Starting phenix.real_space_refine on Tue Nov 19 20:19:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zhm_60108/11_2024/8zhm_60108.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zhm_60108/11_2024/8zhm_60108.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zhm_60108/11_2024/8zhm_60108.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zhm_60108/11_2024/8zhm_60108.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zhm_60108/11_2024/8zhm_60108.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zhm_60108/11_2024/8zhm_60108.cif" } resolution = 3.39 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9222 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 180 5.16 5 C 28617 2.51 5 N 7473 2.21 5 O 9003 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 45273 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 8344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 8344 Classifications: {'peptide': 1066} Link IDs: {'PTRANS': 56, 'TRANS': 1009} Chain breaks: 5 Chain: "B" Number of atoms: 8344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 8344 Classifications: {'peptide': 1066} Link IDs: {'PTRANS': 56, 'TRANS': 1009} Chain breaks: 5 Chain: "C" Number of atoms: 8344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 8344 Classifications: {'peptide': 1066} Link IDs: {'PTRANS': 56, 'TRANS': 1009} Chain breaks: 5 Chain: "H" Number of atoms: 1661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1661 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 214} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1557 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 196} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 1661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1661 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 214} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1557 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 196} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 1661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1661 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 214} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "O" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1557 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 196} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1593 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 197} Chain breaks: 1 Chain: "E" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1670 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 209} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1593 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 197} Chain breaks: 1 Chain: "J" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1670 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 209} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1593 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 197} Chain breaks: 1 Chain: "M" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1670 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 209} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" 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: "W" 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: "X" 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: "Y" 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: "Z" 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: "a" 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: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 25.22, per 1000 atoms: 0.56 Number of scatterers: 45273 At special positions: 0 Unit cell: (221.712, 203.856, 205.344, 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 180 16.00 O 9003 8.00 N 7473 7.00 C 28617 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=66, symmetry=0 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 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 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 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " 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 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 151 " - pdb=" SG CYS H 207 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 198 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 151 " - pdb=" SG CYS G 207 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 90 " distance=2.03 Simple disulfide: pdb=" SG CYS I 139 " - pdb=" SG CYS I 198 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 151 " - pdb=" SG CYS N 207 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 90 " distance=2.03 Simple disulfide: pdb=" SG CYS O 139 " - pdb=" SG CYS O 198 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 91 " distance=2.03 Simple disulfide: pdb=" SG CYS D 145 " - pdb=" SG CYS D 204 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 97 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 203 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 91 " distance=2.03 Simple disulfide: pdb=" SG CYS F 145 " - pdb=" SG CYS F 204 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 97 " distance=2.03 Simple disulfide: pdb=" SG CYS J 147 " - pdb=" SG CYS J 203 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 91 " distance=2.03 Simple disulfide: pdb=" SG CYS K 145 " - pdb=" SG CYS K 204 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 97 " distance=2.03 Simple disulfide: pdb=" SG CYS M 147 " - pdb=" SG CYS M 203 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 616 " " NAG A1309 " - " ASN A 657 " " NAG A1310 " - " ASN A 709 " " NAG A1311 " - " ASN A1074 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 657 " " NAG B1310 " - " ASN B 709 " " NAG B1311 " - " ASN B1074 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 616 " " NAG C1309 " - " ASN C 657 " " NAG C1310 " - " ASN C 709 " " NAG C1311 " - " ASN C1074 " " NAG P 1 " - " ASN A 717 " " NAG Q 1 " - " ASN A 801 " " NAG R 1 " - " ASN A1098 " " NAG S 1 " - " ASN A1134 " " NAG T 1 " - " ASN B 717 " " NAG U 1 " - " ASN B 801 " " NAG V 1 " - " ASN B1098 " " NAG W 1 " - " ASN B1134 " " NAG X 1 " - " ASN C 717 " " NAG Y 1 " - " ASN C 801 " " NAG Z 1 " - " ASN C1098 " " NAG a 1 " - " ASN C1134 " Time building additional restraints: 10.55 Conformation dependent library (CDL) restraints added in 5.5 seconds 11526 Ramachandran restraints generated. 5763 Oldfield, 0 Emsley, 5763 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10788 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 122 sheets defined 13.3% alpha, 34.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.41 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 342 Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.911A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.987A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 782 removed outlier: 3.819A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.669A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 887 through 891 removed outlier: 4.083A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.696A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 4.115A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 913 through 918' Processing helix chain 'A' and resid 919 through 939 Processing helix chain 'A' and resid 945 through 966 removed outlier: 3.549A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 4.113A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1032 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 339 through 344 Processing helix chain 'B' and resid 383 through 387 removed outlier: 4.170A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 746 through 753 removed outlier: 4.022A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 782 removed outlier: 3.899A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.621A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.672A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 4.095A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN B 919 " --> pdb=" O VAL B 915 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 913 through 919' Processing helix chain 'B' and resid 919 through 939 Processing helix chain 'B' and resid 946 through 966 removed outlier: 3.854A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 4.013A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 989 through 1033 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 342 Processing helix chain 'C' and resid 383 through 387 removed outlier: 4.209A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.506A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 746 through 752 removed outlier: 3.918A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 753 through 755 No H-bonds generated for 'chain 'C' and resid 753 through 755' Processing helix chain 'C' and resid 756 through 782 removed outlier: 3.784A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.726A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 887 through 891 removed outlier: 4.068A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.664A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 916 removed outlier: 3.540A pdb=" N LEU C 916 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 removed outlier: 3.577A pdb=" N SER C 940 " --> pdb=" O ASP C 936 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 966 removed outlier: 3.852A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 4.201A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 989 through 1032 Processing helix chain 'H' and resid 198 through 200 No H-bonds generated for 'chain 'H' and resid 198 through 200' Processing helix chain 'L' and resid 126 through 133 removed outlier: 3.965A pdb=" N GLN L 131 " --> pdb=" O GLU L 128 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA L 132 " --> pdb=" O GLU L 129 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASN L 133 " --> pdb=" O LEU L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 186 through 191 removed outlier: 3.971A pdb=" N LYS L 191 " --> pdb=" O PRO L 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 198 through 200 No H-bonds generated for 'chain 'G' and resid 198 through 200' Processing helix chain 'I' and resid 129 through 133 removed outlier: 3.669A pdb=" N ASN I 133 " --> pdb=" O LEU I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 186 through 191 removed outlier: 4.057A pdb=" N LYS I 191 " --> pdb=" O PRO I 187 " (cutoff:3.500A) Processing helix chain 'N' and resid 198 through 200 No H-bonds generated for 'chain 'N' and resid 198 through 200' Processing helix chain 'O' and resid 127 through 131 removed outlier: 3.923A pdb=" N GLN O 131 " --> pdb=" O GLU O 128 " (cutoff:3.500A) Processing helix chain 'O' and resid 186 through 191 removed outlier: 3.985A pdb=" N LYS O 191 " --> pdb=" O PRO O 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 132 through 138 Processing helix chain 'D' and resid 192 through 199 removed outlier: 3.540A pdb=" N LYS D 197 " --> pdb=" O PRO D 193 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N HIS D 199 " --> pdb=" O GLN D 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 34 removed outlier: 4.088A pdb=" N GLY E 33 " --> pdb=" O SER E 30 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N TYR E 34 " --> pdb=" O SER E 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 30 through 34' Processing helix chain 'E' and resid 88 through 92 removed outlier: 3.875A pdb=" N THR E 92 " --> pdb=" O ALA E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 196 No H-bonds generated for 'chain 'E' and resid 194 through 196' Processing helix chain 'F' and resid 132 through 138 Processing helix chain 'F' and resid 192 through 199 removed outlier: 3.612A pdb=" N LYS F 197 " --> pdb=" O PRO F 193 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N HIS F 199 " --> pdb=" O GLN F 195 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 92 removed outlier: 3.893A pdb=" N THR J 92 " --> pdb=" O ALA J 89 " (cutoff:3.500A) Processing helix chain 'J' and resid 134 through 138 removed outlier: 3.717A pdb=" N THR J 