Starting phenix.real_space_refine on Thu Mar 21 02:21:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q9g_13869/03_2024/7q9g_13869.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q9g_13869/03_2024/7q9g_13869.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q9g_13869/03_2024/7q9g_13869.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q9g_13869/03_2024/7q9g_13869.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q9g_13869/03_2024/7q9g_13869.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q9g_13869/03_2024/7q9g_13869.pdb" } resolution = 3.3 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= 0.004 sd= 0.034 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 128 5.16 5 C 18420 2.51 5 N 4771 2.21 5 O 5654 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 28973 Number of models: 1 Model: "" Number of chains: 22 Chain: "B" Number of atoms: 8281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1060, 8281 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 54, 'TRANS': 1005} Chain breaks: 6 Chain: "C" Number of atoms: 8273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1059, 8273 Classifications: {'peptide': 1059} Link IDs: {'PTRANS': 53, 'TRANS': 1005} Chain breaks: 6 Chain: "A" Number of atoms: 8287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8287 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 54, 'TRANS': 1006} Chain breaks: 6 Chain: "H" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 889 Classifications: {'peptide': 119} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 114} Chain: "L" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 98} Chain: "E" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 889 Classifications: {'peptide': 119} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 114} Chain: "F" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 98} 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: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 15.18, per 1000 atoms: 0.52 Number of scatterers: 28973 At special positions: 0 Unit cell: (150.384, 159.783, 215.454, 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 128 16.00 O 5654 8.00 N 4771 7.00 C 18420 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, symmetry=0 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.03 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " distance=2.03 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 587 " distance=2.03 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.03 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.03 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS C 376 " - pdb=" SG CYS C 429 " distance=2.03 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 522 " distance=2.03 Simple disulfide: pdb=" SG CYS C 477 " - pdb=" SG CYS C 485 " distance=2.03 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 587 " distance=2.03 Simple disulfide: pdb=" SG CYS C 614 " - pdb=" SG CYS C 646 " distance=2.03 Simple disulfide: pdb=" SG CYS C 659 " - pdb=" SG CYS C 668 " distance=2.03 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 757 " distance=2.03 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.03 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=2.03 Simple disulfide: pdb=" SG CYS 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=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 89 " 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 J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " NAG-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 J 1 " - " ASN B1131 " " NAG K 1 " - " ASN C 714 " " NAG M 1 " - " ASN C 798 " " NAG N 1 " - " ASN C1095 " " NAG O 1 " - " ASN C1131 " " NAG P 1 " - " ASN A 714 " " NAG Q 1 " - " ASN A 798 " " NAG R 1 " - " ASN A1095 " " NAG S 1 " - " ASN A1131 " Time building additional restraints: 11.70 Conformation dependent library (CDL) restraints added in 5.1 seconds 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6738 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 63 sheets defined 22.6% alpha, 33.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.92 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: 3.803A pdb=" N ASN B 385 " --> pdb=" O THR B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 407 Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 435 through 440 Processing helix chain 'B' and resid 734 through 740 Processing helix chain 'B' and resid 743 through 752 removed outlier: 3.934A 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: 3.835A pdb=" N ALA B 887 " --> pdb=" O TRP B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 906 removed outlier: 3.602A pdb=" N ILE B 906 " --> pdb=" O ARG B 902 " (cutoff:3.500A) Processing helix chain 'B' and resid 909 through 916 removed outlier: 4.224A pdb=" N LEU B 913 " --> pdb=" O THR B 909 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 938 Processing helix chain 'B' and resid 942 through 962 Processing helix chain 'B' and resid 963 through 965 No H-bonds generated for 'chain 'B' and resid 963 through 965' Processing helix chain 'B' and resid 973 through 981 Processing helix chain 'B' and resid 982 through 1029 removed outlier: 4.466A pdb=" N VAL B 988 " --> pdb=" O PRO B 984 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLN B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG B 992 " --> pdb=" O VAL B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1137 through 1144 removed outlier: 3.954A 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 387 removed outlier: 3.781A pdb=" N ASN C 385 " --> pdb=" O THR C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 407 removed outlier: 4.095A 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 734 through 740 Processing helix chain 'C' and resid 743 through 751 Processing helix chain 'C' and resid 752 through 754 No H-bonds generated for 'chain 'C' and resid 752 through 754' Processing helix chain 'C' and resid 755 through 780 removed outlier: 3.671A pdb=" N GLN C 759 " --> pdb=" O SER C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 823 Processing helix chain 'C' and resid 863 through 882 Processing helix chain 'C' and resid 883 through 887 Processing helix chain 'C' and resid 894 through 906 Processing helix chain 'C' and resid 910 through 916 Processing helix chain 'C' and resid 916 through 938 Processing helix chain 'C' and resid 942 through 962 Processing helix chain 'C' and resid 963 through 965 No H-bonds generated for 'chain 'C' and resid 963 through 965' Processing helix chain 'C' and resid 973 through 981 Processing helix chain 'C' and resid 982 through 1029 removed outlier: 4.408A pdb=" N VAL C 988 " --> pdb=" O PRO C 984 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLN C 989 " --> pdb=" O GLU C 985 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG C 992 " --> pdb=" O VAL C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1144 removed outlier: 3.751A 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 386 removed outlier: 3.651A pdb=" N LEU A 384 " --> pdb=" O PRO A 381 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASN A 385 " --> pdb=" O THR A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 435 