removed outlier: 3.531A pdb=" N VAL C 948 " --> pdb=" O LYS C 944 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 981 Processing helix chain 'C' and resid 982 through 1029 removed outlier: 4.290A pdb=" N VAL C 988 " --> pdb=" O PRO C 984 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLN C 989 " --> pdb=" O GLU C 985 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG C 992 " --> pdb=" O VAL C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1144 removed outlier: 3.759A pdb=" N GLU C1141 " --> pdb=" O PRO C1137 " (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: 3.654A pdb=" N LEU A 384 " --> pdb=" O PRO A 381 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASN A 385 " --> pdb=" O THR A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 removed outlier: 3.858A pdb=" N ARG A 405 " --> pdb=" O ASP A 402 " (cutoff:3.500A) 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 741 Processing helix chain 'A' and resid 743 through 752 removed outlier: 3.651A 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: 4.022A 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 909 through 916 removed outlier: 3.971A pdb=" N LEU A 913 " --> pdb=" O THR A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 938 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 964 Processing helix chain 'A' and resid 973 through 981 Processing helix chain 'A' and resid 982 through 1029 removed outlier: 4.343A pdb=" N VAL A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN A 989 " --> pdb=" O GLU A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1144 removed outlier: 3.729A pdb=" N GLU A1141 " --> pdb=" O PRO A1137 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 92 removed outlier: 3.694A pdb=" N THR H 92 " --> pdb=" O ALA H 89 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.162A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 92 removed outlier: 3.703A pdb=" N THR E 92 " --> pdb=" O ALA E 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 83 removed outlier: 4.160A pdb=" N PHE F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 92 removed outlier: 3.641A pdb=" N THR J 92 " --> pdb=" O ALA J 89 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 83 removed outlier: 4.132A pdb=" N PHE K 83 " --> pdb=" O PRO K 80 " (cutoff:3.500A) 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: 7.688A pdb=" N ASN B 61 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N TYR B 266 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.024A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.067A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 11.241A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 9.820A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.315A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.347A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 9.476A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 10.845A pdb=" N PHE B 140 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N SER B 155 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N GLY B 142 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N MET B 153 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N TYR B 144 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N SER B 151 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.067A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N SER B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N LEU B 141 " --> pdb=" O SER B 244 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LEU B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL B 143 " --> pdb=" O LEU B 246 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 308 through 315 removed outlier: 5.533A pdb=" N ILE B 309 " --> pdb=" O THR B 596 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N THR B 596 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLN B 311 " --> pdb=" O VAL B 594 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL B 594 " --> pdb=" O GLN B 311 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLY B 591 " --> pdb=" O GLN B 610 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 321 through 325 removed outlier: 4.504A pdb=" N GLU B 321 " --> pdb=" O CYS B 535 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 351 through 355 Processing sheet with id=AA9, first strand: chain 'B' and resid 358 through 359 removed outlier: 6.726A pdb=" N CYS B 358 " --> pdb=" O CYS B 522 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AB2, first strand: chain 'B' and resid 470 through 471 Processing sheet with id=AB3, first strand: chain 'B' and resid 651 through 652 removed outlier: 6.454A pdb=" N ALA B 669 " --> pdb=" O PRO B 662 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 699 through 701 removed outlier: 3.731A pdb=" N LYS C 787 " --> pdb=" O ASN B 700 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 708 through 725 removed outlier: 6.602A pdb=" N SER B 708 " --> pdb=" O THR B1073 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR B1073 " --> pdb=" O SER B 708 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ALA B 710 " --> pdb=" O ASN B1071 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASN B1071 " --> pdb=" O ALA B 710 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLU B1069 " --> pdb=" O PRO B 712 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ASN B 714 " --> pdb=" O ALA B1067 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N TYR B1064 " --> pdb=" O HIS B1045 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N HIS B1045 " --> pdb=" O TYR B1064 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 730 through 733 removed outlier: 4.385A pdb=" N LYS B 730 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 785 through 787 removed outlier: 6.041A pdb=" N ILE B 785 " --> pdb=" O ASN A 700 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 1117 through 1122 removed outlier: 4.988A pdb=" N ALA B1084 " --> pdb=" O SER B1120 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 1091 through 1094 Processing sheet with id=AC1, first strand: chain 'C' and resid 21 through 22 Processing sheet with id=AC2, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.308A pdb=" N ASN C 61 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N TYR C 266 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.685A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 83 through 85 removed outlier: 5.948A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 11.328A pdb=" N VAL C 126 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 9.829A pdb=" N GLU C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 11.257A pdb=" N ILE C 128 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 8.597A pdb=" N THR C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N VAL C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ASN C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.132A 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: 9.440A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 10.895A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 8.728A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N GLY C 142 " --> pdb=" O MET C 153 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N MET C 153 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N TYR C 144 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N SER C 151 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 308 through 316 removed outlier: 5.462A pdb=" N ILE C 309 " --> pdb=" O THR C 596 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N THR C 596 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N GLN C 311 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL C 594 " --> pdb=" O GLN C 311 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLY C 591 " --> pdb=" O GLN C 610 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 322 through 325 removed outlier: 5.435A pdb=" N ASP C 571 " --> pdb=" O ILE C 584 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLY C 563 " --> pdb=" O ASP C 571 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 351 through 355 removed outlier: 3.863A pdb=" N ASN C 391 " --> pdb=" O GLU C 513 