138 " --> pdb=" O SER J 135 " (cutoff:3.500A) Processing helix chain 'J' and resid 194 through 196 No H-bonds generated for 'chain 'J' and resid 194 through 196' Processing helix chain 'K' and resid 132 through 138 Processing helix chain 'K' and resid 192 through 199 removed outlier: 3.567A pdb=" N LYS K 197 " --> pdb=" O PRO K 193 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N HIS K 199 " --> pdb=" O GLN K 195 " (cutoff:3.500A) Processing helix chain 'M' and resid 88 through 92 removed outlier: 3.925A pdb=" N THR M 92 " --> pdb=" O ALA M 89 " (cutoff:3.500A) Processing helix chain 'M' and resid 134 through 138 removed outlier: 3.768A pdb=" N THR M 138 " --> pdb=" O SER M 135 " (cutoff:3.500A) Processing helix chain 'M' and resid 194 through 196 No H-bonds generated for 'chain 'M' and resid 194 through 196' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.335A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.732A pdb=" N GLU C 583 " --> pdb=" O ASP C 578 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.802A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 12.942A pdb=" N PHE A 135 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 12.716A pdb=" N THR A 240 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 10.563A pdb=" N ASN A 137 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 10.709A pdb=" N LEU A 242 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ASP A 138 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL A 159 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.943A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL A 127 " --> pdb=" O VAL A 120 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 313 removed outlier: 3.757A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.632A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 466 through 467 removed outlier: 3.695A pdb=" N ARG A 466 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY H 104 " --> pdb=" O ARG A 466 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 575 through 578 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.381A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE A 664 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 727 removed outlier: 3.500A pdb=" N VAL A1068 " --> pdb=" O THR A 719 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.216A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.605A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.701A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.622A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 9.058A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 50 through 55 removed outlier: 4.050A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.206A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.780A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 317 removed outlier: 6.516A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 324 through 326 removed outlier: 6.387A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.152A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 466 through 467 removed outlier: 3.838A pdb=" N ARG B 466 " --> pdb=" O GLY N 104 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLY N 104 " --> pdb=" O ARG B 466 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.533A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 565 through 566 removed outlier: 6.887A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 575 through 578 removed outlier: 3.534A pdb=" N GLU B 583 " --> pdb=" O ASP B 578 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.555A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE B 666 " --> pdb=" O ILE B 670 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE B 664 " --> pdb=" O ALA B 672 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AD7, first strand: chain 'B' and resid 711 through 727 removed outlier: 6.498A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 711 through 727 removed outlier: 6.498A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.154A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE2, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.389A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.592A pdb=" N HIS C 49 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 removed outlier: 12.608A pdb=" N PHE C 238 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 12.412A pdb=" N ASN C 137 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 9.573A pdb=" N THR C 240 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N LEU C 242 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 10.609A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG C 158 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.098A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 311 through 317 removed outlier: 3.671A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR C 313 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR C 315 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 325 through 326 Processing sheet with id=AE8, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.793A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TRP C 436 " --> pdb=" O ARG C 509 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'C' and resid 466 through 467 removed outlier: 3.667A pdb=" N ARG C 466 " --> pdb=" O GLY G 104 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLY G 104 " --> pdb=" O ARG C 466 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.489A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.800A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE C 664 " --> pdb=" O ALA C 672 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 711 through 712 removed outlier: 3.688A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 718 through 727 removed outlier: 3.807A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 733 through 735 removed outlier: 4.192A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.502A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 3 through 6 removed outlier: 4.405A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU H 83 " --> pdb=" O VAL H 18 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL H 20 " --> pdb=" O MET H 81 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 10 through 11 removed outlier: 4.669A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE H 52 " --> pdb=" O ILE H 57 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE H 57 " --> pdb=" O ILE H 52 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 10 through 11 removed outlier: 4.107A pdb=" N LEU H 113 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'H' and resid 131 through 135 removed outlier: 3.525A pdb=" N GLY H 150 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL H 195 " --> pdb=" O ALA H 147 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU H 149 " --> pdb=" O VAL H 193 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER H 191 " --> pdb=" O CYS H 151 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL H 153 " --> pdb=" O LEU H 189 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU H 189 " --> pdb=" O VAL H 153 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASP H 155 " --> pdb=" O TYR H 187 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N TYR H 187 " --> pdb=" O ASP H 155 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL H 192 " --> pdb=" O HIS H 175 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N HIS H 175 " --> pdb=" O VAL H 192 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'H' and resid 162 through 165 removed outlier: 3.624A pdb=" N THR H 162 " --> pdb=" O ASN H 210 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N CYS H 207 " --> pdb=" O LYS H 220 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LYS H 220 " --> pdb=" O CYS H 207 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 17 through 23 Processing sheet with id=AG5, first strand: chain 'L' and resid 47 through 51 removed outlier: 6.907A pdb=" N LEU L 48 " --> pdb=" O GLN L 39 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N GLN L 39 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ILE L 50 " --> pdb=" O TRP L 37 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TRP L 37 " --> pdb=" O ILE L 50 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR L 38 " --> pdb=" O TYR L 89 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER L 92 " --> pdb=" O VAL L 101 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 47 through 51 removed outlier: 6.907A pdb=" N LEU L 48 " --> pdb=" O GLN L 39 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N GLN L 39 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ILE L 50 " --> pdb=" O TRP L 37 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TRP L 37 " --> pdb=" O ILE L 50 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR L 38 " --> pdb=" O TYR L 89 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR L 88 " --> pdb=" O THR L 106 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'L' and resid 119 through 123 removed outlier: 4.277A pdb=" N VAL L 138 " --> pdb=" O PHE L 123 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N TYR L 177 " --> pdb=" O ASP L 143 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA L 178 " --> pdb=" O SER L 170 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER L 170 " --> pdb=" O ALA L 178 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'L' and resid 135 through 136 Processing sheet with id=AG9, first strand: chain 'L' and resid 159 through 160 removed outlier: 4.627A pdb=" N TRP L 153 " --> pdb=" O VAL L 160 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N THR L 150 " --> pdb=" O THR L 201 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR L 201 " --> pdb=" O THR L 150 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR L 196 " --> pdb=" O VAL L 211 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N CYS L 198 " --> pdb=" O LYS L 209 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LYS L 209 " --> pdb=" O CYS L 198 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL L 200 " --> pdb=" O VAL L 207 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL L 207 " --> pdb=" O VAL L 200 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'G' and resid 3 through 6 removed outlier: 3.691A pdb=" N GLN G 3 " --> pdb=" O SER G 25 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS G 23 " --> pdb=" O VAL G 5 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR G 78 " --> pdb=" O ASP G 73 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.989A pdb=" N LYS G 12 " --> pdb=" O THR G 121 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE G 34 " --> pdb=" O GLY G 50 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N GLY G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET G 48 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE G 52 " --> pdb=" O ILE G 57 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE G 57 " --> pdb=" O ILE G 52 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.989A pdb=" N LYS G 12 " --> pdb=" O THR G 121 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LEU G 113 " --> pdb=" O ARG G 98 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'G' and resid 131 through 135 removed outlier: 3.589A pdb=" N SER G 131 " --> pdb=" O LYS G 154 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLY G 150 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU G 149 " --> pdb=" O VAL G 193 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER G 191 " --> pdb=" O CYS G 151 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL G 153 " --> pdb=" O LEU G 189 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU G 189 " --> pdb=" O VAL G 153 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP G 155 " --> pdb=" O TYR G 187 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N TYR G 187 " --> pdb=" O ASP G 155 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'G' and resid 162 through 165 removed outlier: 3.515A pdb=" N THR G 162 " --> pdb=" O ASN G 210 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N CYS G 207 " --> pdb=" O LYS G 220 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS G 220 " --> pdb=" O CYS G 207 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'I' and resid 17 through 23 Processing sheet with id=AH7, first strand: chain 'I' and resid 47 through 51 removed outlier: 6.834A pdb=" N LEU I 48 " --> pdb=" O GLN I 39 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N GLN I 39 " --> pdb=" O LEU I 48 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ILE I 50 " --> pdb=" O TRP I 37 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TRP I 37 " --> pdb=" O ILE I 50 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR I 38 " --> pdb=" O TYR I 89 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER I 92 " --> pdb=" O VAL I 101 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'I' and resid 47 through 51 removed outlier: 6.834A pdb=" N LEU I 48 " --> pdb=" O GLN I 39 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N GLN I 39 " --> pdb=" O LEU I 48 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ILE I 50 " --> pdb=" O TRP I 37 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TRP I 37 " --> pdb=" O ILE I 50 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR I 38 " --> pdb=" O TYR I 89 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR I 88 " --> pdb=" O THR I 106 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'I' and resid 119 through 123 removed outlier: 3.990A pdb=" N PHE I 123 " --> pdb=" O VAL I 138 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL I 138 " --> pdb=" O PHE I 123 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N TYR I 177 " --> pdb=" O ASP I 143 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA I 178 " --> pdb=" O SER I 170 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER I 170 " --> pdb=" O ALA I 178 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'I' and resid 135 through 136 Processing sheet with id=AI2, first strand: chain 'I' and resid 159 through 160 removed outlier: 4.554A pdb=" N TRP I 153 " --> pdb=" O VAL I 160 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N THR I 150 " --> pdb=" O THR I 201 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N THR I 201 " --> pdb=" O THR I 150 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TYR I 196 " --> pdb=" O VAL I 211 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N CYS I 198 " --> pdb=" O LYS I 209 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LYS I 209 " --> pdb=" O CYS I 198 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL I 200 " --> pdb=" O VAL I 207 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL I 207 " --> pdb=" O VAL I 200 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'N' and resid 3 through 5 removed outlier: 3.969A pdb=" N GLN N 3 " --> pdb=" O SER N 25 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'N' and resid 10 through 11 removed outlier: 3.516A pdb=" N TYR N 94 " --> pdb=" O THR N 118 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLY N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE N 52 " --> pdb=" O ILE N 57 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE N 57 " --> pdb=" O ILE N 52 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'N' and resid 131 through 135 removed outlier: 3.755A pdb=" N GLY N 150 " --> pdb=" O LEU N 135 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU N 149 " --> pdb=" O VAL N 193 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER N 191 " --> pdb=" O CYS N 151 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL N 153 " --> pdb=" O LEU N 189 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU N 189 " --> pdb=" O VAL N 153 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ASP N 155 " --> pdb=" O TYR N 187 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N TYR N 187 " --> pdb=" O ASP N 155 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'N' and resid 162 through 165 removed outlier: 3.747A pdb=" N THR N 162 " --> pdb=" O ASN N 210 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS N 220 " --> pdb=" O CYS N 207 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'O' and resid 17 through 22 removed outlier: 3.558A pdb=" N LEU O 75 " --> pdb=" O ILE O 20 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER O 72 " --> pdb=" O SER O 69 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'O' and resid 47 through 51 removed outlier: 6.852A pdb=" N LEU O 48 " --> pdb=" O GLN O 39 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N GLN O 39 " --> pdb=" O LEU O 48 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE O 50 " --> pdb=" O TRP O 37 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR O 38 " --> pdb=" O TYR O 89 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER O 92 " --> pdb=" O VAL O 101 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'O' and resid 47 through 51 removed outlier: 6.852A pdb=" N LEU O 48 " --> pdb=" O GLN O 39 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N GLN O 39 " --> pdb=" O LEU O 48 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE O 50 " --> pdb=" O TRP O 37 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR O 38 " --> pdb=" O TYR O 89 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'O' and resid 119 through 123 removed outlier: 4.253A pdb=" N VAL O 138 " --> pdb=" O PHE O 123 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N TYR O 177 " --> pdb=" O ASP O 143 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'O' and resid 135 through 136 Processing sheet with id=AJ3, first strand: chain 'O' and resid 150 through 154 removed outlier: 4.178A pdb=" N THR O 150 " --> pdb=" O THR O 201 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR O 201 " --> pdb=" O THR O 150 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS O 154 " --> pdb=" O SER O 197 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR O 196 " --> pdb=" O VAL O 211 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N CYS O 198 " --> pdb=" O LYS O 209 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LYS O 209 " --> pdb=" O CYS O 198 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL O 200 " --> pdb=" O VAL O 207 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL O 207 " --> pdb=" O VAL O 200 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'D' and resid 4 through 5 removed outlier: 3.546A pdb=" N SER D 73 " --> pdb=" O ASP D 68 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP D 68 " --> pdb=" O SER D 73 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'D' and resid 9 through 11 removed outlier: 6.752A pdb=" N VAL D 10 " --> pdb=" O THR D 108 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'D' and resid 9 through 11 removed outlier: 6.752A pdb=" N VAL D 10 " --> pdb=" O THR D 108 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'D' and resid 125 through 129 removed outlier: 3.718A pdb=" N PHE D 129 " --> pdb=" O VAL D 144 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL D 144 " --> pdb=" O PHE D 129 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N TYR D 183 " --> pdb=" O ASP D 149 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'D' and resid 125 through 129 removed outlier: 3.718A pdb=" N PHE D 129 " --> pdb=" O VAL D 144 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL D 144 " --> pdb=" O PHE D 129 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N TYR D 183 " --> pdb=" O ASP D 149 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'D' and resid 164 through 166 removed outlier: 4.081A pdb=" N TRP D 159 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS D 215 " --> pdb=" O CYS D 204 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AK2, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.742A pdb=" N VAL E 12 " --> pdb=" O THR E 117 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK2 Processing sheet with id=AK3, first strand: chain 'E' and resid 59 through 61 removed outlier: 5.070A pdb=" N TRP E 49 " --> pdb=" O ARG E 40 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ARG E 40 " --> pdb=" O TRP E 49 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY E 51 " --> pdb=" O TRP E 38 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR E 109 " --> pdb=" O ARG E 99 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'E' and resid 59 through 61 removed outlier: 5.070A pdb=" N TRP E 49 " --> pdb=" O ARG E 40 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ARG E 40 " --> pdb=" O TRP E 49 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY E 51 " --> pdb=" O TRP E 38 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'E' and resid 127 through 131 removed outlier: 3.638A pdb=" N GLY E 146 " --> pdb=" O LEU E 131 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N TYR E 183 " --> pdb=" O ASP E 151 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'E' and resid 127 through 131 removed outlier: 3.638A pdb=" N GLY E 146 " --> pdb=" O LEU E 131 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N TYR E 183 " --> pdb=" O ASP E 151 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'E' and resid 158 through 161 removed outlier: 4.240A pdb=" N TYR E 201 " --> pdb=" O VAL E 218 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'F' and resid 4 through 5 Processing sheet with id=AK9, first strand: chain 'F' and resid 9 through 11 removed outlier: 6.866A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'F' and resid 9 through 11 Processing sheet with id=AL2, first strand: chain 'F' and resid 125 through 129 removed outlier: 3.543A pdb=" N VAL F 144 " --> pdb=" O PHE F 129 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N TYR F 183 " --> pdb=" O ASP F 149 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'F' and resid 125 through 129 removed outlier: 3.543A pdb=" N VAL F 144 " --> pdb=" O PHE F 129 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N TYR F 183 " --> pdb=" O ASP F 149 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'F' and resid 164 through 166 removed outlier: 4.120A pdb=" N TRP F 159 " --> pdb=" O VAL F 166 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AL6, first strand: chain 'J' and resid 11 through 12 Processing sheet with id=AL7, first strand: chain 'J' and resid 59 through 61 removed outlier: 5.068A pdb=" N TRP J 49 " --> pdb=" O ARG J 40 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ARG J 40 " --> pdb=" O TRP J 49 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY J 51 " --> pdb=" O TRP J 38 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER J 37 " --> pdb=" O ALA J 98 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA J 98 " --> pdb=" O SER J 37 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TYR J 109 " --> pdb=" O ARG J 99 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'J' and resid 59 through 61 removed outlier: 5.068A pdb=" N TRP J 49 " --> pdb=" O ARG J 40 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ARG J 40 " --> pdb=" O TRP J 49 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY J 51 " --> pdb=" O TRP J 38 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER J 37 " --> pdb=" O ALA J 98 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA J 98 " --> pdb=" O SER J 37 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'J' and resid 127 through 131 removed outlier: 3.853A pdb=" N GLY J 146 " --> pdb=" O LEU J 131 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N TYR J 183 " --> pdb=" O ASP J 151 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'J' and resid 127 through 131 removed outlier: 3.853A pdb=" N GLY J 146 " --> pdb=" O LEU J 131 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N TYR J 183 " --> pdb=" O ASP J 151 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'J' and resid 158 through 161 removed outlier: 4.204A pdb=" N TYR J 201 " --> pdb=" O VAL J 218 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'K' and resid 4 through 5 Processing sheet