through 440 Processing helix chain 'A' and resid 734 through 740 Processing helix chain 'A' and resid 743 through 752 removed outlier: 3.803A pdb=" N GLN A 752 " --> pdb=" O ASN A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 780 Processing helix chain 'A' and resid 813 through 823 Processing helix chain 'A' and resid 863 through 882 Processing helix chain 'A' and resid 883 through 888 removed outlier: 3.632A pdb=" N ALA A 887 " --> pdb=" O TRP A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 907 Processing helix chain 'A' and resid 910 through 938 removed outlier: 3.507A pdb=" N TYR A 914 " --> pdb=" O GLN A 910 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LYS A 918 " --> pdb=" O TYR A 914 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LEU A 919 " --> pdb=" O GLU A 915 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR A 938 " --> pdb=" O SER A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 941 No H-bonds generated for 'chain 'A' and resid 939 through 941' Processing helix chain 'A' and resid 942 through 962 removed outlier: 3.532A pdb=" N VAL A 948 " --> pdb=" O LYS A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 965 No H-bonds generated for 'chain 'A' and resid 963 through 965' Processing helix chain 'A' and resid 973 through 981 removed outlier: 3.612A pdb=" N ILE A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 1029 removed outlier: 4.874A pdb=" N VAL A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLN A 989 " --> pdb=" O GLU A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1144 removed outlier: 3.673A pdb=" N GLU A1141 " --> pdb=" O PRO A1137 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'L' and resid 30 through 32 No H-bonds generated for 'chain 'L' and resid 30 through 32' Processing helix chain 'L' and resid 80 through 84 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 86 through 90 Processing helix chain 'F' and resid 30 through 32 No H-bonds generated for 'chain 'F' and resid 30 through 32' Processing helix chain 'F' and resid 80 through 84 Processing sheet with id=AA1, first strand: chain 'B' and resid 21 through 22 Processing sheet with id=AA2, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.626A pdb=" N ASN B 61 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N TYR B 266 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.981A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.005A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 11.277A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 9.877A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.359A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.655A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.413A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 9.548A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 10.863A pdb=" N PHE B 140 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N SER B 155 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N GLY B 142 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N MET B 153 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N TYR B 144 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N SER B 151 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.005A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N SER B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU B 141 " --> pdb=" O SER B 244 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL B 143 " --> pdb=" O LEU B 246 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 308 through 316 removed outlier: 5.416A pdb=" N ILE B 309 " --> pdb=" O THR B 596 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N THR B 596 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N GLN B 311 " --> pdb=" O VAL B 594 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL B 594 " --> pdb=" O GLN B 311 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLY B 591 " --> pdb=" O GLN B 610 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 322 through 325 removed outlier: 6.778A pdb=" N PHE B 562 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 351 through 355 Processing sheet with id=AB1, first strand: chain 'B' and resid 358 through 359 removed outlier: 6.738A pdb=" N CYS B 358 " --> pdb=" O CYS B 522 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AB3, first strand: chain 'B' and resid 470 through 471 Processing sheet with id=AB4, first strand: chain 'B' and resid 661 through 664 removed outlier: 6.509A pdb=" N ALA B 669 " --> pdb=" O PRO B 662 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 699 through 701 removed outlier: 3.765A pdb=" N LYS C 787 " --> pdb=" O ASN B 700 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 709 through 712 Processing sheet with id=AB7, first strand: chain 'B' and resid 715 through 725 removed outlier: 6.935A pdb=" N GLY B1056 " --> pdb=" O SER B1052 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N SER B1052 " --> pdb=" O GLY B1056 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL B1058 " --> pdb=" O PRO B1050 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU B1060 " --> pdb=" O SER B1048 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N SER B1048 " --> pdb=" O LEU B1060 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL B1062 " --> pdb=" O LEU B1046 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 730 through 733 removed outlier: 4.371A pdb=" N LYS B 730 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 785 through 787 removed outlier: 5.831A pdb=" N ILE B 785 " --> pdb=" O ASN A 700 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 1117 through 1122 removed outlier: 4.863A pdb=" N ALA B1084 " --> pdb=" O SER B1120 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 21 through 22 Processing sheet with id=AC3, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.110A pdb=" N ASN C 61 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N TYR C 266 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA C 260 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.731A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.520A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 11.373A pdb=" N VAL C 126 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 9.893A pdb=" N GLU C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 11.278A pdb=" N ILE C 128 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N THR C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N VAL C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ASN C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 11.419A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 9.531A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 10.918A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N GLY C 142 " --> pdb=" O MET C 153 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N MET C 153 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N TYR C 144 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N SER C 151 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.520A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N TYR C 145 " --> pdb=" O LEU C 246 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 308 through 