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 358 through 359 removed outlier: 6.408A pdb=" N CYS C 358 " --> pdb=" O CYS C 522 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 449 through 451 Processing sheet with id=AD1, first strand: chain 'C' and resid 470 through 471 Processing sheet with id=AD2, first strand: chain 'C' and resid 651 through 652 removed outlier: 6.496A pdb=" N ILE C 667 " --> pdb=" O ILE C 663 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 708 through 712 Processing sheet with id=AD4, first strand: chain 'C' and resid 715 through 725 removed outlier: 6.101A pdb=" N TYR C1064 " --> pdb=" O HIS C1045 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N HIS C1045 " --> pdb=" O TYR C1064 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 731 through 733 Processing sheet with id=AD6, first strand: chain 'C' and resid 804 through 805 removed outlier: 3.950A pdb=" N ARG C 812 " --> pdb=" O ASP C 805 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 1117 through 1122 removed outlier: 4.537A pdb=" N ALA C1084 " --> pdb=" O SER C1120 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 1091 through 1094 Processing sheet with id=AD9, first strand: chain 'A' and resid 21 through 22 Processing sheet with id=AE1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.856A pdb=" N ASN A 61 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N TYR A 266 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.447A pdb=" N THR A 271 " --> pdb=" O ASP A 287 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ASP A 287 " --> pdb=" O THR A 271 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU A 273 " --> pdb=" O ALA A 285 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ALA A 285 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LYS A 275 " --> pdb=" O THR A 283 " (cutoff:3.500A) Processing sheet with id=AE3, 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: 5.963A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 11.303A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.812A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.222A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.247A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 9.359A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 10.820A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 8.677A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N GLY A 142 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N MET A 153 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N TYR A 144 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N SER A 151 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 308 through 316 removed outlier: 5.809A pdb=" N ILE A 309 " --> pdb=" O THR A 596 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N THR A 596 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLN A 311 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL A 594 " --> pdb=" O GLN A 311 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLY A 591 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 321 through 325 removed outlier: 6.667A pdb=" N GLU A 321 " --> pdb=" O ASN A 537 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N ASN A 539 " --> pdb=" O GLU A 321 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE A 323 " --> pdb=" O ASN A 539 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 351 through 355 Processing sheet with id=AE7, first strand: chain 'A' and resid 358 through 359 removed outlier: 6.725A pdb=" N CYS A 358 " --> pdb=" O CYS A 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AE9, first strand: chain 'A' and resid 470 through 471 Processing sheet with id=AF1, first strand: chain 'A' and resid 651 through 652 removed outlier: 6.516A pdb=" N ALA A 669 " --> pdb=" O PRO A 662 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'A' and resid 708 through 712 Processing sheet with id=AF3, first strand: chain 'A' and resid 715 through 725 removed outlier: 7.065A pdb=" N GLY A1056 " --> pdb=" O SER A1052 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N SER A1052 " --> pdb=" O GLY A1056 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL A1058 " --> pdb=" O PRO A1050 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU A1060 " --> pdb=" O SER A1048 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N SER A1048 " --> pdb=" O LEU A1060 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL A1062 " --> pdb=" O LEU A1046 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'A' and resid 731 through 733 Processing sheet with id=AF5, first strand: chain 'A' and resid 1117 through 1122 removed outlier: 4.537A pdb=" N ALA A1084 " --> pdb=" O SER A1120 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'A' and resid 1091 through 1094 Processing sheet with id=AF7, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AF8, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.738A pdb=" N VAL H 12 " --> pdb=" O THR H 120 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N TRP H 36 " --> pdb=" O SER H 52 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N SER H 52 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N TRP H 38 " --> pdb=" O ILE H 50 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.738A pdb=" N VAL H 12 " --> pdb=" O THR H 120 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N CYS H 97 " --> pdb=" O TRP H 113 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N TRP H 113 " --> pdb=" O CYS H 97 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ARG H 99 " --> pdb=" O ASP H 111 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.659A pdb=" N THR L 72 " --> pdb=" O SER L 65 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.441A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 10 through 12 Processing sheet with id=AG4, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AG5, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.719A pdb=" N VAL E 12 " --> pdb=" O THR E 120 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N TRP E 36 " --> pdb=" O SER E 52 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N SER E 52 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TRP E 38 " --> pdb=" O ILE E 50 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.719A pdb=" N VAL E 12 " --> pdb=" O THR E 120 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.679A pdb=" N THR F 72 " --> pdb=" O SER F 65 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.447A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'F' and resid 10 through 13 Processing sheet with id=AH1, first strand: chain 'J' and resid 4 through 7 removed outlier: 5.388A pdb=" N GLU J 16 " --> pdb=" O SER J 86 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER J 86 " --> pdb=" O GLU J 16 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.603A pdb=" N VAL J 12 " --> pdb=" O THR J 120 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N TRP J 36 " --> pdb=" O SER J 52 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N SER J 52 " --> pdb=" O TRP J 36 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N TRP J 38 " --> pdb=" O ILE J 50 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.603A pdb=" N VAL J 12 " --> pdb=" O THR J 120 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N CYS J 97 " --> pdb=" O TRP J 113 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N TRP J 113 " --> pdb=" O CYS J 97 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ARG J 99 " --> pdb=" O ASP J 111 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR J 109 " --> pdb=" O THR J 101 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'K' and resid 4 through 7 removed outlier: 3.640A pdb=" N THR K 72 " --> pdb=" O SER K 65 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.467A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'K' and resid 10 through 13 1288 hydrogen bonds defined for protein. 