with id=AM4, first strand: chain 'K' and resid 9 through 12 removed outlier: 3.578A pdb=" N VAL K 10 " --> pdb=" O LYS K 106 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'K' and resid 125 through 129 removed outlier: 3.510A pdb=" N PHE K 129 " --> pdb=" O VAL K 144 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL K 144 " --> pdb=" O PHE K 129 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N TYR K 183 " --> pdb=" O ASP K 149 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'K' and resid 125 through 129 removed outlier: 3.510A pdb=" N PHE K 129 " --> pdb=" O VAL K 144 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL K 144 " --> pdb=" O PHE K 129 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N TYR K 183 " --> pdb=" O ASP K 149 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'K' and resid 164 through 166 removed outlier: 4.121A pdb=" N TRP K 159 " --> pdb=" O VAL K 166 " (cutoff:3.500A) Processing sheet with id=AM8, first strand: chain 'M' and resid 3 through 6 Processing sheet with id=AM9, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.665A pdb=" N VAL M 12 " --> pdb=" O THR M 117 " (cutoff:3.500A) No H-bonds generated for sheet with id=AM9 Processing sheet with id=AN1, first strand: chain 'M' and resid 59 through 61 removed outlier: 6.927A pdb=" N TRP M 38 " --> pdb=" O ILE M 50 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N CYS M 52 " --> pdb=" O TRP M 36 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N TRP M 36 " --> pdb=" O CYS M 52 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TYR M 109 " --> pdb=" O ARG M 99 " (cutoff:3.500A) Processing sheet with id=AN2, first strand: chain 'M' and resid 59 through 61 removed outlier: 6.927A pdb=" N TRP M 38 " --> pdb=" O ILE M 50 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N CYS M 52 " --> pdb=" O TRP M 36 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N TRP M 36 " --> pdb=" O CYS M 52 " (cutoff:3.500A) Processing sheet with id=AN3, first strand: chain 'M' and resid 127 through 131 removed outlier: 3.651A pdb=" N GLY M 146 " --> pdb=" O LEU M 131 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N TYR M 183 " --> pdb=" O ASP M 151 " (cutoff:3.500A) Processing sheet with id=AN4, first strand: chain 'M' and resid 127 through 131 removed outlier: 3.651A pdb=" N GLY M 146 " --> pdb=" O LEU M 131 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N TYR M 183 " --> pdb=" O ASP M 151 " (cutoff:3.500A) Processing sheet with id=AN5, first strand: chain 'M' and resid 158 through 161 removed outlier: 4.227A pdb=" N TYR M 201 " --> pdb=" O VAL M 218 " (cutoff:3.500A) 1647 hydrogen bonds defined for protein. 4272 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: 26.46 Time building geometry restraints manager: 12.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 14406 1.35 - 1.47: 11533 1.47 - 1.59: 20168 1.59 - 1.71: 0 1.71 - 1.83: 219 Bond restraints: 46326 Sorted by residual: bond pdb=" N ILE B 235 " pdb=" CA ILE B 235 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.17e-02 7.31e+03 1.09e+01 bond pdb=" N ILE B 233 " pdb=" CA ILE B 233 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.85e+00 bond pdb=" N ASN B 657 " pdb=" CA ASN B 657 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.28e-02 6.10e+03 7.18e+00 bond pdb=" C LYS N 212 " pdb=" N PRO N 213 " ideal model delta sigma weight residual 1.336 1.367 -0.031 1.20e-02 6.94e+03 6.87e+00 bond pdb=" N ASN B 234 " pdb=" CA ASN B 234 " ideal model delta sigma weight residual 1.455 1.487 -0.031 1.21e-02 6.83e+03 6.74e+00 ... (remaining 46321 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 61888 1.83 - 3.65: 1090 3.65 - 5.48: 92 5.48 - 7.31: 45 7.31 - 9.14: 11 Bond angle restraints: 63126 Sorted by residual: angle pdb=" O GLY C 526 " pdb=" C GLY C 526 " pdb=" N PRO C 527 " ideal model delta sigma weight residual 121.77 113.78 7.99 1.00e+00 1.00e+00 6.38e+01 angle pdb=" CA LYS C 558 " pdb=" CB LYS C 558 " pdb=" CG LYS C 558 " ideal model delta sigma weight residual 114.10 121.45 -7.35 2.00e+00 2.50e-01 1.35e+01 angle pdb=" CA GLN J 3 " pdb=" CB GLN J 3 " pdb=" CG GLN J 3 " ideal model delta sigma weight residual 114.10 121.27 -7.17 2.00e+00 2.50e-01 1.28e+01 angle pdb=" C GLY H 27 " pdb=" N THR H 28 " pdb=" CA THR H 28 " ideal model delta sigma weight residual 121.54 128.24 -6.70 1.91e+00 2.74e-01 1.23e+01 angle pdb=" C GLY N 27 " pdb=" N THR N 28 " pdb=" CA THR N 28 " ideal model delta sigma weight residual 121.54 128.23 -6.69 1.91e+00 2.74e-01 1.23e+01 ... (remaining 63121 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 25468 18.00 - 35.99: 2207 35.99 - 53.99: 577 53.99 - 71.99: 89 71.99 - 89.98: 45 Dihedral angle restraints: 28386 sinusoidal: 11541 harmonic: 16845 Sorted by residual: dihedral pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " pdb=" CB CYS B 649 " ideal model delta sinusoidal sigma weight residual -86.00 -173.63 87.63 1 1.00e+01 1.00e-02 9.20e+01 dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual 93.00 5.40 87.60 1 1.00e+01 1.00e-02 9.20e+01 dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual -86.00 -171.05 85.05 1 1.00e+01 1.00e-02 8.77e+01 ... (remaining 28383 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.239: 7331 0.239 - 0.478: 4 0.478 - 0.718: 2 0.718 - 0.957: 0 0.957 - 1.196: 1 Chirality restraints: 7338 Sorted by residual: chirality pdb=" C1 NAG B1309 " pdb=" ND2 ASN B 657 " pdb=" C2 NAG B1309 " pdb=" O5 NAG B1309 " both_signs ideal model delta sigma weight residual False -2.40 -1.20 -1.20 2.00e-01 2.50e+01 3.58e+01 chirality pdb=" C1 NAG C1302 " pdb=" ND2 ASN C 122 " pdb=" C2 NAG C1302 " pdb=" O5 NAG C1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.16e+00 chirality pdb=" C1 NAG C1303 " pdb=" ND2 ASN C 165 " pdb=" C2 NAG C1303 " pdb=" O5 NAG C1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.89 -0.51 2.00e-01 2.50e+01 6.45e+00 ... (remaining 7335 not shown) Planarity restraints: 8106 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY C 526 " 0.053 2.00e-02 2.50e+03 1.01e-01 1.02e+02 pdb=" C GLY C 526 " -0.175 2.00e-02 2.50e+03 pdb=" O GLY C 526 " 0.065 2.00e-02 2.50e+03 pdb=" N PRO C 527 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY O 112 " 0.033 2.00e-02 2.50e+03 6.46e-02 4.18e+01 pdb=" C GLY O 112 " -0.112 2.00e-02 2.50e+03 pdb=" O GLY O 112 " 0.042 2.00e-02 2.50e+03 pdb=" N GLN O 113 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 102 " 0.014 2.00e-02 2.50e+03 1.41e-02 4.98e+00 pdb=" CG TRP E 102 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP E 102 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP E 102 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 102 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP E 102 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP E 102 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 102 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 102 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP E 102 " 0.004 2.00e-02 2.50e+03 ... (remaining 8103 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 2229 2.72 - 3.27: 41518 3.27 - 3.81: 74047 3.81 - 4.36: 85210 4.36 - 4.90: 148594 Nonbonded interactions: 351598 Sorted by model distance: nonbonded pdb=" CB SER K 13 " pdb=" CB LEU K 110 " model vdw 2.181 3.840 nonbonded pdb=" CA SER K 13 " pdb=" CB LEU K 110 " model vdw 2.196 3.870 nonbonded pdb=" OG SER M 7 " pdb=" OG1 THR M 21 " model vdw 2.248 3.040 nonbonded pdb=" OG SER K 28 " pdb=" OG SER K 31 " model vdw 2.250 3.040 nonbonded pdb=" OG1 THR C 333 " pdb=" OD2 ASP C 364 " model vdw 2.251 3.040 ... (remaining 351593 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'K' } ncs_group { reference = chain 'E' selection = chain 'J' selection = chain 'M' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'N' } ncs_group { reference = chain 'I' selection = chain 'L' selection = chain 'O' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.310 Construct map_model_manager: 0.060 Extract box with map and model: 1.710 Check model and map are aligned: 0.330 Set scattering table: 0.400 Process input model: 105.880 Find NCS groups from input model: 2.060 Set up NCS constraints: 0.430 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 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 0.048 46326 Z= 0.199 Angle : 0.566 9.136 63126 Z= 0.292 Chirality : 0.048 1.196 7338 Planarity : 0.005 0.101 8061 Dihedral : 14.344 89.983 17400 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.68 % Favored : 96.30 % Rotamer: Outliers : 0.80 % Allowed : 18.37 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.11), residues: 5763 helix: 0.66 (0.20), residues: 648 sheet: 0.21 (0.13), residues: 1673 loop : -1.49 (0.10), residues: 3442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP E 102 HIS 0.003 0.001 HIS G 211 PHE 0.020 0.001 PHE B 133 TYR 0.027 0.001 TYR E 54 ARG 0.009 0.000 ARG M 106 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11526 Ramachandran restraints generated. 5763 Oldfield, 0 Emsley, 5763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11526 Ramachandran restraints generated. 5763 Oldfield, 0 Emsley, 5763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 246 time to evaluate : 4.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 LYS cc_start: 0.8250 (mmtt) cc_final: 0.7825 (mmtm) REVERT: B 137 ASN cc_start: 0.5908 (m110) cc_final: 0.5401 (t0) REVERT: B 177 MET cc_start: 0.1452 (mtm) cc_final: -0.1688 (mmt) REVERT: B 523 THR cc_start: 0.5982 (OUTLIER) cc_final: 0.5686 (p) REVERT: B 524 VAL cc_start: 0.1745 (OUTLIER) cc_final: 0.1427 (p) REVERT: B 869 MET cc_start: 0.9057 (mtt) cc_final: 0.8842 (mtp) REVERT: B 1130 ILE cc_start: 0.7880 (pt) cc_final: 0.7620 (mt) REVERT: C 144 TYR cc_start: 0.6869 (t80) cc_final: 0.6089 (t80) REVERT: H 204 THR cc_start: 0.7742 (p) cc_final: 0.7371 (m) REVERT: L 71 THR cc_start: 0.5711 (OUTLIER) cc_final: 0.5447 (m) REVERT: G 207 CYS cc_start: 0.3606 (OUTLIER) cc_final: 0.3311 (t) REVERT: N 207 CYS cc_start: 0.4950 (OUTLIER) cc_final: 0.3362 (t) REVERT: O 16 GLN cc_start: 0.4630 (pp30) cc_final: 0.4282 (mt0) REVERT: O 111 LEU cc_start: 0.3849 (tp) cc_final: 0.3536 (mt) REVERT: O 165 GLU cc_start: 0.2670 (pp20) cc_final: 0.1937 (mm-30) REVERT: O 171 LYS cc_start: 0.1936 (mmtt) cc_final: 0.1447 (tttp) REVERT: F 12 GLU cc_start: 0.7877 (tp30) cc_final: 0.6500 (tt0) REVERT: J 153 PHE cc_start: 0.4754 (t80) cc_final: 0.4532 (t80) REVERT: J 180 SER cc_start: 0.4952 (p) cc_final: 0.4588 (m) REVERT: J 183 TYR cc_start: 0.6084 (m-80) cc_final: 0.5805 (m-80) REVERT: M 3 GLN cc_start: 0.8167 (tm-30) cc_final: 0.7643 (pp30) outliers start: 40 outliers final: 8 residues processed: 283 average time/residue: 0.6321 time to fit residues: 287.7076 Evaluate side-chains 150 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 137 time to evaluate : 4.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain G residue 207 CYS Chi-restraints excluded: chain N residue 207 CYS Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain J residue 99 ARG Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 110 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 486 optimal weight: 30.0000 chunk 436 optimal weight: 7.9990 chunk 242 optimal weight: 0.0770 chunk 149 optimal weight: 30.0000 chunk 294 optimal weight: 0.8980 chunk 233 optimal weight: 9.9990 chunk 451 optimal weight: 0.7980 chunk 174 optimal weight: 4.9990 chunk 274 optimal weight: 1.9990 chunk 336 optimal weight: 40.0000 chunk 523 optimal weight: 20.0000 overall best weight: 1.