316 removed outlier: 5.413A pdb=" N ILE C 309 " --> pdb=" O THR C 596 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N THR C 596 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 5.956A 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: 4.165A pdb=" N GLY C 591 " --> pdb=" O GLN C 610 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 322 through 325 removed outlier: 5.225A pdb=" N ASP C 571 " --> pdb=" O ILE C 584 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N PHE C 562 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 351 through 355 removed outlier: 3.852A pdb=" N ASN C 391 " --> pdb=" O GLU C 513 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 358 through 359 removed outlier: 6.599A pdb=" N CYS C 358 " --> pdb=" O CYS C 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 449 through 451 Processing sheet with id=AD3, first strand: chain 'C' and resid 470 through 471 Processing sheet with id=AD4, first strand: chain 'C' and resid 651 through 652 removed outlier: 6.587A pdb=" N ALA C 669 " --> pdb=" O PRO C 662 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 708 through 712 Processing sheet with id=AD6, first strand: chain 'C' and resid 715 through 725 removed outlier: 7.093A pdb=" N GLY C1056 " --> pdb=" O SER C1052 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N SER C1052 " --> pdb=" O GLY C1056 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL C1058 " --> pdb=" O PRO C1050 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU C1060 " --> pdb=" O SER C1048 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N SER C1048 " --> pdb=" O LEU C1060 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL C1062 " --> pdb=" O LEU C1046 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 731 through 733 Processing sheet with id=AD8, first strand: chain 'C' and resid 1117 through 1122 removed outlier: 4.584A pdb=" N ALA C1084 " --> pdb=" O SER C1120 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 1091 through 1094 Processing sheet with id=AE1, first strand: chain 'A' and resid 21 through 22 Processing sheet with id=AE2, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.726A pdb=" N ASN A 61 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N TYR A 266 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA A 260 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.865A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.551A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 11.292A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.789A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.210A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.327A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 9.412A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 10.819A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 8.675A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N GLY A 142 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N MET A 153 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N TYR A 144 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N SER A 151 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.551A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N SER A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU A 141 " --> pdb=" O SER A 244 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL A 143 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 308 through 316 removed outlier: 5.493A pdb=" N ILE A 309 " --> pdb=" O THR A 596 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N THR A 596 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N GLN A 311 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL A 594 " --> pdb=" O GLN A 311 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY A 591 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 322 through 325 Processing sheet with id=AE8, first strand: chain 'A' and resid 351 through 355 Processing sheet with id=AE9, first strand: chain 'A' and resid 358 through 359 removed outlier: 6.643A pdb=" N CYS A 358 " --> pdb=" O CYS A 522 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AF2, first strand: chain 'A' and resid 470 through 471 Processing sheet with id=AF3, first strand: chain 'A' and resid 651 through 652 removed outlier: 6.427A pdb=" N ALA A 669 " --> pdb=" O PRO A 662 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'A' and resid 708 through 712 Processing sheet with id=AF5, first strand: chain 'A' and resid 715 through 725 removed outlier: 7.069A pdb=" N GLY A1056 " --> pdb=" O SER A1052 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N SER A1052 " --> pdb=" O GLY A1056 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL A1058 " --> pdb=" O PRO A1050 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU A1060 " --> pdb=" O SER A1048 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N SER A1048 " --> pdb=" O LEU A1060 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL A1062 " --> pdb=" O LEU A1046 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'A' and resid 730 through 733 removed outlier: 4.589A pdb=" N LYS A 730 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'A' and resid 1117 through 1122 removed outlier: 4.520A pdb=" N ALA A1084 " --> pdb=" O SER A1120 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'A' and resid 1091 through 1094 Processing sheet with id=AF9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AG1, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.220A pdb=" N GLY H 10 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AG3, first strand: chain 'L' and resid 10 through 13 removed outlier: 5.862A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA L 85 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 10 through 13 removed outlier: 5.862A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA L 85 " --> pdb=" O VAL L 104 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AG6, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.245A pdb=" N GLY E 10 " --> pdb=" O THR E 116 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N MET E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N VAL E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 4 through 7 removed outlier: 5.044A pdb=" N THR F 70 " --> pdb=" O ALA F 25 " (cutoff:3.500A) removed outlier: 9.331A pdb=" N GLN F 27 " --> pdb=" O SER F 68 " (cutoff:3.500A) removed outlier: 9.447A pdb=" N SER F 68 " --> pdb=" O GLN F 27 " (cutoff:3.500A) removed outlier: 11.349A pdb=" N VAL F 29 " --> pdb=" O SER F 66 " (cutoff:3.500A) removed outlier: 11.558A pdb=" N SER F 66 " --> pdb=" O VAL F 29 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'F' and resid 10 through 13 removed outlier: 5.873A pdb=" N LEU F 11 " --> pdb=" O ASP F 105 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N LEU F 34 " --> pdb=" O TYR F 50 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N TYR F 50 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TRP F 36 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'F' and resid 10 through 13 removed outlier: 5.873A pdb=" N LEU F 11 " --> pdb=" O ASP F 105 " (cutoff:3.500A) 1243 hydrogen bonds defined for protein. 