3444 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: 14.55 Time building geometry restraints manager: 13.12 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: 9639 1.34 - 1.46: 7411 1.46 - 1.58: 13986 1.58 - 1.70: 3 1.70 - 1.82: 165 Bond restraints: 31204 Sorted by residual: bond pdb=" CB VAL A 698 " pdb=" CG1 VAL A 698 " ideal model delta sigma weight residual 1.521 1.620 -0.099 3.30e-02 9.18e+02 9.02e+00 bond pdb=" C GLY A 697 " pdb=" N VAL A 698 " ideal model delta sigma weight residual 1.332 1.361 -0.029 1.36e-02 5.41e+03 4.67e+00 bond pdb=" N LEU B 229 " pdb=" CA LEU B 229 " ideal model delta sigma weight residual 1.463 1.437 0.025 1.22e-02 6.72e+03 4.32e+00 bond pdb=" CB VAL C 698 " pdb=" CG1 VAL C 698 " ideal model delta sigma weight residual 1.521 1.585 -0.064 3.30e-02 9.18e+02 3.79e+00 bond pdb=" CG LEU C 696 " pdb=" CD1 LEU C 696 " ideal model delta sigma weight residual 1.521 1.581 -0.060 3.30e-02 9.18e+02 3.32e+00 ... (remaining 31199 not shown) Histogram of bond angle deviations from ideal: 75.90 - 87.56: 2 87.56 - 99.21: 3 99.21 - 110.87: 11989 110.87 - 122.53: 25778 122.53 - 134.18: 4709 Bond angle restraints: 42481 Sorted by residual: angle pdb=" N VAL B 317 " pdb=" CA VAL B 317 " pdb=" C VAL B 317 " ideal model delta sigma weight residual 108.17 75.90 32.27 1.46e+00 4.69e-01 4.89e+02 angle pdb=" N GLN B 318 " pdb=" CA GLN B 318 " pdb=" C GLN B 318 " ideal model delta sigma weight residual 108.45 85.56 22.89 1.93e+00 2.68e-01 1.41e+02 angle pdb=" N VAL C 698 " pdb=" CA VAL C 698 " pdb=" C VAL C 698 " ideal model delta sigma weight residual 107.80 92.42 15.38 1.45e+00 4.76e-01 1.13e+02 angle pdb=" N THR L 69 " pdb=" CA THR L 69 " pdb=" C THR L 69 " ideal model delta sigma weight residual 112.04 98.16 13.88 1.44e+00 4.82e-01 9.29e+01 angle pdb=" N VAL C 698 " pdb=" CA VAL C 698 " pdb=" CB VAL C 698 " ideal model delta sigma weight residual 111.46 123.29 -11.83 1.26e+00 6.30e-01 8.81e+01 ... (remaining 42476 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 18250 17.81 - 35.62: 729 35.62 - 53.43: 184 53.43 - 71.24: 48 71.24 - 89.05: 18 Dihedral angle restraints: 19229 sinusoidal: 8147 harmonic: 11082 Sorted by residual: dihedral pdb=" N THR L 69 " pdb=" C THR L 69 " pdb=" CA THR L 69 " pdb=" CB THR L 69 " ideal model delta harmonic sigma weight residual 123.40 100.21 23.19 0 2.50e+00 1.60e-01 8.61e+01 dihedral pdb=" N VAL B 317 " pdb=" C VAL B 317 " pdb=" CA VAL B 317 " pdb=" CB VAL B 317 " ideal model delta harmonic sigma weight residual 123.40 106.86 16.54 0 2.50e+00 1.60e-01 4.37e+01 dihedral pdb=" CA LEU A 696 " pdb=" C LEU A 696 " pdb=" N GLY A 697 " pdb=" CA GLY A 697 " ideal model delta harmonic sigma weight residual -180.00 -148.33 -31.67 0 5.00e+00 4.00e-02 4.01e+01 ... (remaining 19226 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 4858 0.117 - 0.234: 82 0.234 - 0.351: 2 0.351 - 0.468: 1 0.468 - 0.585: 1 Chirality restraints: 4944 Sorted by residual: chirality pdb=" C1 NAG S 2 " pdb=" O4 NAG S 1 " pdb=" C2 NAG S 2 " pdb=" O5 NAG S 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.34 -0.06 2.00e-02 2.50e+03 9.90e+00 chirality pdb=" CA THR L 69 " pdb=" N THR L 69 " pdb=" C THR L 69 " pdb=" CB THR L 69 " both_signs ideal model delta sigma weight residual False 2.53 3.11 -0.59 2.00e-01 2.50e+01 8.56e+00 chirality pdb=" CA VAL B 317 " pdb=" N VAL B 317 " pdb=" C VAL B 317 " pdb=" CB VAL B 317 " both_signs ideal model delta sigma weight residual False 2.44 2.88 -0.43 2.00e-01 2.50e+01 4.72e+00 ... (remaining 4941 not shown) Planarity restraints: 5445 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1303 " 0.025 2.00e-02 2.50e+03 2.09e-02 5.48e+00 pdb=" C7 NAG B1303 " -0.009 2.00e-02 2.50e+03 pdb=" C8 NAG B1303 " 0.020 2.00e-02 2.50e+03 pdb=" N2 NAG B1303 " -0.033 2.00e-02 2.50e+03 pdb=" O7 NAG B1303 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 963 " -0.011 2.00e-02 2.50e+03 2.15e-02 4.63e+00 pdb=" C LEU A 963 " 0.037 2.00e-02 2.50e+03 pdb=" O LEU A 963 " -0.014 2.00e-02 2.50e+03 pdb=" N SER A 964 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 962 " 0.010 2.00e-02 2.50e+03 2.09e-02 4.36e+00 pdb=" C GLN A 962 " -0.036 2.00e-02 2.50e+03 pdb=" O GLN A 962 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU A 963 " 0.012 2.00e-02 2.50e+03 ... (remaining 5442 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 255 2.49 - 3.10: 23757 3.10 - 3.70: 45319 3.70 - 4.30: 69085 4.30 - 4.90: 115495 Nonbonded interactions: 253911 Sorted by model distance: nonbonded pdb=" NZ LYS B1025 " pdb=" O PHE B1039 " model vdw 1.893 2.520 nonbonded pdb=" OE2 GLU A 816 " pdb=" N SER A1052 " model vdw 2.014 2.520 nonbonded pdb=" OG SER J 72 " pdb=" OG SER J 81 " model vdw 2.038 2.440 nonbonded pdb=" OE2 GLU B 816 " pdb=" N SER B1052 " model vdw 2.058 2.520 nonbonded pdb=" OG SER H 72 " pdb=" OG SER H 81 " model vdw 2.061 2.440 ... (remaining 253906 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 66 or resid 77 through 172 or resid 186 through \ 617 or resid 638 through 1144 or resid 1301 through 1308)) selection = (chain 'B' and (resid 13 through 172 or resid 186 through 245 or resid 261 throu \ gh 617 or resid 638 through 1144 or resid 1301 through 1308)) selection = (chain 'C' and (resid 13 through 617 or resid 638 through 1144 or resid 1301 thr \ ough 1308)) } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'I' 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' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'F' selection = chain 'K' selection = chain 'L' } 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: 4.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 20.730 Check model and map are aligned: 0.640 Set scattering table: 0.330 Process input model: 84.400 Find NCS groups from input model: 2.190 Set up NCS constraints: 0.320 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:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 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 : 0.005 0.099 31204 Z= 0.292 Angle : 0.663 32.272 42481 Z= 0.369 Chirality : 0.045 0.585 4944 Planarity : 0.004 0.049 5405 Dihedral : 10.947 89.053 11969 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.40 % Allowed : 4.98 % Favored : 94.62 % Rotamer: Outliers : 1.20 % Allowed : 4.53 % Favored : 94.27 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.13), residues: 3753 helix: 0.63 (0.20), residues: 708 sheet: -0.07 (0.16), residues: 1016 loop : -1.13 (0.13), residues: 2029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 36 HIS 0.005 0.001 HIS A 516 PHE 0.023 0.001 PHE B 303 TYR 0.017 0.001 TYR C 870 ARG 0.008 0.000 ARG C1036 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 3334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 593 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.8523 (m-80) cc_final: 0.8044 (m-10) REVERT: B 313 SER cc_start: 0.9466 (t) cc_final: 0.9231 (p) REVERT: B 314 ASN cc_start: 0.9156 (m110) cc_final: 0.8302 (p0) REVERT: B 729 THR cc_start: 0.8818 (m) cc_final: 0.8073 (p) REVERT: B 802 ILE cc_start: 0.7381 (pt) cc_final: 0.6969 (pt) REVERT: B 932 GLN cc_start: 0.9171 (mt0) cc_final: 0.8915 (tm-30) REVERT: B 985 GLU cc_start: 0.9194 (mt-10) cc_final: 0.8697 (pt0) REVERT: B 1003 THR cc_start: 0.9549 (m) cc_final: 0.8886 (m) REVERT: C 223 LEU cc_start: 0.9426 (mp) cc_final: 0.8813 (tp) REVERT: C 348 TYR cc_start: 0.9151 (p90) cc_final: 0.8564 (p90) REVERT: C 420 TYR cc_start: 0.8213 (t80) cc_final: 0.7635 (t80) REVERT: C 512 PHE cc_start: 0.4743 (m-80) cc_final: 0.4477 (m-80) REVERT: C 605 VAL cc_start: 0.2549 (m) cc_final: 0.2327 (m) REVERT: C 739 ILE cc_start: 0.9279 (mt) cc_final: 0.8990 (tt) REVERT: C 759 GLN cc_start: 0.9612 (pt0) cc_final: 0.9363 (pt0) REVERT: C 767 ILE cc_start: 0.9289 (mt) cc_final: 0.8778 (mt) REVERT: C 799 PHE cc_start: 0.8071 (m-80) cc_final: 0.7857 (m-10) REVERT: C 819 LEU cc_start: 0.9453 (mt) cc_final: 0.9074 (mt) REVERT: C 858 LEU cc_start: 0.8919 (mt) cc_final: 0.8031 (tp) REVERT: C 866 MET cc_start: 0.8757 (mtt) cc_final: 0.8370 (mtt) REVERT: C 870 TYR cc_start: 0.8992 (m-80) cc_final: 0.8636 (m-80) REVERT: C 919 LEU cc_start: 0.9371 (tp) cc_final: 0.8944 (tt) REVERT: C 1049 PHE cc_start: 0.7250 (m-80) cc_final: 0.6775 (m-80) REVERT: C 1110 GLN cc_start: 0.9131 (mt0) cc_final: 0.8750 (mp10) REVERT: A 55 PHE cc_start: 0.8273 (m-80) cc_final: 0.7248 (m-80) REVERT: A 348 TYR cc_start: 0.9621 (p90) cc_final: 0.9330 (p90) REVERT: A 420 TYR cc_start: 0.8628 (t80) cc_final: 0.7512 (t80) REVERT: A 729 THR cc_start: 0.7878 (m) cc_final: 0.7126 (t) REVERT: A 760 LEU cc_start: 0.9311 (mt) cc_final: 0.9046 (mt) REVERT: A 875 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.9056 (mm) REVERT: A 961 LYS cc_start: 0.9625 (mttt) cc_final: 0.9327 (mmtm) REVERT: A 998 LEU cc_start: 0.9549 (tp) cc_final: 0.9233 (tp) REVERT: A 1002 GLN cc_start: 0.9054 (mt0) cc_final: 0.8752 (mm110) REVERT: A 1016 ARG cc_start: 0.8445 (ttp-110) cc_final: 0.8214 (ptp-170) REVERT: A 1026 MET cc_start: 0.8696 (tpp) cc_final: 0.8458 (mmm) REVERT: A 1028 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7974 (mt-10) REVERT: A 1049 PHE cc_start: 0.7603 (m-80) cc_final: 0.7224 (m-10) REVERT: A 1059 PHE cc_start: 0.8798 (m-80) cc_final: 0.7921 (m-10) REVERT: A 1108 GLU cc_start: 0.9033 (tt0) cc_final: 0.8729 (tm-30) REVERT: A 1110 GLN cc_start: 0.9299 (mt0) cc_final: 0.8749 (tp40) REVERT: L 4 MET cc_start: 0.7811 (tpp) cc_final: 0.7527 (mmt) REVERT: L 21 LEU cc_start: 0.5360 (OUTLIER) cc_final: 0.4852 (tt) REVERT: J 71 MET cc_start: 0.7278 (mtp) cc_final: 0.6489 (ttp) REVERT: K 4 MET cc_start: 0.6582 (tpp) cc_final: 0.6370 (ttt) REVERT: K 90 LEU cc_start: 0.8187 (tp) cc_final: 0.7793 (tp) outliers start: 40 outliers final: 9 residues processed: 619 average time/residue: 0.4270 time to fit residues: 414.4075 Evaluate side-chains 336 residues out of total 3334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 325 time to evaluate : 2.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 318 optimal weight: 30.0000 chunk 285 optimal weight: 6.9990 chunk 158 optimal weight: 1.9990 chunk 97 optimal weight: 8.9990 chunk 192 optimal weight: 10.0000 chunk 152 optimal weight: 5.9990 chunk 295 optimal weight: 0.9980 chunk 114 optimal weight: 5.9990 chunk 179 optimal weight: 0.0170 chunk 219 optimal weight: 30.0000 chunk 342 optimal weight: 40.0000 overall best weight: 3.0024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 495 GLN ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN B1008 GLN ** B1020 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1085 HIS ** B1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 318 GLN C 484 ASN C 853 ASN C 910 GLN ** C 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 962 GLN ** C1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 484 ASN A 495 GLN A 610 GLN ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 821 ASN A 898 GLN A 910 GLN ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 78 ASN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN E 78 ASN F 38 GLN J 78 ASN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 31204 Z= 0.272 Angle : 0.642 11.765 42481 Z= 0.341 Chirality : 0.044 0.300 4944 Planarity : 0.005 0.065 5405 Dihedral : 6.825 59.250 5199 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.09 % Favored : 94.67 % Rotamer: Outliers : 0.12 % Allowed : 2.37 % Favored : 97.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % 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: -0.62 (0.13), residues: 3753 helix: 0.80 (0.19), residues: 708 sheet: 0.07 (0.16), residues: 1007 loop : -1.10 (0.13), residues: 2038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 105 HIS 0.009 0.001 HIS C1055 PHE 0.034 0.002 PHE C 65 TYR 0.035 0.002 TYR A 263 ARG 0.008 0.001 ARG B 34 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 3334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 400 time to evaluate : 3.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 PHE cc_start: 0.8340 (m-80) cc_final: 0.7175 (m-10) REVERT: B 272 PHE cc_start: 0.8828 (m-80) cc_final: 0.7982 (m-80) REVERT: B 782 VAL cc_start: 0.7990 (m) cc_final: 0.7506 (m) REVERT: B 866 MET cc_start: 0.9279 (mpp) cc_final: 0.8926 (mmm) REVERT: B 999 GLN cc_start: 0.9445 (tp-100) cc_final: 0.8944 (tp-100) REVERT: B 1003 THR cc_start: 0.9387 (m) cc_final: 0.8975 (m) REVERT: C 223 LEU cc_start: 0.9365 (mp) cc_final: 0.8770 (tp) REVERT: C 348 TYR cc_start: 0.9247 (p90) cc_final: 0.8604 (p90) REVERT: C 420 TYR cc_start: 0.8584 (t80) cc_final: 0.8087 (t80) REVERT: C 737 MET cc_start: 0.9179 (tpp) cc_final: 0.8979 (tpp) REVERT: C 739 ILE cc_start: 0.9178 (mt) cc_final: 0.8855 (tp) REVERT: C 755 SER cc_start: 0.9448 (p) cc_final: 0.9135 (p) REVERT: C 799 PHE cc_start: 0.8179 (m-80) cc_final: 0.7942 (m-10) REVERT: C 819 LEU cc_start: 0.9528 (mt) cc_final: 0.9195 (mt) REVERT: C 858 LEU cc_start: 0.9010 (mt) cc_final: 0.8522 (tp) REVERT: C 866 MET cc_start: 0.8774 (mtt) cc_final: 0.8452 (mtt) REVERT: C 870 TYR cc_start: 0.8996 (m-80) cc_final: 0.8658 (m-80) REVERT: C 928 ILE cc_start: 0.9284 (mm) cc_final: 0.8996 (mm) REVERT: C 985 GLU cc_start: 0.9401 (mt-10) cc_final: 0.9035 (mp0) REVERT: C 1059 PHE cc_start: 0.8323 (m-10) cc_final: 0.8109 (m-10) REVERT: C 1110 GLN cc_start: 0.9068 (mt0) cc_final: 0.8675 (mp10) REVERT: A 348 TYR cc_start: 0.9664 (p90) cc_final: 0.9405 (p90) REVERT: A 420 TYR cc_start: 0.8572 (t80) cc_final: 0.7514 (t80) REVERT: A 583 ASP cc_start: 0.8748 (m-30) cc_final: 0.8305 (t0) REVERT: A 704 TYR cc_start: 0.3519 (t80) cc_final: 0.2524 (t80) REVERT: A 729 THR cc_start: 0.8249 (m) cc_final: 0.8025 (t) REVERT: A 744 THR cc_start: 0.9445 (p) cc_final: 0.9234 (p) REVERT: A 752 GLN cc_start: 0.8452 (tm-30) cc_final: 0.8046 (tm-30) REVERT: A 951 GLN cc_start: 0.9192 (mt0) cc_final: 0.8838 (mt0) REVERT: A 961 LYS cc_start: 0.9386 (mttt) cc_final: 0.9079 (mmtm) REVERT: A 977 ILE cc_start: 0.9509 (tt) cc_final: 0.9114 (tt) REVERT: A 1016 ARG cc_start: 0.8519 (ttp-110) cc_final: 0.8090 (ptp-170) REVERT: A 1108 GLU cc_start: 0.9123 (tt0) cc_final: 0.8474 (tm-30) REVERT: L 4 MET cc_start: 0.7749 (tpp) cc_final: 0.7253 (mmt) REVERT: J 71 MET cc_start: 0.7415 (mtp) cc_final: 0.7177 (ttp) REVERT: K 4 MET cc_start: 0.7180 (tpp) cc_final: 0.6859 (ttm) outliers start: 4 outliers final: 1 residues processed: 404 average time/residue: 0.3993 time to fit residues: 263.2305 Evaluate side-chains 283 residues out of total 3334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 282 time to evaluate : 3.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 190 optimal weight: 5.9990 chunk 106 optimal weight: 0.7980 chunk 284 optimal weight: 0.8980 chunk 233 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 342 optimal weight: 10.0000 chunk 370 optimal weight: 5.9990 chunk 305 optimal weight: 2.9990 chunk 340 optimal weight: 50.0000 chunk 116 optimal weight: 3.9990 chunk 275 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 484 ASN ** B 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 950 ASN ** B 952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 ASN B 999 GLN ** B1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1008 GLN ** C1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1139 GLN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 946 GLN A 950 ASN A1008 GLN A1116 ASN A1132 ASN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 31204 Z= 0.180 Angle : 0.563 9.331 42481 Z= 0.295 Chirality : 0.043 0.179 4944 Planarity : 0.004 0.066 5405 Dihedral : 5.993 59.646 5199 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.09 % Favored : 94.70 % Rotamer: Outliers : 0.09 % Allowed : 2.67 % Favored : 97.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % 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 (0.13), residues: 3753 helix: 1.25 (0.19), residues: 699 sheet: 0.16 (0.16), residues: 1000 loop : -1.05 (0.13), residues: 2054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 883 HIS 0.007 0.001 HIS B1061 PHE 0.026 0.002 PHE A 272 TYR 0.024 0.001 TYR A 263 ARG 0.008 0.000 ARG B 574 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 3334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 375 time to evaluate : 3.