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN A 388 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN B 613 GLN B 751 ASN B 895 GLN B 913 GLN C 66 HIS ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 ASN C 506 GLN L 81 GLN ** L 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 GLN I 113 GLN I 202 HIS N 3 GLN ** O 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 GLN ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 206 ASN K 119 GLN ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 46326 Z= 0.249 Angle : 0.563 9.640 63126 Z= 0.292 Chirality : 0.045 0.495 7338 Planarity : 0.004 0.050 8061 Dihedral : 5.401 59.850 7435 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.28 % Allowed : 17.97 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % 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: -0.82 (0.11), residues: 5763 helix: 0.98 (0.21), residues: 709 sheet: 0.24 (0.13), residues: 1791 loop : -1.40 (0.10), residues: 3263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP O 37 HIS 0.019 0.001 HIS N 175 PHE 0.020 0.001 PHE B 133 TYR 0.023 0.001 TYR A 170 ARG 0.013 0.001 ARG C 214 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11526 Ramachandran restraints generated. 5763 Oldfield, 0 Emsley, 5763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11526 Ramachandran restraints generated. 5763 Oldfield, 0 Emsley, 5763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 148 time to evaluate : 5.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ILE cc_start: 0.7573 (OUTLIER) cc_final: 0.7297 (mt) REVERT: A 202 LYS cc_start: 0.7955 (mmtt) cc_final: 0.7531 (mmtm) REVERT: A 215 ASP cc_start: 0.6174 (m-30) cc_final: 0.5362 (p0) REVERT: A 598 ILE cc_start: 0.8808 (OUTLIER) cc_final: 0.8535 (mp) REVERT: B 137 ASN cc_start: 0.6021 (m110) cc_final: 0.5559 (p0) REVERT: B 177 MET cc_start: 0.2132 (mtm) cc_final: 0.1810 (pmm) REVERT: B 234 ASN cc_start: 0.6037 (OUTLIER) cc_final: 0.5831 (t0) REVERT: B 869 MET cc_start: 0.9016 (mtt) cc_final: 0.8762 (mtp) REVERT: B 1086 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.7978 (pttp) REVERT: B 1130 ILE cc_start: 0.8298 (pt) cc_final: 0.8070 (mt) REVERT: C 105 ILE cc_start: 0.7429 (OUTLIER) cc_final: 0.7207 (pt) REVERT: C 166 CYS cc_start: 0.3698 (OUTLIER) cc_final: 0.3236 (p) REVERT: C 740 MET cc_start: 0.7854 (mmm) cc_final: 0.7466 (mmm) REVERT: C 993 ILE cc_start: 0.8911 (OUTLIER) cc_final: 0.8554 (tp) REVERT: H 6 GLU cc_start: 0.4447 (OUTLIER) cc_final: 0.2670 (mt-10) REVERT: H 157 PHE cc_start: -0.0884 (OUTLIER) cc_final: -0.1089 (t80) REVERT: L 71 THR cc_start: 0.5717 (OUTLIER) cc_final: 0.5474 (m) REVERT: L 81 GLN cc_start: 0.3855 (OUTLIER) cc_final: 0.3476 (pm20) REVERT: L 107 LYS cc_start: 0.4218 (tttp) cc_final: 0.3792 (mmtt) REVERT: N 170 LEU cc_start: 0.5226 (OUTLIER) cc_final: 0.4696 (pp) REVERT: N 207 CYS cc_start: 0.4951 (OUTLIER) cc_final: 0.2797 (t) REVERT: O 16 GLN cc_start: 0.5104 (pp30) cc_final: 0.4516 (mt0) REVERT: O 110 VAL cc_start: 0.1413 (OUTLIER) cc_final: 0.1093 (t) REVERT: O 111 LEU cc_start: 0.3967 (tp) cc_final: 0.3721 (mt) REVERT: O 113 GLN cc_start: -0.1856 (mm-40) cc_final: -0.2376 (pm20) REVERT: O 171 LYS cc_start: 0.2408 (mmtt) cc_final: 0.1998 (tttp) REVERT: D 204 CYS cc_start: 0.4392 (OUTLIER) cc_final: 0.3341 (p) REVERT: E 3 GLN cc_start: 0.7815 (mm110) cc_final: 0.7216 (mm110) REVERT: E 176 VAL cc_start: -0.0026 (OUTLIER) cc_final: -0.0578 (t) REVERT: J 5 GLN cc_start: 0.8425 (tm-30) cc_final: 0.8180 (pp30) REVERT: J 180 SER cc_start: 0.4747 (p) cc_final: 0.4439 (m) REVERT: J 183 TYR cc_start: 0.5917 (m-80) cc_final: 0.5711 (m-80) outliers start: 114 outliers final: 33 residues processed: 254 average time/residue: 0.5523 time to fit residues: 245.0451 Evaluate side-chains 171 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 122 time to evaluate : 4.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 157 PHE Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 81 GLN Chi-restraints excluded: chain L residue 186 THR Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 207 CYS Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain O residue 139 CYS Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 204 CYS Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain M residue 79 GLN Chi-restraints excluded: chain M residue 122 SER Chi-restraints excluded: chain M residue 176 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 290 optimal weight: 2.9990 chunk 162 optimal weight: 7.9990 chunk 435 optimal weight: 30.0000 chunk 356 optimal weight: 20.0000 chunk 144 optimal weight: 7.9990 chunk 524 optimal weight: 20.0000 chunk 566 optimal weight: 50.0000 chunk 466 optimal weight: 20.0000 chunk 519 optimal weight: 5.9990 chunk 178 optimal weight: 0.8980 chunk 420 optimal weight: 0.3980 overall best weight: 3.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1054 GLN C 66 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN C 580 GLN C 895 GLN ** C 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN ** L 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN ** O 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 171 HIS ** K 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 46326 Z= 0.431 Angle : 0.641 11.851 63126 Z= 0.330 Chirality : 0.047 0.497 7338 Planarity : 0.005 0.147 8061 Dihedral : 5.663 109.661 7422 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.42 % Favored : 95.54 % Rotamer: Outliers : 3.08 % Allowed : 17.81 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % 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: -0.90 (0.11), residues: 5763 helix: 0.61 (0.20), residues: 699 sheet: 0.18 (0.12), residues: 1871 loop : -1.39 (0.11), residues: 3193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP N 36 HIS 0.011 0.001 HIS A 49 PHE 0.025 0.002 PHE C 92 TYR 0.028 0.002 TYR A 380 ARG 0.011 0.001 ARG B 905 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11526 Ramachandran restraints generated. 5763 Oldfield, 0 Emsley, 5763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11526 Ramachandran restraints generated. 5763 Oldfield, 0 Emsley, 5763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 129 time to evaluate : 4.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.8402 (OUTLIER) cc_final: 0.8069 (t80) REVERT: A 238 PHE cc_start: 0.6525 (OUTLIER) cc_final: 0.5588 (p90) REVERT: A 1037 SER cc_start: 0.9073 (OUTLIER) cc_final: 0.8865 (p) REVERT: B 238 PHE cc_start: 0.7470 (OUTLIER) cc_final: 0.6841 (p90) REVERT: B 324 GLU cc_start: 0.6828 (OUTLIER) cc_final: 0.6548 (mp0) REVERT: B 969 ASN cc_start: 0.9228 (OUTLIER) cc_final: 0.8377 (p0) REVERT: B 1072 GLU cc_start: 0.9006 (OUTLIER) cc_final: 0.8562 (pm20) REVERT: B 1086 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.7958 (pttp) REVERT: C 105 ILE cc_start: 0.7497 (OUTLIER) cc_final: 0.7272 (pt) REVERT: C 166 CYS cc_start: 0.4512 (OUTLIER) cc_final: 0.4095 (p) REVERT: C 745 ASP cc_start: 0.8788 (OUTLIER) cc_final: 0.8453 (p0) REVERT: C 993 ILE cc_start: 0.9061 (OUTLIER) cc_final: 0.8653 (tp) REVERT: C 1063 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7951 (mt) REVERT: C 1072 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8568 (pt0) REVERT: C 1105 THR cc_start: 0.9388 (OUTLIER) cc_final: 0.9179 (p) REVERT: H 6 GLU cc_start: 0.5628 (OUTLIER) cc_final: 0.4271 (mt-10) REVERT: H 157 PHE cc_start: -0.0577 (OUTLIER) cc_final: -0.0807 (t80) REVERT: L 63 ARG cc_start: 0.4911 (OUTLIER) cc_final: 0.4567 (tmm-80) REVERT: L 71 THR cc_start: 0.5680 (OUTLIER) cc_final: 0.5435 (m) REVERT: L 107 LYS cc_start: 0.4451 (tttp) cc_final: 0.4085 (mmtt) REVERT: N 170 LEU cc_start: 0.5286 (OUTLIER) cc_final: 0.4612 (pp) REVERT: O 16 GLN cc_start: 0.5318 (pp30) cc_final: 0.4505 (mt0) REVERT: O 110 VAL cc_start: 0.1550 (OUTLIER) cc_final: 0.1186 (t) REVERT: O 113 GLN cc_start: -0.1772 (mm-40) cc_final: -0.2267 (pm20) REVERT: O 171 LYS cc_start: 0.2678 (mmtt) cc_final: 0.2238 (tttp) REVERT: O 176 LYS cc_start: 0.3224 (pttp) cc_final: 0.2970 (tmmt) REVERT: E 3 GLN cc_start: 0.7916 (mm110) cc_final: 0.7427 (mm110) REVERT: E 24 VAL cc_start: -0.0853 (OUTLIER) cc_final: -0.1334 (t) REVERT: E 176 VAL cc_start: -0.0099 (OUTLIER) cc_final: -0.0624 (t) REVERT: J 180 SER cc_start: 0.4822 (p) cc_final: 0.4522 (m) REVERT: K 147 ILE cc_start: 0.1504 (OUTLIER) cc_final: 0.1235 (tt) REVERT: M 109 TYR cc_start: 0.8655 (OUTLIER) cc_final: 0.8435 (t80) REVERT: M 155 GLU cc_start: 0.3712 (mt-10) cc_final: 0.3449 (mm-30) outliers start: 154 outliers final: 71 residues processed: 273 average time/residue: 0.5141 time to fit residues: 248.0405 Evaluate side-chains 206 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 110 time to evaluate : 4.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 157 PHE Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain O residue 139 CYS Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 135 SER Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 34 TYR Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 128 LEU Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain M residue 109 TYR Chi-restraints excluded: chain M residue 145 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 517 optimal weight: 20.0000 chunk 393 optimal weight: 50.0000 chunk 271 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 250 optimal weight: 30.0000 chunk 351 optimal weight: 40.0000 chunk 525 optimal weight: 30.0000 chunk 556 optimal weight: 7.9990 chunk 274 optimal weight: 0.7980 chunk 498 optimal weight: 40.0000 chunk 150 optimal weight: 9.9990 overall best weight: 4.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 189 GLN ** O 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 46326 Z= 0.455 Angle : 0.640 10.007 63126 Z= 0.328 Chirality : 0.047 0.471 7338 Planarity : 0.005 0.078 8061 Dihedral : 5.555 99.984 7419 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.72 % Favored : 95.23 % Rotamer: Outliers : 3.38 % Allowed : 18.49 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % 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: -0.99 (0.11), residues: 5763 helix: 0.54 (0.20), residues: 715 sheet: 0.06 (0.12), residues: 1781 loop : -1.38 (0.10), residues: 3267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 36 HIS 0.010 0.001 HIS A1058 PHE 0.025 0.002 PHE A 377 TYR 0.020 0.002 TYR A 380 ARG 0.010 0.001 ARG B 905 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11526 Ramachandran restraints generated. 5763 Oldfield, 0 Emsley, 5763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11526 Ramachandran restraints generated. 5763 Oldfield, 0 Emsley, 5763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 126 time to evaluate : 4.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.8090 (m-80) cc_final: 0.7736 (m-80) REVERT: A 144 TYR cc_start: 0.8283 (t80) cc_final: 0.8043 (t80) REVERT: A 200 TYR cc_start: 0.8323 (OUTLIER) cc_final: 0.8004 (t80) REVERT: A 205 SER cc_start: 0.8757 (OUTLIER) cc_final: 0.8480 (t) REVERT: A 227 VAL cc_start: 0.8977 (p) cc_final: 0.8769 (t) REVERT: A 238 PHE cc_start: 0.6667 (OUTLIER) cc_final: 0.5613 (p90) REVERT: A 740 MET cc_start: 0.8469 (mmm) cc_final: 0.8261 (mmm) REVERT: A 995 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.8303 (mtm110) REVERT: A 1031 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.8000 (mt-10) REVERT: A 1037 SER cc_start: 0.9051 (OUTLIER) cc_final: 0.8805 (p) REVERT: A 1092 GLU cc_start: 0.8133 (pm20) cc_final: 0.7899 (pm20) REVERT: B 177 MET cc_start: 0.2722 (mtm) cc_final: -0.1158 (mmt) REVERT: B 238 PHE cc_start: 0.7506 (OUTLIER) cc_final: 0.6576 (p90) REVERT: B 329 PHE cc_start: 0.7311 (m-10) cc_final: 0.6931 (m-10) REVERT: B 714 ILE cc_start: 0.9277 (OUTLIER) cc_final: 0.9061 (mt) REVERT: B 745 ASP cc_start: 0.8916 (m-30) cc_final: 0.7968 (t0) REVERT: B 959 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8922 (mt) REVERT: B 969 ASN cc_start: 0.9177 (OUTLIER) cc_final: 0.8453 (p0) REVERT: B 1031 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7260 (mt-10) REVERT: B 1072 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8533 (pm20) REVERT: C 105 ILE cc_start: 0.7361 (OUTLIER) cc_final: 0.7133 (pt) REVERT: C 136 CYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7795 (p) REVERT: C 166 CYS cc_start: 0.3798 (OUTLIER) cc_final: 0.3340 (p) REVERT: C 231 ILE cc_start: 0.7910 (OUTLIER) cc_final: 0.7692 (mp) REVERT: C 565 PHE cc_start: 0.8035 (OUTLIER) cc_final: 0.7700 (m-80) REVERT: C 592 PHE cc_start: 0.5776 (OUTLIER) cc_final: 0.4718 (m-80) REVERT: C 730 SER cc_start: 0.9411 (OUTLIER) cc_final: 0.9145 (p) REVERT: C 740 MET cc_start: 0.8379 (mmm) cc_final: 0.8114 (mmm) REVERT: C 745 ASP cc_start: 0.8893 (OUTLIER) cc_final: 0.8601 (p0) REVERT: C 993 ILE cc_start: 0.9197 (OUTLIER) cc_final: 0.8782 (tp) REVERT: C 1063 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.7992 (mt) REVERT: C 1072 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8623 (pt0) REVERT: C 1115 ILE cc_start: 0.8920 (OUTLIER) cc_final: 0.8553 (mm) REVERT: H 6 GLU cc_start: 0.5841 (OUTLIER) cc_final: 0.4977 (mt-10) REVERT: H 157 PHE cc_start: -0.0507 (OUTLIER) cc_final: -0.0708 (t80) REVERT: L 71 THR cc_start: 0.5564 (OUTLIER) cc_final: 0.5339 (m) REVERT: L 107 LYS cc_start: 0.4802 (tttp) cc_final: 0.4485 (mmtt) REVERT: N 170 LEU cc_start: 0.5640 (OUTLIER) cc_final: 0.4966 (pp) REVERT: O 16 GLN cc_start: 0.5859 (pp30) cc_final: 0.4850 (mt0) REVERT: O 113 GLN cc_start: -0.1486 (mm-40) cc_final: -0.2306 (pm20) REVERT: D 12 GLU cc_start: 0.4476 (OUTLIER) cc_final: 0.3932 (tt0) REVERT: D 204 CYS cc_start: 0.4811 (OUTLIER) cc_final: 0.4144 (p) REVERT: E 3 GLN cc_start: 0.7662 (mm110) cc_final: 0.7234 (mm110) REVERT: E 24 VAL cc_start: -0.0194 (OUTLIER) cc_final: -0.0668 (t) REVERT: E 176 VAL cc_start: 0.0051 (OUTLIER) cc_final: -0.0486 (t) REVERT: J 180 SER cc_start: 0.4830 (p) cc_final: 0.4571 (m) REVERT: K 147 ILE cc_start: 0.2049 (OUTLIER) cc_final: 0.1542 (tt) REVERT: M 155 GLU cc_start: 0.3770 (mt-10) cc_final: 0.3457 (mm-30) outliers start: 169 outliers final: 80 residues processed: 287 average time/residue: 0.5448 time to fit residues: 274.9355 Evaluate side-chains 220 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 107 time to evaluate : 4.