3354 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: 21.51 Time building geometry restraints manager: 12.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9232 1.34 - 1.46: 7379 1.46 - 1.58: 12859 1.58 - 1.70: 0 1.70 - 1.82: 164 Bond restraints: 29634 Sorted by residual: bond pdb=" N GLU E 1 " pdb=" CA GLU E 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.11e+00 bond pdb=" N ASP F 1 " pdb=" CA ASP F 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.99e+00 bond pdb=" N GLU H 1 " pdb=" CA GLU H 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.94e+00 bond pdb=" N ASP L 1 " pdb=" CA ASP L 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.84e+00 bond pdb=" C1 NAG A1308 " pdb=" O5 NAG A1308 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.72e+00 ... (remaining 29629 not shown) Histogram of bond angle deviations from ideal: 100.11 - 106.89: 927 106.89 - 113.67: 16408 113.67 - 120.44: 10675 120.44 - 127.22: 12021 127.22 - 134.00: 288 Bond angle restraints: 40319 Sorted by residual: angle pdb=" N ASP L 93 " pdb=" CA ASP L 93 " pdb=" C ASP L 93 " ideal model delta sigma weight residual 112.93 109.32 3.61 1.33e+00 5.65e-01 7.35e+00 angle pdb=" N ASP F 93 " pdb=" CA ASP F 93 " pdb=" C ASP F 93 " ideal model delta sigma weight residual 112.93 109.41 3.52 1.33e+00 5.65e-01 6.99e+00 angle pdb=" CA GLY A 413 " pdb=" C GLY A 413 " pdb=" N ASN A 414 " ideal model delta sigma weight residual 114.52 117.27 -2.75 1.09e+00 8.42e-01 6.35e+00 angle pdb=" N ILE B 407 " pdb=" CA ILE B 407 " pdb=" C ILE B 407 " ideal model delta sigma weight residual 106.21 108.82 -2.61 1.07e+00 8.73e-01 5.94e+00 angle pdb=" N GLY B 590 " pdb=" CA GLY B 590 " pdb=" C GLY B 590 " ideal model delta sigma weight residual 110.63 113.76 -3.13 1.45e+00 4.76e-01 4.67e+00 ... (remaining 40314 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 17496 17.73 - 35.47: 565 35.47 - 53.20: 164 53.20 - 70.94: 42 70.94 - 88.67: 9 Dihedral angle restraints: 18276 sinusoidal: 7763 harmonic: 10513 Sorted by residual: dihedral pdb=" CA THR A 596 " pdb=" C THR A 596 " pdb=" N PRO A 597 " pdb=" CA PRO A 597 " ideal model delta harmonic sigma weight residual 180.00 161.58 18.42 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CB CYS C1079 " pdb=" SG CYS C1079 " pdb=" SG CYS C1123 " pdb=" CB CYS C1123 " ideal model delta sinusoidal sigma weight residual -86.00 -115.14 29.14 1 1.00e+01 1.00e-02 1.21e+01 dihedral pdb=" CA THR B 596 " pdb=" C THR B 596 " pdb=" N PRO B 597 " pdb=" CA PRO B 597 " ideal model delta harmonic sigma weight residual 180.00 162.78 17.22 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 18273 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2748 0.028 - 0.057: 1259 0.057 - 0.085: 264 0.085 - 0.113: 312 0.113 - 0.142: 110 Chirality restraints: 4693 Sorted by residual: chirality pdb=" CA ILE C 119 " pdb=" N ILE C 119 " pdb=" C ILE C 119 " pdb=" CB ILE C 119 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.03e-01 chirality pdb=" CA ILE B 128 " pdb=" N ILE B 128 " pdb=" C ILE B 128 " pdb=" CB ILE B 128 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.92e-01 chirality pdb=" CA ILE C 203 " pdb=" N ILE C 203 " pdb=" C ILE C 203 " pdb=" CB ILE C 203 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.72e-01 ... (remaining 4690 not shown) Planarity restraints: 5193 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A1086 " 0.022 5.00e-02 4.00e+02 3.38e-02 1.83e+00 pdb=" N PRO A1087 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO A1087 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A1087 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 957 " 0.007 2.00e-02 2.50e+03 1.35e-02 1.81e+00 pdb=" C ASN A 957 " -0.023 2.00e-02 2.50e+03 pdb=" O ASN A 957 " 0.009 2.00e-02 2.50e+03 pdb=" N THR A 958 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 952 " 0.007 2.00e-02 2.50e+03 1.33e-02 1.77e+00 pdb=" C ASN B 952 " -0.023 2.00e-02 2.50e+03 pdb=" O ASN B 952 " 0.009 2.00e-02 2.50e+03 pdb=" N ALA B 953 " 0.008 2.00e-02 2.50e+03 ... (remaining 5190 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 320 2.61 - 3.18: 25687 3.18 - 3.75: 43817 3.75 - 4.33: 64123 4.33 - 4.90: 107060 Nonbonded interactions: 241007 Sorted by model distance: nonbonded pdb=" OD1 ASN A 537 " pdb=" OG1 THR A 546 " model vdw 2.034 2.440 nonbonded pdb=" OD2 ASP B 575 " pdb=" OG1 THR B 578 " model vdw 2.039 2.440 nonbonded pdb=" OG1 THR B 109 " pdb=" OD1 ASP B 111 " model vdw 2.044 2.440 nonbonded pdb=" O ASN B 436 " pdb=" OG SER B 440 " model vdw 2.070 2.440 nonbonded pdb=" O ASN A 436 " pdb=" OG SER A 440 " model vdw 2.079 2.440 ... (remaining 241002 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 617 or resid 638 through 1144 or resid 1301 thr \ ough 1308)) selection = (chain 'B' and (resid 13 through 617 or resid 638 through 1144 or resid 1301 thr \ ough 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 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } ncs_group { reference = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 35.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 17.790 Check model and map are aligned: 1.260 Set scattering table: 0.000 Process input model: 88.940 Find NCS groups from input model: 2.390 Set up NCS constraints: 0.360 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 149.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 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 : 0.003 0.034 29634 Z= 0.221 Angle : 0.497 4.852 40319 Z= 0.256 Chirality : 0.043 0.142 4693 Planarity : 0.003 0.034 5153 Dihedral : 10.010 88.670 11400 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.67 % Allowed : 3.46 % Favored : 95.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % 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: -0.07 (0.14), residues: 3582 helix: 0.71 (0.21), residues: 701 sheet: 0.03 (0.16), residues: 938 loop : -0.28 (0.14), residues: 1943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 883 HIS 0.003 0.001 HIS A1061 PHE 0.014 0.001 PHE C 756 TYR 0.014 0.001 TYR B1064 ARG 0.002 0.000 ARG B1016 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 353 time to evaluate : 3.036 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: B 96 GLU cc_start: 0.5596 (OUTLIER) cc_final: 0.5357 (pm20) REVERT: B 133 PHE cc_start: 0.7463 (m-80) cc_final: 0.7162 (m-80) REVERT: B 205 SER cc_start: 0.8601 (p) cc_final: 0.7868 (p) REVERT: B 820 PHE cc_start: 0.7456 (m-80) cc_final: 0.7210 (m-10) REVERT: C 562 PHE cc_start: 0.7277 (p90) cc_final: 0.6066 (p90) REVERT: C 564 ARG cc_start: 0.5982 (mtt-85) cc_final: 0.5732 (mtt-85) REVERT: C 853 ASN cc_start: 0.8341 (t0) cc_final: 0.8059 (t0) REVERT: A 86 PHE cc_start: 0.8402 (t80) cc_final: 0.7757 (t80) REVERT: A 281 THR cc_start: 0.8339 (m) cc_final: 0.8133 (p) REVERT: H 80 LEU cc_start: 0.5504 (tp) cc_final: 0.4466 (tp) REVERT: L 4 MET cc_start: -0.0224 (mmt) cc_final: -0.1239 (mtm) REVERT: F 4 MET cc_start: -0.1786 (mmt) cc_final: -0.3123 (mtt) outliers start: 21 outliers final: 11 residues processed: 372 average time/residue: 0.4100 time to fit residues: 242.2844 Evaluate side-chains 211 residues out of total 3146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 199 time to evaluate : 3.