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 PHE cc_start: 0.8221 (m-80) cc_final: 0.7155 (m-10) REVERT: B 272 PHE cc_start: 0.8553 (m-80) cc_final: 0.7791 (m-80) REVERT: B 866 MET cc_start: 0.9264 (mpp) cc_final: 0.8935 (mmm) REVERT: B 966 ASN cc_start: 0.9478 (m-40) cc_final: 0.8871 (p0) REVERT: B 999 GLN cc_start: 0.9416 (tp40) cc_final: 0.9049 (tp-100) REVERT: C 128 ILE cc_start: 0.8978 (mp) cc_final: 0.8681 (mp) REVERT: C 168 PHE cc_start: 0.8932 (t80) cc_final: 0.8545 (t80) REVERT: C 223 LEU cc_start: 0.9324 (mp) cc_final: 0.8754 (tp) REVERT: C 348 TYR cc_start: 0.9242 (p90) cc_final: 0.8632 (p90) REVERT: C 420 TYR cc_start: 0.8581 (t80) cc_final: 0.7994 (t80) REVERT: C 512 PHE cc_start: 0.4921 (m-80) cc_final: 0.4585 (m-80) REVERT: C 737 MET cc_start: 0.9208 (tpp) cc_final: 0.8977 (tpp) REVERT: C 866 MET cc_start: 0.8817 (mtt) cc_final: 0.8536 (mtt) REVERT: C 870 TYR cc_start: 0.8977 (m-80) cc_final: 0.8622 (m-80) REVERT: C 930 LYS cc_start: 0.9379 (mptt) cc_final: 0.9070 (mttt) REVERT: C 932 GLN cc_start: 0.9028 (tm-30) cc_final: 0.8790 (tm-30) REVERT: C 985 GLU cc_start: 0.9395 (mt-10) cc_final: 0.9048 (mp0) REVERT: C 1010 ILE cc_start: 0.9575 (pt) cc_final: 0.9239 (pt) REVERT: C 1110 GLN cc_start: 0.9141 (mt0) cc_final: 0.8737 (mp10) REVERT: A 420 TYR cc_start: 0.8486 (t80) cc_final: 0.7393 (t80) REVERT: A 583 ASP cc_start: 0.8738 (m-30) cc_final: 0.8408 (t0) REVERT: A 704 TYR cc_start: 0.3495 (t80) cc_final: 0.2725 (t80) REVERT: A 744 THR cc_start: 0.9437 (p) cc_final: 0.9237 (p) REVERT: A 752 GLN cc_start: 0.8468 (tm-30) cc_final: 0.8085 (tm-30) REVERT: A 816 GLU cc_start: 0.9088 (mt-10) cc_final: 0.7754 (mt-10) REVERT: A 875 LEU cc_start: 0.9405 (mm) cc_final: 0.9200 (mm) REVERT: A 982 ASP cc_start: 0.8450 (m-30) cc_final: 0.7854 (p0) REVERT: A 999 GLN cc_start: 0.8919 (tp-100) cc_final: 0.8686 (tp-100) REVERT: A 1003 THR cc_start: 0.8700 (m) cc_final: 0.8279 (m) REVERT: A 1108 GLU cc_start: 0.9094 (tt0) cc_final: 0.8450 (tm-30) REVERT: L 4 MET cc_start: 0.7720 (tpp) cc_final: 0.7122 (mmt) outliers start: 3 outliers final: 1 residues processed: 378 average time/residue: 0.4169 time to fit residues: 265.8147 Evaluate side-chains 270 residues out of total 3334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 269 time to evaluate : 3.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 338 optimal weight: 10.0000 chunk 257 optimal weight: 0.1980 chunk 177 optimal weight: 0.9980 chunk 37 optimal weight: 40.0000 chunk 163 optimal weight: 7.9990 chunk 230 optimal weight: 5.9990 chunk 344 optimal weight: 5.9990 chunk 364 optimal weight: 20.0000 chunk 179 optimal weight: 5.9990 chunk 326 optimal weight: 8.9990 chunk 98 optimal weight: 5.9990 overall best weight: 3.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 801 GLN B 898 GLN B 925 ASN B 999 GLN ** B1020 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1055 HIS ** B1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 904 ASN C 946 GLN C 950 ASN C1020 ASN ** C1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1051 GLN C1055 HIS ** C1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 GLN ** A1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 GLN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 31204 Z= 0.329 Angle : 0.701 13.523 42481 Z= 0.375 Chirality : 0.046 0.226 4944 Planarity : 0.005 0.065 5405 Dihedral : 5.876 59.156 5199 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 20.78 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.78 % Favored : 94.00 % Rotamer: Outliers : 0.09 % Allowed : 3.33 % Favored : 96.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % 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: -0.83 (0.13), residues: 3753 helix: 0.29 (0.19), residues: 675 sheet: 0.07 (0.16), residues: 1020 loop : -1.16 (0.13), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C1099 HIS 0.015 0.002 HIS C1055 PHE 0.037 0.002 PHE B1049 TYR 0.044 0.002 TYR C 738 ARG 0.006 0.001 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 338 time to evaluate : 3.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 PHE cc_start: 0.8221 (m-80) cc_final: 0.7137 (m-10) REVERT: B 272 PHE cc_start: 0.8744 (m-80) cc_final: 0.7949 (m-10) REVERT: B 749 LEU cc_start: 0.8892 (mt) cc_final: 0.8650 (mp) REVERT: B 866 MET cc_start: 0.9275 (mpp) cc_final: 0.8972 (mmm) REVERT: B 957 ASN cc_start: 0.9100 (m110) cc_final: 0.8871 (m-40) REVERT: B 999 GLN cc_start: 0.9513 (tp-100) cc_final: 0.9189 (tp-100) REVERT: B 1124 ASP cc_start: 0.6843 (p0) cc_final: 0.6630 (p0) REVERT: C 223 LEU cc_start: 0.9314 (mp) cc_final: 0.8794 (tp) REVERT: C 420 TYR cc_start: 0.8794 (t80) cc_final: 0.8041 (t80) REVERT: C 512 PHE cc_start: 0.5020 (m-80) cc_final: 0.4748 (m-80) REVERT: C 694 MET cc_start: 0.7841 (ppp) cc_final: 0.7356 (ppp) REVERT: C 870 TYR cc_start: 0.9056 (m-80) cc_final: 0.8795 (m-80) REVERT: C 916 ASN cc_start: 0.9270 (t0) cc_final: 0.9029 (t0) REVERT: C 918 LYS cc_start: 0.9464 (mttt) cc_final: 0.9115 (mppt) REVERT: C 930 LYS cc_start: 0.9484 (mptt) cc_final: 0.9197 (mttt) REVERT: C 931 ILE cc_start: 0.8977 (mm) cc_final: 0.8775 (mm) REVERT: C 948 VAL cc_start: 0.9592 (t) cc_final: 0.9151 (p) REVERT: A 53 ASP cc_start: 0.7701 (t0) cc_final: 0.7490 (t70) REVERT: A 54 LEU cc_start: 0.6817 (tp) cc_final: 0.6497 (tp) REVERT: A 55 PHE cc_start: 0.7702 (m-10) cc_final: 0.7053 (m-10) REVERT: A 117 LEU cc_start: 0.9638 (tp) cc_final: 0.9308 (tp) REVERT: A 348 TYR cc_start: 0.9708 (p90) cc_final: 0.9473 (p90) REVERT: A 420 TYR cc_start: 0.8665 (t80) cc_final: 0.7606 (t80) REVERT: A 583 ASP cc_start: 0.8859 (m-30) cc_final: 0.8649 (t0) REVERT: A 694 MET cc_start: 0.8156 (ppp) cc_final: 0.7820 (ppp) REVERT: A 717 ILE cc_start: 0.8343 (mm) cc_final: 0.7940 (mm) REVERT: A 737 MET cc_start: 0.9221 (tpt) cc_final: 0.8704 (tpp) REVERT: A 752 GLN cc_start: 0.8799 (tm-30) cc_final: 0.8393 (tm-30) REVERT: A 759 GLN cc_start: 0.9345 (pt0) cc_final: 0.9133 (pt0) REVERT: A 816 GLU cc_start: 0.8658 (mt-10) cc_final: 0.8456 (mt-10) REVERT: A 999 GLN cc_start: 0.8986 (tp-100) cc_final: 0.8655 (tp-100) REVERT: A 1003 THR cc_start: 0.8724 (m) cc_final: 0.8256 (m) REVERT: A 1028 GLU cc_start: 0.8322 (mt-10) cc_final: 0.8038 (pt0) REVERT: A 1039 PHE cc_start: 0.6439 (t80) cc_final: 0.5939 (t80) REVERT: A 1108 GLU cc_start: 0.9186 (tt0) cc_final: 0.8605 (tm-30) REVERT: L 87 TYR cc_start: 0.9338 (m-10) cc_final: 0.9125 (m-10) REVERT: J 120 THR cc_start: 0.7339 (p) cc_final: 0.7026 (p) outliers start: 3 outliers final: 1 residues processed: 341 average time/residue: 0.3757 time to fit residues: 214.2900 Evaluate side-chains 243 residues out of total 3334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 242 time to evaluate : 3.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 303 optimal weight: 3.9990 chunk 206 optimal weight: 6.9990 chunk 5 optimal weight: 40.0000 chunk 271 optimal weight: 4.9990 chunk 150 optimal weight: 9.9990 chunk 310 optimal weight: 3.9990 chunk 251 optimal weight: 40.0000 chunk 0 optimal weight: 20.0000 chunk 186 optimal weight: 3.9990 chunk 327 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 484 ASN ** B 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 ASN ** B 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 898 GLN ** B1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 910 GLN C 932 GLN C 946 GLN ** C1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1132 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 GLN E 41 GLN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.4679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 31204 Z= 0.264 Angle : 0.617 9.615 42481 Z= 0.328 Chirality : 0.044 0.325 4944 Planarity : 0.004 0.063 5405 Dihedral : 5.508 54.132 5199 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 17.44 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.38 % Favored : 94.46 % Rotamer: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % 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: -0.74 (0.13), residues: 3753 helix: 0.46 (0.19), residues: 668 sheet: 0.07 (0.16), residues: 1011 loop : -1.10 (0.14), residues: 2074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 883 HIS 0.011 0.001 HIS B1045 PHE 0.029 0.002 PHE A 272 TYR 0.023 0.002 TYR C 738 ARG 0.006 0.000 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 3334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 326 time to evaluate : 3.628 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: 0.8080 (m-80) cc_final: 0.7098 (m-10) REVERT: B 272 PHE cc_start: 0.8531 (m-80) cc_final: 0.7918 (m-10) REVERT: B 745 GLU cc_start: 0.9282 (mp0) cc_final: 