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 157 PHE Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 218 VAL Chi-restraints excluded: chain O residue 196 TYR Chi-restraints excluded: chain D residue 12 GLU Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 204 CYS Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 54 TYR Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain J residue 5 GLN Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain M residue 145 LEU Chi-restraints excluded: chain M residue 176 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 463 optimal weight: 3.9990 chunk 316 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 414 optimal weight: 10.0000 chunk 229 optimal weight: 2.9990 chunk 475 optimal weight: 40.0000 chunk 384 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 284 optimal weight: 0.7980 chunk 499 optimal weight: 50.0000 chunk 140 optimal weight: 7.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN A 957 GLN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 920 GLN ** H 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 189 GLN I 193 HIS ** O 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 46326 Z= 0.242 Angle : 0.527 9.692 63126 Z= 0.271 Chirality : 0.044 0.449 7338 Planarity : 0.004 0.071 8061 Dihedral : 5.165 98.528 7418 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.99 % Favored : 95.96 % Rotamer: Outliers : 2.54 % Allowed : 19.60 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.11), residues: 5763 helix: 1.15 (0.20), residues: 691 sheet: 0.09 (0.12), residues: 1796 loop : -1.30 (0.11), residues: 3276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 110 HIS 0.005 0.001 HIS C1088 PHE 0.029 0.001 PHE F 150 TYR 0.017 0.001 TYR A 170 ARG 0.008 0.000 ARG K 62 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11526 Ramachandran restraints generated. 5763 Oldfield, 0 Emsley, 5763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11526 Ramachandran restraints generated. 5763 Oldfield, 0 Emsley, 5763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 113 time to evaluate : 5.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.8023 (m-80) cc_final: 0.7791 (m-80) REVERT: A 144 TYR cc_start: 0.8351 (t80) cc_final: 0.8127 (t80) REVERT: A 153 MET cc_start: 0.7720 (pmm) cc_final: 0.7514 (pmm) REVERT: A 200 TYR cc_start: 0.8294 (OUTLIER) cc_final: 0.7947 (t80) REVERT: A 205 SER cc_start: 0.8720 (OUTLIER) cc_final: 0.8385 (t) REVERT: A 995 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.8289 (mtm110) REVERT: A 1092 GLU cc_start: 0.7994 (pm20) cc_final: 0.7749 (pm20) REVERT: B 177 MET cc_start: 0.1941 (mtm) cc_final: -0.1781 (mmt) REVERT: B 179 LEU cc_start: 0.4271 (OUTLIER) cc_final: 0.4056 (tp) REVERT: B 200 TYR cc_start: 0.8285 (m-80) cc_final: 0.7713 (t80) REVERT: B 238 PHE cc_start: 0.7508 (OUTLIER) cc_final: 0.6562 (p90) REVERT: B 242 LEU cc_start: 0.8624 (mp) cc_final: 0.8221 (tp) REVERT: B 745 ASP cc_start: 0.8898 (m-30) cc_final: 0.7952 (t0) REVERT: B 969 ASN cc_start: 0.9131 (OUTLIER) cc_final: 0.8409 (p0) REVERT: B 1072 GLU cc_start: 0.8973 (OUTLIER) cc_final: 0.8631 (pm20) REVERT: C 105 ILE cc_start: 0.7219 (OUTLIER) cc_final: 0.6951 (pt) REVERT: C 166 CYS cc_start: 0.3814 (OUTLIER) cc_final: 0.3346 (p) REVERT: C 592 PHE cc_start: 0.5633 (OUTLIER) cc_final: 0.4447 (m-80) REVERT: C 993 ILE cc_start: 0.9134 (OUTLIER) cc_final: 0.8626 (tp) REVERT: H 6 GLU cc_start: 0.6017 (OUTLIER) cc_final: 0.5219 (mt-10) REVERT: H 20 VAL cc_start: -0.4378 (OUTLIER) cc_final: -0.4910 (t) REVERT: H 157 PHE cc_start: -0.0473 (OUTLIER) cc_final: -0.0707 (t80) REVERT: L 107 LYS cc_start: 0.4844 (tttp) cc_final: 0.4499 (mmtt) REVERT: N 170 LEU cc_start: 0.5654 (OUTLIER) cc_final: 0.5119 (pp) REVERT: O 171 LYS cc_start: 0.2715 (mmtm) cc_final: 0.2157 (tttp) REVERT: D 12 GLU cc_start: 0.4149 (OUTLIER) cc_final: 0.3550 (tt0) REVERT: D 204 CYS cc_start: 0.4814 (OUTLIER) cc_final: 0.4156 (p) REVERT: E 3 GLN cc_start: 0.7689 (mm110) cc_final: 0.7264 (mm110) REVERT: E 24 VAL cc_start: -0.0142 (OUTLIER) cc_final: -0.0768 (t) REVERT: E 176 VAL cc_start: -0.0009 (OUTLIER) cc_final: -0.0565 (t) REVERT: J 180 SER cc_start: 0.5041 (p) cc_final: 0.4820 (m) REVERT: K 147 ILE cc_start: 0.1984 (OUTLIER) cc_final: 0.1436 (tt) REVERT: M 155 GLU cc_start: 0.3775 (mt-10) cc_final: 0.3470 (mm-30) outliers start: 127 outliers final: 65 residues processed: 232 average time/residue: 0.5146 time to fit residues: 212.1002 Evaluate side-chains 191 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 106 time to evaluate : 4.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 157 PHE Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain I residue 10 VAL Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 218 VAL Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain O residue 139 CYS Chi-restraints excluded: chain D residue 12 GLU Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 204 CYS Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 54 TYR Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 34 TYR Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 136 LYS Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain M residue 122 SER Chi-restraints excluded: chain M residue 145 LEU Chi-restraints excluded: chain M residue 176 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 187 optimal weight: 0.6980 chunk 501 optimal weight: 40.0000 chunk 110 optimal weight: 2.9990 chunk 326 optimal weight: 50.0000 chunk 137 optimal weight: 2.9990 chunk 557 optimal weight: 50.0000 chunk 462 optimal weight: 20.0000 chunk 258 optimal weight: 40.0000 chunk 46 optimal weight: 3.9990 chunk 184 optimal weight: 3.9990 chunk 292 optimal weight: 1.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 ASN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN I 91 GLN I 189 GLN I 193 HIS ** O 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 189 GLN E 5 GLN ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN ** J 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 137 GLN ** K 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 46326 Z= 0.308 Angle : 0.552 8.646 63126 Z= 0.282 Chirality : 0.045 0.446 7338 Planarity : 0.004 0.070 8061 Dihedral : 5.029 92.112 7417 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.67 % Favored : 95.28 % Rotamer: Outliers : 2.92 % Allowed : 19.52 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % 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: -0.79 (0.11), residues: 5763 helix: 1.05 (0.20), residues: 691 sheet: 0.10 (0.12), residues: 1795 loop : -1.26 (0.11), residues: 3277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 110 HIS 0.006 0.001 HIS C 49 PHE 0.017 0.001 PHE A 238 TYR 0.017 0.001 TYR E 54 ARG 0.005 0.000 ARG B 905 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11526 Ramachandran restraints generated. 5763 Oldfield, 0 Emsley, 5763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11526 Ramachandran restraints generated. 5763 Oldfield, 0 Emsley, 5763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 109 time to evaluate : 4.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.8237 (m-80) cc_final: 0.7884 (m-80) REVERT: A 144 TYR cc_start: 0.8216 (t80) cc_final: 0.7936 (t80) REVERT: A 153 MET cc_start: 0.7894 (pmm) cc_final: 0.7263 (pmm) REVERT: A 200 TYR cc_start: 0.8256 (OUTLIER) cc_final: 0.7977 (t80) REVERT: A 205 SER cc_start: 0.8748 (OUTLIER) cc_final: 0.8436 (t) REVERT: A 820 ASP cc_start: 0.8690 (OUTLIER) cc_final: 0.7955 (m-30) REVERT: A 995 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.8300 (mtm110) REVERT: A 1037 SER cc_start: 0.9038 (OUTLIER) cc_final: 0.8826 (p) REVERT: A 1092 GLU cc_start: 0.8043 (pm20) cc_final: 0.7751 (pm20) REVERT: A 1106 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.8498 (pt0) REVERT: B 177 MET cc_start: 0.1906 (mtm) cc_final: 0.1692 (pmm) REVERT: B 200 TYR cc_start: 0.8358 (m-80) cc_final: 0.7763 (t80) REVERT: B 278 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8508 (tptp) REVERT: B 324 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.7002 (mp0) REVERT: B 745 ASP cc_start: 0.8829 (m-30) cc_final: 0.7890 (t0) REVERT: B 969 ASN cc_start: 0.9171 (OUTLIER) cc_final: 0.8474 (p0) REVERT: B 1072 GLU cc_start: 0.9013 (OUTLIER) cc_final: 0.8640 (pm20) REVERT: C 105 ILE cc_start: 0.7267 (OUTLIER) cc_final: 0.6992 (pt) REVERT: C 136 CYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8126 (p) REVERT: C 166 CYS cc_start: 0.3772 (OUTLIER) cc_final: 0.3356 (p) REVERT: C 592 PHE cc_start: 0.5819 (OUTLIER) cc_final: 0.4615 (m-80) REVERT: C 730 SER cc_start: 0.9345 (OUTLIER) cc_final: 0.9090 (p) REVERT: C 740 MET cc_start: 0.8567 (mmm) cc_final: 0.8286 (mmm) REVERT: H 6 GLU cc_start: 0.6274 (OUTLIER) cc_final: 0.5609 (mt-10) REVERT: H 20 VAL cc_start: -0.4250 (OUTLIER) cc_final: -0.4806 (t) REVERT: H 157 PHE cc_start: -0.0461 (OUTLIER) cc_final: -0.0687 (t80) REVERT: L 71 THR cc_start: 0.5314 (OUTLIER) cc_final: 0.5078 (m) REVERT: L 107 LYS cc_start: 0.4534 (tttp) cc_final: 0.4229 (mmtt) REVERT: N 170 LEU cc_start: 0.5658 (OUTLIER) cc_final: 0.5126 (pp) REVERT: O 171 LYS cc_start: 0.1765 (mmtm) cc_final: 0.1155 (tttp) REVERT: O 176 LYS cc_start: 0.3639 (tmmt) cc_final: 0.3384 (tmmt) REVERT: D 12 GLU cc_start: 0.4080 (OUTLIER) cc_final: 0.3479 (tt0) REVERT: D 204 CYS cc_start: 0.4848 (OUTLIER) cc_final: 0.4200 (p) REVERT: E 3 GLN cc_start: 0.7756 (mm110) cc_final: 0.7337 (mm110) REVERT: E 24 VAL cc_start: 0.0699 (OUTLIER) cc_final: 0.0237 (t) REVERT: E 176 VAL cc_start: -0.1038 (OUTLIER) cc_final: -0.1538 (t) REVERT: J 180 SER cc_start: 0.4545 (p) cc_final: 0.4248 (m) REVERT: K 147 ILE cc_start: 0.2159 (OUTLIER) cc_final: 0.1700 (tt) REVERT: M 155 GLU cc_start: 0.3801 (mt-10) cc_final: 0.3467 (mm-30) outliers start: 146 outliers final: 93 residues processed: 248 average time/residue: 0.5224 time to fit residues: 230.3537 Evaluate side-chains 221 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 103 time to evaluate : 4.