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 263 TYR Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 1119 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 303 optimal weight: 2.9990 chunk 272 optimal weight: 3.9990 chunk 150 optimal weight: 0.0970 chunk 92 optimal weight: 1.9990 chunk 183 optimal weight: 0.2980 chunk 145 optimal weight: 50.0000 chunk 281 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 chunk 171 optimal weight: 0.6980 chunk 209 optimal weight: 0.0570 chunk 326 optimal weight: 30.0000 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 ASN B 207 HIS B 759 GLN B 801 GLN ** B1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1103 GLN ** C 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 801 GLN C 869 GLN C 932 GLN C 975 ASN A 207 HIS ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 752 GLN ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 911 ASN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 29634 Z= 0.169 Angle : 0.531 11.475 40319 Z= 0.274 Chirality : 0.043 0.203 4693 Planarity : 0.004 0.067 5153 Dihedral : 6.746 75.165 5017 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.62 % Allowed : 7.47 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % 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: 0.35 (0.14), residues: 3582 helix: 1.61 (0.19), residues: 709 sheet: 0.28 (0.16), residues: 961 loop : -0.26 (0.15), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 105 HIS 0.014 0.001 HIS B 207 PHE 0.017 0.001 PHE B 326 TYR 0.020 0.001 TYR B1064 ARG 0.006 0.000 ARG A 992 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 3146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 220 time to evaluate : 3.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 820 PHE cc_start: 0.7417 (m-80) cc_final: 0.7182 (m-10) REVERT: C 160 TYR cc_start: 0.8078 (p90) cc_final: 0.7875 (p90) REVERT: C 229 LEU cc_start: 0.7933 (mt) cc_final: 0.7452 (mp) REVERT: C 556 PHE cc_start: 0.7817 (OUTLIER) cc_final: 0.7549 (t80) REVERT: C 562 PHE cc_start: 0.7274 (p90) cc_final: 0.6633 (p90) REVERT: C 901 TYR cc_start: 0.7631 (m-10) cc_final: 0.7254 (m-10) REVERT: A 86 PHE cc_start: 0.8480 (t80) cc_final: 0.7854 (t80) REVERT: H 34 MET cc_start: 0.7762 (mmm) cc_final: 0.7427 (mmm) REVERT: L 4 MET cc_start: -0.0117 (mmt) cc_final: -0.1115 (mtm) REVERT: F 4 MET cc_start: -0.1950 (mmt) cc_final: -0.3281 (mtt) outliers start: 51 outliers final: 27 residues processed: 258 average time/residue: 0.3624 time to fit residues: 157.5125 Evaluate side-chains 205 residues out of total 3146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 177 time to evaluate : 3.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 588 SER Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 1115 ASP Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 263 TYR Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 556 PHE Chi-restraints excluded: chain C residue 587 CYS Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 1102 THR Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 614 CYS Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1139 GLN Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain L residue 88 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 181 optimal weight: 0.9990 chunk 101 optimal weight: 0.4980 chunk 271 optimal weight: 1.9990 chunk 221 optimal weight: 20.0000 chunk 89 optimal weight: 2.9990 chunk 326 optimal weight: 9.9990 chunk 352 optimal weight: 20.0000 chunk 290 optimal weight: 3.9990 chunk 323 optimal weight: 50.0000 chunk 111 optimal weight: 0.7980 chunk 262 optimal weight: 0.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 748 ASN B 923 GLN B 932 GLN C 561 GLN C 610 GLN C 952 ASN ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29634 Z= 0.201 Angle : 0.509 11.235 40319 Z= 0.262 Chirality : 0.043 0.215 4693 Planarity : 0.003 0.054 5153 Dihedral : 5.970 57.971 5008 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.13 % Allowed : 7.91 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.14), residues: 3582 helix: 1.91 (0.20), residues: 699 sheet: 0.40 (0.16), residues: 949 loop : -0.31 (0.14), residues: 1934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP L 36 HIS 0.003 0.001 HIS B 207 PHE 0.022 0.001 PHE C 106 TYR 0.020 0.001 TYR B1064 ARG 0.009 0.000 ARG C 564 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 3146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 190 time to evaluate : 3.174 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: C 229 LEU cc_start: 0.7946 (mt) cc_final: 0.7483 (mp) REVERT: C 556 PHE cc_start: 0.7802 (OUTLIER) cc_final: 0.7491 (t80) REVERT: C 901 TYR cc_start: 0.7673 (m-10) cc_final: 0.7332 (m-10) REVERT: A 86 PHE cc_start: 0.8489 (t80) cc_final: 0.7893 (t80) REVERT: F 4 MET cc_start: -0.2035 (mmt) cc_final: -0.3316 (mtt) outliers start: 67 outliers final: 42 residues processed: 240 average time/residue: 0.3603 time to fit residues: 146.7573 Evaluate side-chains 210 residues out of total 3146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 167 time to evaluate : 3.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 994 ILE Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1115 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 263 TYR Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 556 PHE Chi-restraints excluded: chain C residue 570 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 587 CYS Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 952 ASN Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 1014 GLU Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1102 THR Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 777 GLU Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 966 ASN Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain L residue 88 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 322 optimal weight: 0.6980 chunk 245 optimal weight: 30.0000 chunk 169 optimal weight: 5.9990 chunk 36 optimal weight: 30.0000 chunk 155 optimal weight: 20.0000 chunk 219 optimal weight: 20.0000 chunk 327 optimal weight: 30.0000 chunk 347 optimal weight: 30.0000 chunk 171 optimal weight: 0.9990 chunk 310 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 923 GLN B 975 ASN C 610 GLN C 761 ASN C 952 ASN C 989 GLN ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 752 GLN ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 29634 Z= 0.318 Angle : 0.535 10.199 40319 Z= 0.275 Chirality : 0.043 0.232 4693 Planarity : 0.004 0.052 5153 Dihedral : 5.624 58.852 5007 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.42 % Allowed : 8.65 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.14), residues: 3582 helix: 1.89 (0.20), residues: 662 sheet: 0.35 (0.16), residues: 959 loop : -0.35 (0.14), residues: 1961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP L 36 HIS 0.005 0.001 HIS A1061 PHE 0.016 0.001 PHE B 65 TYR 0.022 0.001 TYR B1064 ARG 0.006 0.000 ARG C 564 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 3146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 175 time to evaluate : 3.