0.8441 (tt0) REVERT: B 866 MET cc_start: 0.9207 (mpp) cc_final: 0.8897 (mmm) REVERT: B 957 ASN cc_start: 0.9133 (m110) cc_final: 0.8926 (m-40) REVERT: B 985 GLU cc_start: 0.8560 (mp0) cc_final: 0.8332 (mp0) REVERT: B 999 GLN cc_start: 0.9498 (tp-100) cc_final: 0.9091 (tp-100) REVERT: B 1078 ILE cc_start: 0.8740 (mt) cc_final: 0.8323 (mm) REVERT: C 223 LEU cc_start: 0.9264 (mp) cc_final: 0.8743 (tp) REVERT: C 348 TYR cc_start: 0.9319 (p90) cc_final: 0.8702 (p90) REVERT: C 420 TYR cc_start: 0.8687 (t80) cc_final: 0.7920 (t80) REVERT: C 512 PHE cc_start: 0.5003 (m-80) cc_final: 0.4780 (m-80) REVERT: C 866 MET cc_start: 0.8918 (mtt) cc_final: 0.8541 (mtt) REVERT: C 870 TYR cc_start: 0.9083 (m-80) cc_final: 0.8817 (m-80) REVERT: C 916 ASN cc_start: 0.9303 (t0) cc_final: 0.9019 (t0) REVERT: C 918 LYS cc_start: 0.9436 (mttt) cc_final: 0.9076 (mppt) REVERT: C 930 LYS cc_start: 0.9493 (mptt) cc_final: 0.9223 (mttt) REVERT: C 931 ILE cc_start: 0.9090 (mm) cc_final: 0.8870 (mm) REVERT: C 985 GLU cc_start: 0.9359 (mt-10) cc_final: 0.9046 (mp0) REVERT: A 54 LEU cc_start: 0.7100 (tp) cc_final: 0.6791 (tp) REVERT: A 55 PHE cc_start: 0.7546 (m-10) cc_final: 0.6985 (m-10) REVERT: A 348 TYR cc_start: 0.9722 (p90) cc_final: 0.9491 (p90) REVERT: A 717 ILE cc_start: 0.8443 (mm) cc_final: 0.7862 (mm) REVERT: A 737 MET cc_start: 0.9169 (tpt) cc_final: 0.8610 (tpp) REVERT: A 744 THR cc_start: 0.9504 (p) cc_final: 0.9299 (p) REVERT: A 752 GLN cc_start: 0.9047 (tm-30) cc_final: 0.8777 (tm-30) REVERT: A 759 GLN cc_start: 0.9242 (pt0) cc_final: 0.8911 (pt0) REVERT: A 797 PHE cc_start: 0.8235 (m-10) cc_final: 0.8017 (m-10) REVERT: A 816 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8133 (mt-10) REVERT: A 957 ASN cc_start: 0.9292 (t0) cc_final: 0.8954 (p0) REVERT: A 999 GLN cc_start: 0.9027 (tp-100) cc_final: 0.8727 (tp-100) REVERT: A 1003 THR cc_start: 0.8688 (m) cc_final: 0.8268 (m) REVERT: A 1016 ARG cc_start: 0.8686 (ttp-110) cc_final: 0.8329 (ptp-170) REVERT: A 1028 GLU cc_start: 0.8309 (mt-10) cc_final: 0.8054 (pt0) REVERT: A 1039 PHE cc_start: 0.6771 (t80) cc_final: 0.6177 (t80) REVERT: A 1108 GLU cc_start: 0.9213 (tt0) cc_final: 0.8649 (tm-30) REVERT: L 4 MET cc_start: 0.8309 (mmm) cc_final: 0.7968 (tpp) REVERT: J 71 MET cc_start: 0.5158 (ppp) cc_final: 0.4267 (ppp) outliers start: 0 outliers final: 0 residues processed: 326 average time/residue: 0.3794 time to fit residues: 206.8134 Evaluate side-chains 238 residues out of total 3334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 238 time to evaluate : 3.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 122 optimal weight: 5.9990 chunk 328 optimal weight: 30.0000 chunk 72 optimal weight: 6.9990 chunk 213 optimal weight: 7.9990 chunk 89 optimal weight: 0.9990 chunk 364 optimal weight: 7.9990 chunk 302 optimal weight: 0.9990 chunk 168 optimal weight: 1.9990 chunk 30 optimal weight: 50.0000 chunk 120 optimal weight: 10.0000 chunk 191 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 898 GLN ** B1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 932 GLN C1051 GLN ** C1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 781 GLN A 923 GLN H 41 GLN E 41 GLN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.5177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 31204 Z= 0.291 Angle : 0.643 10.862 42481 Z= 0.343 Chirality : 0.044 0.215 4944 Planarity : 0.005 0.083 5405 Dihedral : 5.345 40.545 5199 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 20.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.39 % Favored : 93.47 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % 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: -0.89 (0.13), residues: 3753 helix: 0.15 (0.19), residues: 672 sheet: 0.04 (0.16), residues: 965 loop : -1.14 (0.13), residues: 2116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 883 HIS 0.012 0.001 HIS B1045 PHE 0.034 0.002 PHE A 58 TYR 0.047 0.002 TYR C 914 ARG 0.015 0.001 ARG B1036 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 3334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 308 time to evaluate : 3.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 PHE cc_start: 0.7875 (m-80) cc_final: 0.6889 (m-10) REVERT: B 272 PHE cc_start: 0.8572 (m-80) cc_final: 0.7946 (m-10) REVERT: B 745 GLU cc_start: 0.9345 (mp0) cc_final: 0.8743 (tt0) REVERT: B 866 MET cc_start: 0.9408 (mpp) cc_final: 0.8455 (ptp) REVERT: B 985 GLU cc_start: 0.8484 (mp0) cc_final: 0.8275 (mp0) REVERT: B 999 GLN cc_start: 0.9508 (tp-100) cc_final: 0.9115 (tp-100) REVERT: B 1078 ILE cc_start: 0.8811 (mt) cc_final: 0.8436 (mm) REVERT: C 223 LEU cc_start: 0.9250 (mp) cc_final: 0.8767 (tp) REVERT: C 348 TYR cc_start: 0.9331 (p90) cc_final: 0.8761 (p90) REVERT: C 420 TYR cc_start: 0.8744 (t80) cc_final: 0.8517 (t80) REVERT: C 866 MET cc_start: 0.8872 (mtt) cc_final: 0.8416 (mtt) REVERT: C 870 TYR cc_start: 0.9097 (m-80) cc_final: 0.8860 (m-80) REVERT: C 916 ASN cc_start: 0.9357 (t0) cc_final: 0.9122 (t0) REVERT: C 918 LYS cc_start: 0.9423 (mttt) cc_final: 0.9047 (mppt) REVERT: C 930 LYS cc_start: 0.9498 (mptt) cc_final: 0.9219 (mttt) REVERT: C 931 ILE cc_start: 0.9220 (mm) cc_final: 0.9016 (mm) REVERT: C 989 GLN cc_start: 0.8825 (mm-40) cc_final: 0.8593 (mp10) REVERT: A 33 THR cc_start: 0.6795 (p) cc_final: 0.6214 (p) REVERT: A 54 LEU cc_start: 0.7176 (tp) cc_final: 0.6889 (tp) REVERT: A 55 PHE cc_start: 0.7420 (m-10) cc_final: 0.6945 (m-10) REVERT: A 348 TYR cc_start: 0.9727 (p90) cc_final: 0.9514 (p90) REVERT: A 694 MET cc_start: 0.8318 (ppp) cc_final: 0.8013 (ppp) REVERT: A 737 MET cc_start: 0.9093 (tpt) cc_final: 0.8688 (tpp) REVERT: A 744 THR cc_start: 0.9500 (p) cc_final: 0.9297 (p) REVERT: A 797 PHE cc_start: 0.8350 (m-10) cc_final: 0.8132 (m-10) REVERT: A 816 GLU cc_start: 0.8371 (mt-10) cc_final: 0.8138 (mt-10) REVERT: A 952 ASN cc_start: 0.9172 (t0) cc_final: 0.8820 (t0) REVERT: A 957 ASN cc_start: 0.9399 (t0) cc_final: 0.8969 (p0) REVERT: A 999 GLN cc_start: 0.9016 (tp-100) cc_final: 0.8680 (tp-100) REVERT: A 1003 THR cc_start: 0.8719 (m) cc_final: 0.8287 (m) REVERT: A 1016 ARG cc_start: 0.8743 (ttp-110) cc_final: 0.8368 (ptp-170) REVERT: A 1107 TYR cc_start: 0.8816 (t80) cc_final: 0.8493 (t80) REVERT: A 1108 GLU cc_start: 0.9151 (tt0) cc_final: 0.8486 (tm-30) REVERT: J 71 MET cc_start: 0.5315 (ppp) cc_final: 0.4383 (ppp) REVERT: J 91 ASP cc_start: 0.5711 (m-30) cc_final: 0.5455 (m-30) REVERT: K 90 LEU cc_start: 0.8242 (tp) cc_final: 0.7914 (mt) outliers start: 0 outliers final: 0 residues processed: 308 average time/residue: 0.3788 time to fit residues: 196.5445 Evaluate side-chains 230 residues out of total 3334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 230 time to evaluate : 3.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 351 optimal weight: 50.0000 chunk 41 optimal weight: 50.0000 chunk 207 optimal weight: 40.0000 chunk 266 optimal weight: 6.9990 chunk 206 optimal weight: 0.8980 chunk 307 optimal weight: 7.9990 chunk 203 optimal weight: 6.9990 chunk 363 optimal weight: 0.8980 chunk 227 optimal weight: 4.9990 chunk 221 optimal weight: 20.0000 chunk 167 optimal weight: 7.9990 overall best weight: 4.1586 ------------------------------------------------------------------------------- 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 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 904 ASN B1002 GLN ** B1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN ** C 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 HIS ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1020 ASN H 41 GLN E 41 GLN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.5792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 31204 Z= 0.324 Angle : 0.680 10.145 42481 Z= 0.366 Chirality : 0.045 0.256 4944 Planarity : 0.005 0.061 5405 Dihedral : 5.506 39.836 5199 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 24.12 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.24 % Favored : 93.63 % Rotamer: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.13), residues: 3753 helix: -0.39 (0.18), residues: 684 sheet: -0.07 (0.17), residues: 950 loop : -1.19 (0.13), residues: 2119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 883 HIS 0.014 0.002 HIS C 652 PHE 0.028 0.002 PHE B 315 TYR 0.034 0.002 TYR B1044 ARG 0.008 0.001 ARG A 992 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 3334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 296 time to evaluate : 3.