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 157 PHE Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain N residue 122 VAL Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 218 VAL Chi-restraints excluded: chain O residue 139 CYS Chi-restraints excluded: chain O residue 196 TYR Chi-restraints excluded: chain D residue 12 GLU Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 204 CYS Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 54 TYR Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 136 LYS Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain M residue 122 SER Chi-restraints excluded: chain M residue 145 LEU Chi-restraints excluded: chain M residue 176 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 537 optimal weight: 20.0000 chunk 62 optimal weight: 0.5980 chunk 317 optimal weight: 2.9990 chunk 406 optimal weight: 6.9990 chunk 315 optimal weight: 0.4980 chunk 469 optimal weight: 50.0000 chunk 311 optimal weight: 0.8980 chunk 555 optimal weight: 20.0000 chunk 347 optimal weight: 20.0000 chunk 338 optimal weight: 50.0000 chunk 256 optimal weight: 0.8980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 992 GLN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN C 460 ASN L 91 GLN I 91 GLN I 189 GLN I 193 HIS ** O 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 46326 Z= 0.182 Angle : 0.498 9.000 63126 Z= 0.255 Chirality : 0.043 0.427 7338 Planarity : 0.004 0.066 8061 Dihedral : 4.778 87.571 7417 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.89 % Favored : 96.06 % Rotamer: Outliers : 2.54 % Allowed : 19.92 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % 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: -0.64 (0.11), residues: 5763 helix: 1.30 (0.21), residues: 690 sheet: 0.24 (0.12), residues: 1803 loop : -1.22 (0.11), residues: 3270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 110 HIS 0.005 0.001 HIS C 49 PHE 0.016 0.001 PHE B 329 TYR 0.017 0.001 TYR A 380 ARG 0.005 0.000 ARG K 62 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11526 Ramachandran restraints generated. 5763 Oldfield, 0 Emsley, 5763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11526 Ramachandran restraints generated. 5763 Oldfield, 0 Emsley, 5763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 110 time to evaluate : 4.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.8268 (m-80) cc_final: 0.7866 (m-80) REVERT: A 136 CYS cc_start: 0.7912 (OUTLIER) cc_final: 0.7643 (p) REVERT: A 144 TYR cc_start: 0.8208 (t80) cc_final: 0.7933 (t80) REVERT: A 153 MET cc_start: 0.7885 (pmm) cc_final: 0.7269 (pmm) REVERT: A 200 TYR cc_start: 0.8359 (OUTLIER) cc_final: 0.8114 (t80) REVERT: A 205 SER cc_start: 0.8714 (OUTLIER) cc_final: 0.8376 (t) REVERT: A 995 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.8287 (mtm110) REVERT: A 1031 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7988 (mt-10) REVERT: A 1037 SER cc_start: 0.9071 (OUTLIER) cc_final: 0.8844 (p) REVERT: A 1092 GLU cc_start: 0.8003 (pm20) cc_final: 0.7691 (pm20) REVERT: B 200 TYR cc_start: 0.8465 (m-80) cc_final: 0.7915 (t80) REVERT: B 242 LEU cc_start: 0.8594 (mp) cc_final: 0.8199 (tp) REVERT: B 745 ASP cc_start: 0.8796 (m-30) cc_final: 0.7882 (t0) REVERT: B 969 ASN cc_start: 0.9140 (OUTLIER) cc_final: 0.8455 (p0) REVERT: C 105 ILE cc_start: 0.7061 (OUTLIER) cc_final: 0.6832 (pt) REVERT: C 136 CYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8139 (p) REVERT: C 166 CYS cc_start: 0.3670 (OUTLIER) cc_final: 0.3251 (p) REVERT: C 200 TYR cc_start: 0.8715 (OUTLIER) cc_final: 0.8186 (m-80) REVERT: C 592 PHE cc_start: 0.5586 (OUTLIER) cc_final: 0.4512 (m-80) REVERT: C 730 SER cc_start: 0.9317 (OUTLIER) cc_final: 0.9090 (p) REVERT: C 993 ILE cc_start: 0.8954 (OUTLIER) cc_final: 0.8419 (tp) REVERT: H 6 GLU cc_start: 0.6455 (OUTLIER) cc_final: 0.6067 (mt-10) REVERT: H 20 VAL cc_start: -0.4429 (OUTLIER) cc_final: -0.4669 (t) REVERT: H 70 ILE cc_start: 0.0479 (OUTLIER) cc_final: -0.0101 (mt) REVERT: H 157 PHE cc_start: -0.0454 (OUTLIER) cc_final: -0.0687 (t80) REVERT: L 71 THR cc_start: 0.5144 (OUTLIER) cc_final: 0.4899 (m) REVERT: L 107 LYS cc_start: 0.4557 (tttp) cc_final: 0.4245 (mmtt) REVERT: N 170 LEU cc_start: 0.5582 (OUTLIER) cc_final: 0.5098 (pp) REVERT: D 12 GLU cc_start: 0.4169 (OUTLIER) cc_final: 0.3534 (tt0) REVERT: D 204 CYS cc_start: 0.4829 (OUTLIER) cc_final: 0.4198 (p) REVERT: E 3 GLN cc_start: 0.7752 (mm110) cc_final: 0.7339 (mm110) REVERT: E 24 VAL cc_start: 0.1003 (OUTLIER) cc_final: 0.0506 (t) REVERT: J 180 SER cc_start: 0.4543 (p) cc_final: 0.4317 (m) REVERT: K 147 ILE cc_start: 0.2190 (OUTLIER) cc_final: 0.1643 (tt) REVERT: M 147 CYS cc_start: 0.1778 (p) cc_final: 0.1348 (m) REVERT: M 155 GLU cc_start: 0.3803 (mt-10) cc_final: 0.3475 (mm-30) outliers start: 127 outliers final: 74 residues processed: 231 average time/residue: 0.5476 time to fit residues: 224.4715 Evaluate side-chains 204 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 106 time to evaluate : 5.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 157 PHE Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain I residue 10 VAL Chi-restraints excluded: chain N residue 122 VAL Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 218 VAL Chi-restraints excluded: chain O residue 63 ARG Chi-restraints excluded: chain O residue 139 CYS Chi-restraints excluded: chain O residue 196 TYR Chi-restraints excluded: chain D residue 12 GLU Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 204 CYS Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 54 TYR Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 136 LYS Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain M residue 145 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 343 optimal weight: 50.0000 chunk 221 optimal weight: 2.9990 chunk 331 optimal weight: 40.0000 chunk 167 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 352 optimal weight: 9.9990 chunk 378 optimal weight: 30.0000 chunk 274 optimal weight: 0.0980 chunk 51 optimal weight: 9.9990 chunk 436 optimal weight: 30.0000 overall best weight: 2.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN L 91 GLN I 189 GLN I 193 HIS ** O 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 189 GLN ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.4181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 46326 Z= 0.336 Angle : 0.574 12.705 63126 Z= 0.291 Chirality : 0.045 0.414 7338 Planarity : 0.004 0.069 8061 Dihedral : 4.856 80.140 7417 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.88 % Favored : 95.07 % Rotamer: Outliers : 2.92 % Allowed : 19.72 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % 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: -0.70 (0.11), residues: 5763 helix: 1.09 (0.21), residues: 691 sheet: 0.14 (0.12), residues: 1825 loop : -1.20 (0.11), residues: 3247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 110 HIS 0.009 0.001 HIS B1064 PHE 0.019 0.002 PHE A 238 TYR 0.024 0.001 TYR E 183 ARG 0.005 0.000 ARG B 905 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11526 Ramachandran restraints generated. 5763 Oldfield, 0 Emsley, 5763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11526 Ramachandran restraints generated. 5763 Oldfield, 0 Emsley, 5763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 107 time to evaluate : 5.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.8156 (m-80) cc_final: 0.7729 (m-80) REVERT: A 136 CYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7696 (p) REVERT: A 144 TYR cc_start: 0.8254 (t80) cc_final: 0.7987 (t80) REVERT: A 153 MET cc_start: 0.7985 (pmm) cc_final: 0.7352 (pmm) REVERT: A 200 TYR cc_start: 0.8359 (OUTLIER) cc_final: 0.8060 (t80) REVERT: A 205 SER cc_start: 0.8752 (OUTLIER) cc_final: 0.8459 (t) REVERT: A 820 ASP cc_start: 0.8786 (OUTLIER) cc_final: 0.8198 (m-30) REVERT: A 995 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.8301 (mtm110) REVERT: A 1031 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7916 (mt-10) REVERT: A 1037 SER cc_start: 0.9036 (OUTLIER) cc_final: 0.8809 (p) REVERT: A 1092 GLU cc_start: 0.8088 (pm20) cc_final: 0.7778 (pm20) REVERT: A 1106 GLN cc_start: 0.9108 (OUTLIER) cc_final: 0.8430 (pt0) REVERT: B 200 TYR cc_start: 0.8475 (m-80) cc_final: 0.7878 (t80) REVERT: B 242 LEU cc_start: 0.8625 (mp) cc_final: 0.8214 (tp) REVERT: B 278 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8513 (tptp) REVERT: B 329 PHE cc_start: 0.7900 (m-80) cc_final: 0.7640 (m-80) REVERT: B 553 THR cc_start: 0.8014 (OUTLIER) cc_final: 0.7745 (t) REVERT: B 745 ASP cc_start: 0.8830 (m-30) cc_final: 0.8418 (p0) REVERT: B 969 ASN cc_start: 0.9102 (OUTLIER) cc_final: 0.8453 (p0) REVERT: B 1072 GLU cc_start: 0.9009 (OUTLIER) cc_final: 0.8621 (pm20) REVERT: C 105 ILE cc_start: 0.7154 (OUTLIER) cc_final: 0.6912 (pt) REVERT: C 136 CYS cc_start: 0.8472 (OUTLIER) cc_final: 0.8158 (p) REVERT: C 166 CYS cc_start: 0.3749 (OUTLIER) cc_final: 0.3370 (p) REVERT: C 200 TYR cc_start: 0.8660 (OUTLIER) cc_final: 0.8111 (m-80) REVERT: C 592 PHE cc_start: 0.5878 (OUTLIER) cc_final: 0.4745 (m-80) REVERT: C 730 SER cc_start: 0.9356 (OUTLIER) cc_final: 0.9105 (p) REVERT: H 6 GLU cc_start: 0.6777 (OUTLIER) cc_final: 0.6475 (mt-10) REVERT: H 20 VAL cc_start: -0.4137 (OUTLIER) cc_final: -0.4348 (t) REVERT: H 70 ILE cc_start: 0.0158 (OUTLIER) cc_final: -0.0328 (mt) REVERT: H 157 PHE cc_start: -0.0430 (OUTLIER) cc_final: -0.0657 (t80) REVERT: L 107 LYS cc_start: 0.4752 (tttp) cc_final: 0.4307 (mmtt) REVERT: G 181 LEU cc_start: 0.4643 (mm) cc_final: 0.4412 (tp) REVERT: N 48 MET cc_start: 0.3897 (mpp) cc_final: 0.2194 (ptp) REVERT: N 170 LEU cc_start: 0.5916 (OUTLIER) cc_final: 0.5478 (pp) REVERT: D 12 GLU cc_start: 0.4204 (OUTLIER) cc_final: 0.3563 (tt0) REVERT: D 204 CYS cc_start: 0.4881 (OUTLIER) cc_final: 0.4260 (p) REVERT: E 3 GLN cc_start: 0.7866 (mm110) cc_final: 0.7455 (mm110) REVERT: E 24 VAL cc_start: -0.0310 (OUTLIER) cc_final: -0.0862 (t) REVERT: E 34 TYR cc_start: 0.7843 (OUTLIER) cc_final: 0.7637 (t80) REVERT: J 11 LEU cc_start: 0.6683 (OUTLIER) cc_final: 0.6365 (tp) REVERT: K 147 ILE cc_start: 0.2414 (OUTLIER) cc_final: 0.1938 (tt) REVERT: M 147 CYS cc_start: 0.2434 (p) cc_final: 0.2216 (p) REVERT: M 155 GLU cc_start: 0.3850 (mt-10) cc_final: 0.3482 (mm-30) outliers start: 146 outliers final: 98 residues processed: 247 average time/residue: 0.5308 time to fit residues: 232.7053 Evaluate side-chains 229 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 102 time to evaluate : 4.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 157 PHE Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 91 GLN Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain I residue 10 VAL Chi-restraints excluded: chain N residue 122 VAL Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 218 VAL Chi-restraints excluded: chain O residue 63 ARG Chi-restraints excluded: chain O residue 139 CYS Chi-restraints excluded: chain O residue 189 GLN Chi-restraints excluded: chain D residue 12 GLU Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 204 CYS Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 34 TYR Chi-restraints excluded: chain E residue 54 TYR Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain M residue 122 SER Chi-restraints excluded: chain M residue 145 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 505 optimal weight: 30.0000 chunk 531 optimal weight: 40.0000 chunk 485 optimal weight: 7.9990 chunk 517 optimal weight: 0.0000 chunk 311 optimal weight: 0.5980 chunk 225 optimal weight: 20.0000 chunk 406 optimal weight: 8.9990 chunk 158 optimal weight: 4.9990 chunk 467 optimal weight: 20.0000 chunk 489 optimal weight: 7.9990 chunk 515 optimal weight: 2.9990 overall best weight: 3.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 81 GLN I 189 GLN I 193 HIS N 166 ASN ** O 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 137 GLN K 178 GLN ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 171 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.4392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 46326 Z= 0.380 Angle : 0.588 15.134 63126 Z= 0.299 Chirality : 0.045 0.409 7338 Planarity : 0.004 0.074 8061 Dihedral : 4.913 73.383 7417 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.72 % Favored : 95.23 % Rotamer: Outliers : 2.86 % Allowed : 20.00 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.11), residues: 5763 helix: 0.98 (0.20), residues: 691 sheet: 0.09 (0.12), residues: 1815 loop : -1.20 (0.11), residues: 3257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP G 36 HIS 0.009 0.001 HIS B1064 PHE 0.021 0.002 PHE A 238 TYR 0.024 0.001 TYR A 380 ARG 0.005 0.000 ARG B 905 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11526 Ramachandran restraints generated. 