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 THR cc_start: 0.7446 (m) cc_final: 0.7171 (p) REVERT: C 556 PHE cc_start: 0.7859 (OUTLIER) cc_final: 0.7528 (t80) REVERT: C 742 ASP cc_start: 0.6918 (OUTLIER) cc_final: 0.6717 (p0) REVERT: C 901 TYR cc_start: 0.7679 (m-10) cc_final: 0.7444 (m-10) REVERT: A 86 PHE cc_start: 0.8492 (t80) cc_final: 0.7990 (t80) REVERT: A 177 MET cc_start: -0.5220 (ttt) cc_final: -0.6684 (mmt) REVERT: H 33 TYR cc_start: 0.2313 (m-80) cc_final: 0.1742 (m-80) REVERT: F 4 MET cc_start: -0.1999 (mmt) cc_final: -0.3250 (mtt) outliers start: 76 outliers final: 56 residues processed: 232 average time/residue: 0.3646 time to fit residues: 144.4156 Evaluate side-chains 221 residues out of total 3146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 163 time to evaluate : 3.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 994 ILE Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1110 GLN Chi-restraints excluded: chain B residue 1115 ASP Chi-restraints excluded: chain B residue 1120 SER Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 263 TYR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 556 PHE Chi-restraints excluded: chain C residue 570 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 587 CYS Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 742 ASP Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 964 SER Chi-restraints excluded: chain C residue 1014 GLU Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1102 THR Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 646 CYS Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 777 GLU Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 966 ASN Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain L residue 88 TYR Chi-restraints excluded: chain F residue 93 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 289 optimal weight: 0.6980 chunk 196 optimal weight: 0.9990 chunk 5 optimal weight: 8.9990 chunk 258 optimal weight: 7.9990 chunk 143 optimal weight: 50.0000 chunk 296 optimal weight: 2.9990 chunk 239 optimal weight: 3.9990 chunk 0 optimal weight: 40.0000 chunk 177 optimal weight: 2.9990 chunk 311 optimal weight: 0.5980 chunk 87 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 923 GLN ** B1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 952 ASN ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29634 Z= 0.215 Angle : 0.501 9.554 40319 Z= 0.256 Chirality : 0.042 0.190 4693 Planarity : 0.003 0.049 5153 Dihedral : 5.173 58.582 5005 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.10 % Allowed : 9.79 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % 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: 0.39 (0.14), residues: 3582 helix: 1.83 (0.20), residues: 675 sheet: 0.41 (0.16), residues: 948 loop : -0.34 (0.14), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 36 HIS 0.003 0.001 HIS L 91 PHE 0.015 0.001 PHE A 140 TYR 0.021 0.001 TYR H 52 ARG 0.005 0.000 ARG C 564 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 3146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 179 time to evaluate : 3.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.7840 (mmm) cc_final: 0.7519 (mmm) REVERT: B 177 MET cc_start: -0.4524 (ttt) cc_final: -0.5561 (tpt) REVERT: C 556 PHE cc_start: 0.7855 (OUTLIER) cc_final: 0.7555 (t80) REVERT: C 742 ASP cc_start: 0.6972 (OUTLIER) cc_final: 0.6768 (p0) REVERT: C 901 TYR cc_start: 0.7665 (m-10) cc_final: 0.7435 (m-10) REVERT: A 86 PHE cc_start: 0.8469 (t80) cc_final: 0.7973 (t80) REVERT: A 177 MET cc_start: -0.5374 (ttt) cc_final: -0.6712 (mmt) REVERT: F 4 MET cc_start: -0.1977 (mmt) cc_final: -0.3226 (mtt) outliers start: 66 outliers final: 48 residues processed: 230 average time/residue: 0.3418 time to fit residues: 135.6356 Evaluate side-chains 214 residues out of total 3146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 164 time to evaluate : 3.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 1115 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 263 TYR Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 556 PHE Chi-restraints excluded: chain C residue 570 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 587 CYS Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 742 ASP Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 952 ASN Chi-restraints excluded: chain C residue 1014 GLU Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1102 THR Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 646 CYS Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 777 GLU Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 966 ASN Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain F residue 93 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 116 optimal weight: 9.9990 chunk 312 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 203 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 347 optimal weight: 30.0000 chunk 288 optimal weight: 0.4980 chunk 160 optimal weight: 20.0000 chunk 28 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 chunk 182 optimal weight: 0.0470 overall best weight: 1.0882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 952 ASN A 218 GLN ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1103 GLN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 29634 Z= 0.200 Angle : 0.491 10.363 40319 Z= 0.251 Chirality : 0.042 0.186 4693 Planarity : 0.003 0.047 5153 Dihedral : 4.932 58.682 5005 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.23 % Allowed : 10.24 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % 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: 0.42 (0.14), residues: 3582 helix: 1.87 (0.20), residues: 675 sheet: 0.47 (0.17), residues: 945 loop : -0.35 (0.14), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP L 36 HIS 0.002 0.001 HIS L 91 PHE 0.015 0.001 PHE B 65 TYR 0.019 0.001 TYR B1064 ARG 0.004 0.000 ARG C 564 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 3146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 170 time to evaluate : 3.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.8034 (mmm) cc_final: 0.7670 (mmm) REVERT: B 529 ASN cc_start: 0.8143 (t0) cc_final: 0.7942 (t0) REVERT: C 205 SER cc_start: 0.8456 (p) cc_final: 0.8231 (p) REVERT: C 556 PHE cc_start: 0.7856 (OUTLIER) cc_final: 0.7554 (t80) REVERT: C 742 ASP cc_start: 0.7008 (OUTLIER) cc_final: 0.6793 (p0) REVERT: C 901 TYR cc_start: 0.7679 (m-10) cc_final: 0.7440 (m-10) REVERT: A 86 PHE cc_start: 0.8470 (t80) cc_final: 0.7969 (t80) REVERT: A 177 MET cc_start: -0.5278 (ttt) cc_final: -0.6665 (mmt) REVERT: A 855 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8410 (mt) REVERT: F 4 MET cc_start: -0.2090 (mmt) cc_final: -0.3158 (mtt) outliers start: 70 outliers final: 51 residues processed: 223 average time/residue: 0.3478 time to fit residues: 133.3029 Evaluate side-chains 214 residues out of total 3146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 160 time to evaluate : 3.