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 PHE cc_start: 0.7913 (m-80) cc_final: 0.7024 (m-80) REVERT: B 272 PHE cc_start: 0.8542 (m-80) cc_final: 0.8091 (m-10) REVERT: B 745 GLU cc_start: 0.9218 (mp0) cc_final: 0.8745 (tt0) REVERT: B 866 MET cc_start: 0.9400 (mpp) cc_final: 0.8450 (ptp) REVERT: B 875 LEU cc_start: 0.9704 (mt) cc_final: 0.9375 (tt) REVERT: B 985 GLU cc_start: 0.8464 (mp0) cc_final: 0.8248 (mp0) REVERT: B 999 GLN cc_start: 0.9526 (tp-100) cc_final: 0.9161 (tp-100) REVERT: B 1078 ILE cc_start: 0.8820 (mt) cc_final: 0.8450 (mm) REVERT: B 1124 ASP cc_start: 0.7179 (p0) cc_final: 0.6922 (p0) REVERT: C 223 LEU cc_start: 0.9244 (mp) cc_final: 0.8783 (tp) REVERT: C 694 MET cc_start: 0.7322 (ppp) cc_final: 0.6810 (ppp) REVERT: C 816 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8159 (mt-10) REVERT: C 916 ASN cc_start: 0.9410 (t0) cc_final: 0.9157 (t0) REVERT: C 918 LYS cc_start: 0.9422 (mttt) cc_final: 0.9042 (mppt) REVERT: C 930 LYS cc_start: 0.9529 (mptt) cc_final: 0.9249 (mttt) REVERT: A 54 LEU cc_start: 0.7047 (tp) cc_final: 0.6812 (tp) REVERT: A 694 MET cc_start: 0.8476 (ppp) cc_final: 0.8113 (ppp) REVERT: A 717 ILE cc_start: 0.8524 (mp) cc_final: 0.8271 (pt) REVERT: A 737 MET cc_start: 0.9032 (tpt) cc_final: 0.8679 (tpp) REVERT: A 778 VAL cc_start: 0.8660 (m) cc_final: 0.8333 (m) REVERT: A 797 PHE cc_start: 0.8403 (m-10) cc_final: 0.8192 (m-10) REVERT: A 816 GLU cc_start: 0.8381 (mt-10) cc_final: 0.8178 (mt-10) REVERT: A 952 ASN cc_start: 0.9270 (t0) cc_final: 0.8946 (t0) REVERT: A 999 GLN cc_start: 0.9029 (tp-100) cc_final: 0.8689 (tp-100) REVERT: A 1003 THR cc_start: 0.8787 (m) cc_final: 0.8375 (m) REVERT: A 1016 ARG cc_start: 0.8775 (ttp-110) cc_final: 0.8419 (ptp-170) REVERT: A 1107 TYR cc_start: 0.8741 (t80) cc_final: 0.8364 (t80) REVERT: A 1108 GLU cc_start: 0.9197 (tt0) cc_final: 0.8640 (tm-30) REVERT: A 1110 GLN cc_start: 0.9455 (mt0) cc_final: 0.9039 (tp40) REVERT: J 71 MET cc_start: 0.5583 (ppp) cc_final: 0.4875 (ppp) REVERT: J 91 ASP cc_start: 0.5915 (m-30) cc_final: 0.5691 (m-30) REVERT: K 90 LEU cc_start: 0.8336 (tp) cc_final: 0.8000 (mt) outliers start: 0 outliers final: 0 residues processed: 296 average time/residue: 0.3833 time to fit residues: 191.9684 Evaluate side-chains 219 residues out of total 3334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 3.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 224 optimal weight: 5.9990 chunk 145 optimal weight: 8.9990 chunk 217 optimal weight: 1.9990 chunk 109 optimal weight: 0.3980 chunk 71 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 231 optimal weight: 0.8980 chunk 247 optimal weight: 30.0000 chunk 179 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 285 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 ASN ** B 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 898 GLN ** B1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 932 GLN C 950 ASN C 962 GLN ** C1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 752 GLN ** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1020 ASN ** A1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 GLN ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.5827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 31204 Z= 0.169 Angle : 0.580 8.269 42481 Z= 0.302 Chirality : 0.043 0.173 4944 Planarity : 0.004 0.047 5405 Dihedral : 4.926 35.167 5199 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.06 % Favored : 94.80 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.13), residues: 3753 helix: 0.58 (0.20), residues: 671 sheet: 0.04 (0.16), residues: 988 loop : -1.15 (0.13), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 64 HIS 0.025 0.002 HIS C1045 PHE 0.019 0.001 PHE B1059 TYR 0.032 0.001 TYR L 87 ARG 0.004 0.000 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 3334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 315 time to evaluate : 3.801 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: B 55 PHE cc_start: 0.7783 (m-80) cc_final: 0.6927 (m-10) REVERT: B 272 PHE cc_start: 0.8553 (m-80) cc_final: 0.7978 (m-10) REVERT: B 745 GLU cc_start: 0.9202 (mp0) cc_final: 0.8712 (tt0) REVERT: B 866 MET cc_start: 0.9440 (mpp) cc_final: 0.9122 (mmm) REVERT: B 875 LEU cc_start: 0.9643 (mt) cc_final: 0.9315 (tp) REVERT: B 985 GLU cc_start: 0.8530 (mp0) cc_final: 0.8322 (mp0) REVERT: B 999 GLN cc_start: 0.9457 (tp-100) cc_final: 0.9121 (tp-100) REVERT: B 1078 ILE cc_start: 0.8716 (mt) cc_final: 0.8339 (mm) REVERT: B 1099 TRP cc_start: 0.8312 (m100) cc_final: 0.7707 (m100) REVERT: B 1124 ASP cc_start: 0.7015 (p0) cc_final: 0.6775 (p0) REVERT: C 168 PHE cc_start: 0.8908 (t80) cc_final: 0.8500 (t80) REVERT: C 223 LEU cc_start: 0.9203 (mp) cc_final: 0.8664 (tp) REVERT: C 348 TYR cc_start: 0.9237 (p90) cc_final: 0.8634 (p90) REVERT: C 420 TYR cc_start: 0.8606 (t80) cc_final: 0.8374 (t80) REVERT: C 816 GLU cc_start: 0.8787 (mt-10) cc_final: 0.7160 (mt-10) REVERT: C 866 MET cc_start: 0.9011 (mtt) cc_final: 0.8638 (mtt) REVERT: C 916 ASN cc_start: 0.9346 (t0) cc_final: 0.9109 (t0) REVERT: C 918 LYS cc_start: 0.9383 (mttt) cc_final: 0.8995 (mppt) REVERT: C 930 LYS cc_start: 0.9466 (mptt) cc_final: 0.9170 (mttt) REVERT: C 931 ILE cc_start: 0.9187 (mm) cc_final: 0.8982 (mm) REVERT: C 1007 GLN cc_start: 0.9342 (mp10) cc_final: 0.9097 (mp10) REVERT: A 55 PHE cc_start: 0.7253 (m-10) cc_final: 0.7019 (m-10) REVERT: A 737 MET cc_start: 0.8953 (tpt) cc_final: 0.8644 (tpp) REVERT: A 760 LEU cc_start: 0.9361 (mt) cc_final: 0.8748 (mt) REVERT: A 767 ILE cc_start: 0.9341 (mt) cc_final: 0.8930 (mt) REVERT: A 952 ASN cc_start: 0.9147 (t0) cc_final: 0.8803 (t0) REVERT: A 957 ASN cc_start: 0.9274 (t0) cc_final: 0.8808 (p0) REVERT: A 999 GLN cc_start: 0.9038 (tp-100) cc_final: 0.8640 (tp-100) REVERT: A 1025 LYS cc_start: 0.8749 (mttp) cc_final: 0.8320 (mmtt) REVERT: A 1039 PHE cc_start: 0.6321 (t80) cc_final: 0.4475 (t80) REVERT: A 1061 HIS cc_start: 0.7053 (m90) cc_final: 0.6827 (m170) REVERT: A 1108 GLU cc_start: 0.9098 (tt0) cc_final: 0.8474 (tm-30) REVERT: J 71 MET cc_start: 0.5372 (ppp) cc_final: 0.4667 (ppp) REVERT: K 90 LEU cc_start: 0.8270 (tp) cc_final: 0.7992 (mt) outliers start: 0 outliers final: 0 residues processed: 315 average time/residue: 0.3926 time to fit residues: 206.8477 Evaluate side-chains 224 residues out of total 3334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 3.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 330 optimal weight: 8.9990 chunk 348 optimal weight: 10.0000 chunk 317 optimal weight: 0.4980 chunk 338 optimal weight: 50.0000 chunk 203 optimal weight: 6.9990 chunk 147 optimal weight: 4.9990 chunk 265 optimal weight: 20.0000 chunk 103 optimal weight: 8.9990 chunk 305 optimal weight: 3.9990 chunk 320 optimal weight: 50.0000 chunk 337 optimal weight: 20.0000 overall best weight: 5.