5763 Oldfield, 0 Emsley, 5763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11526 Ramachandran restraints generated. 5763 Oldfield, 0 Emsley, 5763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 106 time to evaluate : 4.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.8120 (m-80) cc_final: 0.7736 (m-80) REVERT: A 144 TYR cc_start: 0.8261 (t80) cc_final: 0.7977 (t80) REVERT: A 153 MET cc_start: 0.7787 (pmm) cc_final: 0.7077 (pmm) REVERT: A 200 TYR cc_start: 0.8363 (OUTLIER) cc_final: 0.8071 (t80) REVERT: A 205 SER cc_start: 0.8770 (OUTLIER) cc_final: 0.8471 (t) REVERT: A 820 ASP cc_start: 0.8771 (OUTLIER) cc_final: 0.8215 (m-30) REVERT: A 995 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.8146 (mtm110) REVERT: A 1031 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7930 (mt-10) REVERT: A 1037 SER cc_start: 0.9066 (OUTLIER) cc_final: 0.8834 (p) REVERT: A 1092 GLU cc_start: 0.8136 (pm20) cc_final: 0.7743 (pm20) REVERT: A 1106 GLN cc_start: 0.9099 (OUTLIER) cc_final: 0.8424 (pt0) REVERT: B 164 ASN cc_start: 0.7167 (OUTLIER) cc_final: 0.6943 (p0) REVERT: B 177 MET cc_start: 0.3474 (pmm) cc_final: -0.0589 (mmt) REVERT: B 200 TYR cc_start: 0.8517 (m-80) cc_final: 0.7925 (t80) REVERT: B 242 LEU cc_start: 0.8669 (mp) cc_final: 0.8224 (mm) REVERT: B 278 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8491 (tptp) REVERT: B 553 THR cc_start: 0.8039 (OUTLIER) cc_final: 0.7772 (t) REVERT: B 745 ASP cc_start: 0.8926 (m-30) cc_final: 0.8553 (p0) REVERT: B 969 ASN cc_start: 0.9108 (OUTLIER) cc_final: 0.8457 (p0) REVERT: B 1072 GLU cc_start: 0.9008 (OUTLIER) cc_final: 0.8626 (pm20) REVERT: C 105 ILE cc_start: 0.7381 (OUTLIER) cc_final: 0.7148 (pt) REVERT: C 136 CYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8188 (p) REVERT: C 166 CYS cc_start: 0.3848 (OUTLIER) cc_final: 0.3499 (p) REVERT: C 200 TYR cc_start: 0.8654 (OUTLIER) cc_final: 0.8138 (m-80) REVERT: C 592 PHE cc_start: 0.5946 (OUTLIER) cc_final: 0.4806 (m-80) REVERT: C 730 SER cc_start: 0.9350 (OUTLIER) cc_final: 0.9099 (p) REVERT: C 740 MET cc_start: 0.8532 (mmm) cc_final: 0.8294 (mmm) REVERT: H 6 GLU cc_start: 0.6980 (OUTLIER) cc_final: 0.6649 (mt-10) REVERT: H 70 ILE cc_start: 0.0362 (OUTLIER) cc_final: -0.0061 (mt) REVERT: H 157 PHE cc_start: -0.0411 (OUTLIER) cc_final: -0.0639 (t80) REVERT: L 81 GLN cc_start: 0.4513 (OUTLIER) cc_final: 0.4304 (pm20) REVERT: L 107 LYS cc_start: 0.4905 (tttp) cc_final: 0.4332 (mppt) REVERT: G 181 LEU cc_start: 0.4910 (mm) cc_final: 0.4677 (tp) REVERT: N 48 MET cc_start: 0.3889 (mpp) cc_final: 0.2253 (ptp) REVERT: N 170 LEU cc_start: 0.5997 (OUTLIER) cc_final: 0.5522 (pp) REVERT: D 12 GLU cc_start: 0.4243 (OUTLIER) cc_final: 0.3620 (tt0) REVERT: D 204 CYS cc_start: 0.4877 (OUTLIER) cc_final: 0.4259 (p) REVERT: E 3 GLN cc_start: 0.7841 (mm110) cc_final: 0.7450 (mm110) REVERT: E 24 VAL cc_start: -0.0193 (OUTLIER) cc_final: -0.0778 (t) REVERT: E 34 TYR cc_start: 0.7895 (OUTLIER) cc_final: 0.7634 (t80) REVERT: J 180 SER cc_start: 0.4583 (p) cc_final: 0.4348 (m) REVERT: K 147 ILE cc_start: 0.2540 (OUTLIER) cc_final: 0.1897 (tt) REVERT: M 109 TYR cc_start: 0.8079 (t80) cc_final: 0.7207 (t80) outliers start: 143 outliers final: 100 residues processed: 243 average time/residue: 0.5373 time to fit residues: 229.8251 Evaluate side-chains 231 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 103 time to evaluate : 5.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 157 PHE Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 81 GLN Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain I residue 10 VAL Chi-restraints excluded: chain N residue 122 VAL Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 218 VAL Chi-restraints excluded: chain O residue 63 ARG Chi-restraints excluded: chain O residue 139 CYS Chi-restraints excluded: chain D residue 12 GLU Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 204 CYS Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 34 TYR Chi-restraints excluded: chain E residue 54 TYR Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain M residue 122 SER Chi-restraints excluded: chain M residue 145 LEU Chi-restraints excluded: chain M residue 171 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 339 optimal weight: 0.7980 chunk 547 optimal weight: 8.9990 chunk 333 optimal weight: 2.9990 chunk 259 optimal weight: 0.1980 chunk 380 optimal weight: 50.0000 chunk 573 optimal weight: 7.9990 chunk 528 optimal weight: 40.0000 chunk 456 optimal weight: 50.0000 chunk 47 optimal weight: 0.9990 chunk 352 optimal weight: 5.9990 chunk 280 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 91 GLN I 189 GLN I 193 HIS ** O 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 171 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.4414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 46326 Z= 0.240 Angle : 0.540 13.039 63126 Z= 0.275 Chirality : 0.044 0.397 7338 Planarity : 0.004 0.071 8061 Dihedral : 4.795 68.439 7417 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.49 % Favored : 95.45 % Rotamer: Outliers : 2.56 % Allowed : 20.24 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % 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: -0.66 (0.11), residues: 5763 helix: 1.17 (0.21), residues: 691 sheet: 0.16 (0.12), residues: 1804 loop : -1.17 (0.11), residues: 3268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP G 36 HIS 0.017 0.001 HIS M 171 PHE 0.031 0.001 PHE B 329 TYR 0.037 0.001 TYR N 187 ARG 0.004 0.000 ARG O 63 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11526 Ramachandran restraints generated. 5763 Oldfield, 0 Emsley, 5763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11526 Ramachandran restraints generated. 5763 Oldfield, 0 Emsley, 5763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 100 time to evaluate : 5.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.8090 (m-80) cc_final: 0.7713 (m-80) REVERT: A 144 TYR cc_start: 0.8257 (t80) cc_final: 0.7976 (t80) REVERT: A 153 MET cc_start: 0.8015 (pmm) cc_final: 0.7493 (pmm) REVERT: A 200 TYR cc_start: 0.8350 (OUTLIER) cc_final: 0.8060 (t80) REVERT: A 205 SER cc_start: 0.8745 (OUTLIER) cc_final: 0.8420 (t) REVERT: A 820 ASP cc_start: 0.8692 (OUTLIER) cc_final: 0.7977 (m-30) REVERT: A 995 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.8315 (mtm110) REVERT: A 1031 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7905 (mt-10) REVERT: A 1037 SER cc_start: 0.9040 (OUTLIER) cc_final: 0.8825 (p) REVERT: A 1092 GLU cc_start: 0.8120 (pm20) cc_final: 0.7727 (pm20) REVERT: A 1106 GLN cc_start: 0.9092 (OUTLIER) cc_final: 0.8375 (pt0) REVERT: B 164 ASN cc_start: 0.7144 (OUTLIER) cc_final: 0.6914 (p0) REVERT: B 177 MET cc_start: 0.3552 (pmm) cc_final: -0.0791 (mmt) REVERT: B 200 TYR cc_start: 0.8611 (m-80) cc_final: 0.8045 (t80) REVERT: B 278 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8404 (tptp) REVERT: B 329 PHE cc_start: 0.7770 (m-80) cc_final: 0.7222 (m-10) REVERT: B 553 THR cc_start: 0.8050 (OUTLIER) cc_final: 0.7796 (t) REVERT: B 745 ASP cc_start: 0.8835 (m-30) cc_final: 0.8473 (p0) REVERT: B 969 ASN cc_start: 0.9078 (OUTLIER) cc_final: 0.8438 (p0) REVERT: B 1072 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8597 (pm20) REVERT: C 105 ILE cc_start: 0.7342 (OUTLIER) cc_final: 0.7114 (pt) REVERT: C 136 CYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8208 (p) REVERT: C 166 CYS cc_start: 0.3846 (OUTLIER) cc_final: 0.3498 (p) REVERT: C 200 TYR cc_start: 0.8644 (OUTLIER) cc_final: 0.8118 (m-80) REVERT: C 592 PHE cc_start: 0.5805 (OUTLIER) cc_final: 0.4675 (m-80) REVERT: C 730 SER cc_start: 0.9331 (OUTLIER) cc_final: 0.9095 (p) REVERT: C 823 PHE cc_start: 0.8356 (OUTLIER) cc_final: 0.7774 (t80) REVERT: H 6 GLU cc_start: 0.6916 (OUTLIER) cc_final: 0.6693 (mt-10) REVERT: H 20 VAL cc_start: -0.3452 (OUTLIER) cc_final: -0.3699 (t) REVERT: H 157 PHE cc_start: -0.0411 (OUTLIER) cc_final: -0.0630 (t80) REVERT: L 107 LYS cc_start: 0.4921 (tttp) cc_final: 0.4345 (mppt) REVERT: G 181 LEU cc_start: 0.4583 (mm) cc_final: 0.4335 (tp) REVERT: N 48 MET cc_start: 0.3819 (mpp) cc_final: 0.2254 (ptp) REVERT: N 170 LEU cc_start: 0.5928 (OUTLIER) cc_final: 0.5502 (pp) REVERT: D 12 GLU cc_start: 0.4249 (OUTLIER) cc_final: 0.3602 (tt0) REVERT: D 204 CYS cc_start: 0.4848 (OUTLIER) cc_final: 0.4231 (p) REVERT: E 3 GLN cc_start: 0.7851 (mm110) cc_final: 0.7464 (mm110) REVERT: E 24 VAL cc_start: -0.0242 (OUTLIER) cc_final: -0.0826 (t) REVERT: E 34 TYR cc_start: 0.7909 (OUTLIER) cc_final: 0.7706 (t80) REVERT: K 147 ILE cc_start: 0.2379 (OUTLIER) cc_final: 0.1480 (tt) REVERT: M 109 TYR cc_start: 0.8086 (t80) cc_final: 0.7209 (t80) outliers start: 128 outliers final: 94 residues processed: 221 average time/residue: 0.5276 time to fit residues: 207.1051 Evaluate side-chains 220 residues out of total 5016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 98 time to evaluate : 4.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 823 PHE Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 157 PHE Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 91 GLN Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain I residue 10 VAL Chi-restraints excluded: chain N residue 122 VAL Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 218 VAL Chi-restraints excluded: chain O residue 63 ARG Chi-restraints excluded: chain O residue 139 CYS Chi-restraints excluded: chain D residue 12 GLU Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 204 CYS Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 34 TYR Chi-restraints excluded: chain E residue 54 TYR Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 34 TYR Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain M residue 122 SER Chi-restraints excluded: chain M residue 145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 362 optimal weight: 30.0000 chunk 486 optimal weight: 50.0000 chunk 139 optimal weight: 40.0000 chunk 421 optimal weight: 20.0000 chunk 67 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 457 optimal weight: 0.0030 chunk 191 optimal weight: 0.8980 chunk 469 optimal weight: 30.0000 chunk 57 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 overall best weight: 1.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 81 GLN L 91 GLN I 189 GLN I 193 HIS ** O 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN ** J 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 137 GLN ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4751 r_free = 0.4751 target = 0.157740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.125621 restraints weight = 151408.182| |-----------------------------------------------------------------------------| r_work (start): 0.4121 rms_B_bonded: 4.30 r_work: 0.3412 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.4434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 46326 Z= 0.199 Angle : 0.517 12.239 63126 Z= 0.263 Chirality : 0.043 0.391 7338 Planarity : 0.004 0.067 8061 Dihedral : 4.618 58.924 7417 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.16 % Favored : 95.78 % Rotamer: Outliers : 2.54 % Allowed : 20.28 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.57 (0.11), residues: 5763 helix: 1.32 (0.21), residues: 691 sheet: 0.24 (0.12), residues: 1796 loop : -1.14 (0.11), residues: 3276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 36 HIS 0.005 0.001 HIS C 49 PHE 0.026 0.001 PHE B 329 TYR 0.035 0.001 TYR N 187 ARG 0.005 0.000 ARG K 62 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8571.21 seconds wall clock time: 156 minutes 45.06 seconds (9405.06 seconds total)