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 1110 GLN Chi-restraints excluded: chain B residue 1115 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 263 TYR Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 556 PHE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 587 CYS Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 742 ASP Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 1014 GLU Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1102 THR Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 646 CYS Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 757 CYS Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 966 ASN Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain F residue 93 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 334 optimal weight: 40.0000 chunk 39 optimal weight: 4.9990 chunk 197 optimal weight: 2.9990 chunk 253 optimal weight: 50.0000 chunk 196 optimal weight: 2.9990 chunk 292 optimal weight: 0.9980 chunk 193 optimal weight: 0.9980 chunk 346 optimal weight: 8.9990 chunk 216 optimal weight: 5.9990 chunk 210 optimal weight: 4.9990 chunk 159 optimal weight: 9.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 932 GLN B1002 GLN ** B1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 952 ASN A 218 GLN ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 999 GLN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 29634 Z= 0.385 Angle : 0.557 10.884 40319 Z= 0.284 Chirality : 0.044 0.182 4693 Planarity : 0.004 0.042 5153 Dihedral : 4.989 59.593 5005 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.64 % Allowed : 10.43 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % 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: 0.25 (0.14), residues: 3582 helix: 1.63 (0.20), residues: 668 sheet: 0.41 (0.16), residues: 965 loop : -0.44 (0.14), residues: 1949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP L 36 HIS 0.005 0.001 HIS A1045 PHE 0.019 0.002 PHE B 65 TYR 0.023 0.001 TYR B1064 ARG 0.012 0.000 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 3146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 169 time to evaluate : 3.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 THR cc_start: 0.7458 (m) cc_final: 0.7079 (p) REVERT: B 133 PHE cc_start: 0.7617 (m-80) cc_final: 0.6804 (m-80) REVERT: C 556 PHE cc_start: 0.7924 (OUTLIER) cc_final: 0.7573 (t80) REVERT: C 742 ASP cc_start: 0.7171 (OUTLIER) cc_final: 0.6919 (p0) REVERT: A 86 PHE cc_start: 0.8492 (t80) cc_final: 0.7912 (t80) REVERT: A 177 MET cc_start: -0.5115 (ttt) cc_final: -0.6671 (mmt) REVERT: F 4 MET cc_start: -0.2027 (mmt) cc_final: -0.3302 (mtt) outliers start: 83 outliers final: 66 residues processed: 231 average time/residue: 0.3504 time to fit residues: 140.0415 Evaluate side-chains 228 residues out of total 3146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 160 time to evaluate : 3.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain B residue 588 SER Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 994 ILE Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1110 GLN Chi-restraints excluded: chain B residue 1115 ASP Chi-restraints excluded: chain B residue 1120 SER Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 263 TYR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 556 PHE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 587 CYS Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 742 ASP Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 1014 GLU Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1102 THR Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 646 CYS Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 777 GLU Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 966 ASN Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 52 TYR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain F residue 93 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 214 optimal weight: 6.9990 chunk 138 optimal weight: 0.8980 chunk 206 optimal weight: 0.5980 chunk 104 optimal weight: 0.0570 chunk 67 optimal weight: 4.9990 chunk 219 optimal weight: 8.9990 chunk 235 optimal weight: 0.5980 chunk 171 optimal weight: 0.8980 chunk 32 optimal weight: 30.0000 chunk 271 optimal weight: 0.9990 chunk 314 optimal weight: 0.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 952 ASN B1002 GLN ** B1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 952 ASN A 218 GLN ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 999 GLN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 29634 Z= 0.155 Angle : 0.498 10.640 40319 Z= 0.251 Chirality : 0.042 0.171 4693 Planarity : 0.003 0.043 5153 Dihedral : 4.654 58.546 5005 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.94 % Allowed : 11.09 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % 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: 0.50 (0.14), residues: 3582 helix: 2.03 (0.20), residues: 656 sheet: 0.53 (0.17), residues: 956 loop : -0.32 (0.14), residues: 1970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP L 36 HIS 0.003 0.001 HIS B1085 PHE 0.019 0.001 PHE A 92 TYR 0.028 0.001 TYR H 94 ARG 0.005 0.000 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 3146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 170 time to evaluate : 2.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 133 PHE cc_start: 0.7570 (m-80) cc_final: 0.6741 (m-80) REVERT: B 153 MET cc_start: 0.7872 (mmm) cc_final: 0.7398 (mmm) REVERT: C 205 SER cc_start: 0.8478 (p) cc_final: 0.8246 (p) REVERT: C 556 PHE cc_start: 0.7902 (OUTLIER) cc_final: 0.7620 (t80) REVERT: C 742 ASP cc_start: 0.7009 (OUTLIER) cc_final: 0.6786 (p0) REVERT: A 86 PHE cc_start: 0.8468 (t80) cc_final: 0.7918 (t80) REVERT: A 177 MET cc_start: -0.5251 (ttt) cc_final: -0.6641 (mmt) REVERT: F 4 MET cc_start: -0.1948 (mmt) cc_final: -0.3082 (mtt) outliers start: 61 outliers final: 53 residues processed: 214 average time/residue: 0.3581 time to fit residues: 131.3164 Evaluate side-chains 218 residues out of total 3146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 163 time to evaluate : 3.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 1115 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 263 TYR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 556 PHE Chi-restraints excluded: chain C residue 570 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 587 CYS Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain C residue 742 ASP Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 1014 GLU Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1102 THR Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 646 CYS Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 966 ASN Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 52 TYR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain F residue 93 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 331 optimal weight: 50.0000 chunk 302 optimal weight: 0.9990 chunk 322 optimal weight: 6.9990 chunk 194 optimal weight: 5.9990 chunk 140 optimal weight: 50.0000 chunk 253 optimal weight: 40.0000 chunk 98 optimal weight: 0.5980 chunk 291 optimal weight: 2.9990 chunk 304 optimal weight: 1.9990 chunk 321 optimal weight: 9.9990 chunk 211 optimal weight: 40.0000 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1002 GLN ** B1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 952 ASN ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 999 GLN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 29634 Z= 0.372 Angle : 0.556 10.555 40319 Z= 0.282 Chirality : 0.044 0.164 4693 Planarity : 0.003 0.041 5153 Dihedral : 4.778 59.554 5005 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.16 % Allowed : 11.03 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % 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: 0.33 (0.14), residues: 3582 helix: 1.77 (0.20), residues: 655 sheet: 0.45 (0.17), residues: 968 loop : -0.40 (0.14), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP L 36 HIS 0.005 0.001 HIS A1045 PHE 0.018 0.001 PHE B 65 TYR 0.040 0.001 TYR H 94 ARG 0.005 0.000 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 3146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 168 time to evaluate : 3.