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 188 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 687 GLN ** B 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 898 GLN ** B1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 GLN ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 GLN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.6442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.144 31204 Z= 0.388 Angle : 0.753 12.343 42481 Z= 0.405 Chirality : 0.047 0.267 4944 Planarity : 0.005 0.087 5405 Dihedral : 5.536 39.050 5199 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 27.67 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.03 % Favored : 92.81 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.13), residues: 3753 helix: -0.56 (0.18), residues: 678 sheet: -0.15 (0.16), residues: 957 loop : -1.25 (0.13), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 883 HIS 0.031 0.003 HIS C1045 PHE 0.051 0.003 PHE C 55 TYR 0.039 0.002 TYR B1044 ARG 0.015 0.001 ARG C1036 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 3334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 287 time to evaluate : 3.532 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: B 272 PHE cc_start: 0.8679 (m-80) cc_final: 0.8277 (m-10) REVERT: B 866 MET cc_start: 0.9464 (mpp) cc_final: 0.8567 (ptp) REVERT: B 950 ASN cc_start: 0.9519 (t0) cc_final: 0.9193 (t0) REVERT: B 999 GLN cc_start: 0.9537 (tp-100) cc_final: 0.9224 (tp-100) REVERT: B 1078 ILE cc_start: 0.8808 (mt) cc_final: 0.8466 (mm) REVERT: B 1124 ASP cc_start: 0.7056 (p0) cc_final: 0.6801 (p0) REVERT: C 223 LEU cc_start: 0.9136 (mp) cc_final: 0.8670 (tp) REVERT: C 817 ASP cc_start: 0.8951 (m-30) cc_final: 0.8646 (m-30) REVERT: C 916 ASN cc_start: 0.9479 (t0) cc_final: 0.9273 (t0) REVERT: C 918 LYS cc_start: 0.9418 (mttt) cc_final: 0.9023 (mppt) REVERT: C 930 LYS cc_start: 0.9517 (mptt) cc_final: 0.9290 (mttt) REVERT: C 989 GLN cc_start: 0.8942 (mm-40) cc_final: 0.8477 (mp10) REVERT: C 1028 GLU cc_start: 0.7392 (mt-10) cc_final: 0.7082 (mt-10) REVERT: A 33 THR cc_start: 0.6932 (p) cc_final: 0.6266 (p) REVERT: A 54 LEU cc_start: 0.7263 (tp) cc_final: 0.6938 (tp) REVERT: A 55 PHE cc_start: 0.6958 (m-10) cc_final: 0.6679 (m-10) REVERT: A 737 MET cc_start: 0.8993 (tpt) cc_final: 0.8720 (tpp) REVERT: A 752 GLN cc_start: 0.9022 (tm-30) cc_final: 0.8813 (tm-30) REVERT: A 772 ASP cc_start: 0.8638 (m-30) cc_final: 0.7859 (m-30) REVERT: A 797 PHE cc_start: 0.8505 (m-10) cc_final: 0.8278 (m-10) REVERT: A 999 GLN cc_start: 0.9046 (tp-100) cc_final: 0.8685 (tp-100) REVERT: A 1003 THR cc_start: 0.8851 (m) cc_final: 0.8424 (m) REVERT: A 1016 ARG cc_start: 0.9041 (ptm160) cc_final: 0.8779 (ptp-170) REVERT: A 1108 GLU cc_start: 0.9279 (tt0) cc_final: 0.8738 (tm-30) REVERT: A 1110 GLN cc_start: 0.9502 (mt0) cc_final: 0.9079 (tp40) REVERT: A 1111 ILE cc_start: 0.8899 (mm) cc_final: 0.7995 (mm) REVERT: H 55 TYR cc_start: 0.9502 (p90) cc_final: 0.9279 (p90) REVERT: J 71 MET cc_start: 0.5333 (ppp) cc_final: 0.4594 (ppp) REVERT: J 91 ASP cc_start: 0.5903 (m-30) cc_final: 0.5660 (m-30) REVERT: K 90 LEU cc_start: 0.8402 (tp) cc_final: 0.8029 (mt) outliers start: 0 outliers final: 0 residues processed: 287 average time/residue: 0.3759 time to fit residues: 181.8064 Evaluate side-chains 207 residues out of total 3334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 3.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 222 optimal weight: 9.9990 chunk 358 optimal weight: 40.0000 chunk 218 optimal weight: 10.0000 chunk 169 optimal weight: 0.8980 chunk 248 optimal weight: 0.3980 chunk 375 optimal weight: 50.0000 chunk 345 optimal weight: 20.0000 chunk 299 optimal weight: 2.9990 chunk 31 optimal weight: 20.0000 chunk 231 optimal weight: 0.9980 chunk 183 optimal weight: 0.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 687 GLN ** B 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 898 GLN B 904 ASN ** B1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 962 GLN ** C1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 318 GLN ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 GLN ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.6443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 31204 Z= 0.191 Angle : 0.616 11.213 42481 Z= 0.321 Chirality : 0.044 0.304 4944 Planarity : 0.004 0.044 5405 Dihedral : 5.056 35.463 5199 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 17.60 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.20 % Favored : 94.67 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % 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: -0.94 (0.13), residues: 3753 helix: 0.27 (0.20), residues: 658 sheet: -0.07 (0.16), residues: 969 loop : -1.18 (0.13), residues: 2126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 64 HIS 0.024 0.002 HIS C1045 PHE 0.018 0.002 PHE C 272 TYR 0.023 0.001 TYR L 87 ARG 0.004 0.000 ARG L 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 3334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 294 time to evaluate : 3.752 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: 0.7782 (m-80) cc_final: 0.6953 (m-10) REVERT: B 272 PHE cc_start: 0.8557 (m-80) cc_final: 0.8024 (m-10) REVERT: B 315 PHE cc_start: 0.7726 (t80) cc_final: 0.7506 (t80) REVERT: B 762 ARG cc_start: 0.8932 (ttm110) cc_final: 0.8629 (ttm110) REVERT: B 866 MET cc_start: 0.9463 (mpp) cc_final: 0.9148 (mmm) REVERT: B 950 ASN cc_start: 0.9428 (t0) cc_final: 0.9119 (t0) REVERT: B 957 ASN cc_start: 0.9121 (m110) cc_final: 0.8839 (m110) REVERT: B 985 GLU cc_start: 0.8475 (mp0) cc_final: 0.8262 (mp0) REVERT: B 999 GLN cc_start: 0.9460 (tp-100) cc_final: 0.9112 (tp-100) REVERT: B 1078 ILE cc_start: 0.8697 (mt) cc_final: 0.8391 (mm) REVERT: B 1099 TRP cc_start: 0.8498 (m100) cc_final: 0.7882 (m100) REVERT: B 1124 ASP cc_start: 0.7104 (p0) cc_final: 0.6878 (p0) REVERT: C 168 PHE cc_start: 0.8908 (t80) cc_final: 0.8511 (t80) REVERT: C 223 LEU cc_start: 0.9128 (mp) cc_final: 0.8663 (tp) REVERT: C 348 TYR cc_start: 0.9252 (p90) cc_final: 0.8708 (p90) REVERT: C 817 ASP cc_start: 0.8850 (m-30) cc_final: 0.8609 (m-30) REVERT: C 866 MET cc_start: 0.9027 (mtt) cc_final: 0.8564 (mtt) REVERT: C 916 ASN cc_start: 0.9407 (t0) cc_final: 0.9175 (t0) REVERT: C 918 LYS cc_start: 0.9377 (mttt) cc_final: 0.8995 (mppt) REVERT: C 930 LYS cc_start: 0.9495 (mptt) cc_final: 0.9231 (mttt) REVERT: C 989 GLN cc_start: 0.8791 (mm-40) cc_final: 0.8361 (mp10) REVERT: C 1007 GLN cc_start: 0.9361 (mp10) cc_final: 0.9066 (mp10) REVERT: A 55 PHE cc_start: 0.7345 (m-10) cc_final: 0.7018 (m-10) REVERT: A 694 MET cc_start: 0.8380 (ppp) cc_final: 0.7905 (ppp) REVERT: A 744 THR cc_start: 0.9594 (p) cc_final: 0.9375 (p) REVERT: A 869 GLN cc_start: 0.9098 (mt0) cc_final: 0.8630 (tm-30) REVERT: A 957 ASN cc_start: 0.9357 (t0) cc_final: 0.8791 (p0) REVERT: A 999 GLN cc_start: 0.9001 (tp-100) cc_final: 0.8592 (tp-100) REVERT: A 1003 THR cc_start: 0.8726 (m) cc_final: 0.8302 (m) REVERT: A 1108 GLU cc_start: 0.9191 (tt0) cc_final: 0.8620 (tm-30) REVERT: J 71 MET cc_start: 0.5120 (ppp) cc_final: 0.4399 (ppp) REVERT: K 90 LEU cc_start: 0.8335 (tp) cc_final: 0.8028 (mt) outliers start: 0 outliers final: 0 residues processed: 294 average time/residue: 0.3852 time to fit residues: 189.3737 Evaluate side-chains 213 residues out of total 3334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 3.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 237 optimal weight: 4.9990 chunk 318 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 275 optimal weight: 5.9990 chunk 44 optimal weight: 40.0000 chunk 83 optimal weight: 9.9990 chunk 299 optimal weight: 3.9990 chunk 125 optimal weight: 8.9990 chunk 307 optimal weight: 0.6980 chunk 37 optimal weight: 50.0000 chunk 55 optimal weight: 30.0000 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 164 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 898 GLN ** B1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 ASN ** C 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 932 GLN ** C1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 GLN ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.088194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.060946 restraints weight = 206475.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.062447 restraints weight = 126881.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.062419 restraints weight = 87645.290| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.6787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 31204 Z= 0.315 Angle : 0.688 11.542 42481 Z= 0.366 Chirality : 0.045 0.296 4944 Planarity : 0.005 0.068 5405 Dihedral : 5.291 36.863 5199 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 24.76 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.77 % Favored : 93.07 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.13), residues: 3753 helix: -0.23 (0.19), residues: 653 sheet: -0.20 (0.17), residues: 965 loop : -1.22 (0.13), residues: 2135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 883 HIS 0.026 0.002 HIS C1045 PHE 0.038 0.002 PHE C1049 TYR 0.030 0.002 TYR B1044 ARG 0.010 0.001 ARG C1036 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6451.26 seconds wall clock time: 119 minutes 33.63 seconds (7173.63 seconds total)