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 THR cc_start: 0.7489 (m) cc_final: 0.7085 (p) REVERT: B 133 PHE cc_start: 0.7694 (m-80) cc_final: 0.6827 (m-80) REVERT: B 975 ASN cc_start: 0.7916 (t0) cc_final: 0.7570 (t0) REVERT: C 556 PHE cc_start: 0.7963 (OUTLIER) cc_final: 0.7614 (t80) REVERT: C 742 ASP cc_start: 0.7215 (OUTLIER) cc_final: 0.6978 (p0) REVERT: A 86 PHE cc_start: 0.8475 (t80) cc_final: 0.7896 (t80) REVERT: A 177 MET cc_start: -0.5055 (ttt) cc_final: -0.6567 (mmt) REVERT: F 4 MET cc_start: -0.1890 (mmt) cc_final: -0.2958 (mtt) outliers start: 68 outliers final: 61 residues processed: 219 average time/residue: 0.3548 time to fit residues: 134.4350 Evaluate side-chains 224 residues out of total 3146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 161 time to evaluate : 3.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain B residue 588 SER Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 1110 GLN Chi-restraints excluded: chain B residue 1115 ASP Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain B residue 1120 SER Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 263 TYR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 556 PHE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 587 CYS Chi-restraints excluded: chain C residue 593 SER Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 742 ASP Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 1014 GLU Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1102 THR Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 646 CYS Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 966 ASN Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 52 TYR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain F residue 93 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 340 optimal weight: 20.0000 chunk 208 optimal weight: 0.9980 chunk 161 optimal weight: 6.9990 chunk 237 optimal weight: 0.7980 chunk 357 optimal weight: 40.0000 chunk 329 optimal weight: 9.9990 chunk 284 optimal weight: 0.6980 chunk 29 optimal weight: 5.9990 chunk 219 optimal weight: 9.9990 chunk 174 optimal weight: 4.9990 chunk 226 optimal weight: 40.0000 overall best weight: 2.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1002 GLN ** B1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 952 ASN ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 999 GLN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 29634 Z= 0.393 Angle : 0.570 10.620 40319 Z= 0.290 Chirality : 0.044 0.156 4693 Planarity : 0.004 0.041 5153 Dihedral : 4.868 59.151 5005 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.35 % Allowed : 11.03 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % 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: 0.21 (0.14), residues: 3582 helix: 1.69 (0.20), residues: 650 sheet: 0.33 (0.16), residues: 977 loop : -0.45 (0.14), residues: 1955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP L 36 HIS 0.006 0.001 HIS A1045 PHE 0.019 0.002 PHE B 65 TYR 0.034 0.001 TYR H 94 ARG 0.006 0.000 ARG B 812 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 3146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 166 time to evaluate : 3.242 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: B 63 THR cc_start: 0.7438 (m) cc_final: 0.7065 (p) REVERT: B 133 PHE cc_start: 0.7827 (m-80) cc_final: 0.7012 (m-80) REVERT: B 975 ASN cc_start: 0.7965 (t0) cc_final: 0.7641 (t0) REVERT: C 556 PHE cc_start: 0.8038 (OUTLIER) cc_final: 0.7665 (t80) REVERT: C 742 ASP cc_start: 0.7241 (OUTLIER) cc_final: 0.7006 (p0) REVERT: A 86 PHE cc_start: 0.8471 (t80) cc_final: 0.7891 (t80) REVERT: A 177 MET cc_start: -0.4986 (ttt) cc_final: -0.6489 (mmt) REVERT: A 205 SER cc_start: 0.8130 (p) cc_final: 0.7795 (m) REVERT: F 4 MET cc_start: -0.1780 (mmt) cc_final: -0.2971 (mtt) outliers start: 74 outliers final: 64 residues processed: 219 average time/residue: 0.3464 time to fit residues: 131.2283 Evaluate side-chains 230 residues out of total 3146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 164 time to evaluate : 2.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 1110 GLN Chi-restraints excluded: chain B residue 1115 ASP Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain B residue 1120 SER Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 263 TYR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 556 PHE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 587 CYS Chi-restraints excluded: chain C residue 593 SER Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 742 ASP Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 1014 GLU Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1102 THR Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 646 CYS Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 966 ASN Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 52 TYR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain F residue 93 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 303 optimal weight: 0.8980 chunk 87 optimal weight: 0.0570 chunk 262 optimal weight: 3.9990 chunk 42 optimal weight: 50.0000 chunk 79 optimal weight: 0.9980 chunk 285 optimal weight: 0.9990 chunk 119 optimal weight: 30.0000 chunk 292 optimal weight: 0.6980 chunk 36 optimal weight: 40.0000 chunk 52 optimal weight: 4.9990 chunk 250 optimal weight: 5.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1002 GLN ** B1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 952 ASN ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 999 GLN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.180010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.122921 restraints weight = 56358.100| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 4.90 r_work: 0.3236 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 29634 Z= 0.165 Angle : 0.507 10.784 40319 Z= 0.255 Chirality : 0.042 0.162 4693 Planarity : 0.003 0.038 5153 Dihedral : 4.526 57.340 5005 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.97 % Allowed : 11.38 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.14), residues: 3582 helix: 1.99 (0.20), residues: 652 sheet: 0.42 (0.17), residues: 975 loop : -0.32 (0.14), residues: 1955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP L 36 HIS 0.003 0.001 HIS B1085 PHE 0.023 0.001 PHE A 201 TYR 0.030 0.001 TYR H 94 ARG 0.004 0.000 ARG C 564 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5978.86 seconds wall clock time: 110 minutes 42.59 seconds (6642.59 seconds total)