Starting phenix.real_space_refine on Wed Mar 20 02:25:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6crx_7575/03_2024/6crx_7575.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6crx_7575/03_2024/6crx_7575.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6crx_7575/03_2024/6crx_7575.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6crx_7575/03_2024/6crx_7575.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6crx_7575/03_2024/6crx_7575.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6crx_7575/03_2024/6crx_7575.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 138 5.16 5 C 16550 2.51 5 N 4197 2.21 5 O 5127 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 26012 Number of models: 1 Model: "" Number of chains: 33 Chain: "B" Number of atoms: 8342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1068, 8342 Classifications: {'peptide': 1068} Link IDs: {'PCIS': 2, 'PTRANS': 51, 'TRANS': 1014} Chain breaks: 6 Chain: "C" Number of atoms: 8346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1069, 8346 Classifications: {'peptide': 1069} Link IDs: {'PCIS': 2, 'PTRANS': 51, 'TRANS': 1015} Chain breaks: 6 Chain: "A" Number of atoms: 8327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 8327 Classifications: {'peptide': 1066} Link IDs: {'PCIS': 2, 'PTRANS': 51, 'TRANS': 1012} Chain breaks: 6 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "O" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 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: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 13.69, per 1000 atoms: 0.53 Number of scatterers: 26012 At special positions: 0 Unit cell: (150.38, 146.26, 187.46, 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 138 16.00 O 5127 8.00 N 4197 7.00 C 16550 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 133 " distance=2.04 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 159 " distance=2.02 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 288 " distance=2.04 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 348 " distance=2.02 Simple disulfide: pdb=" SG CYS B 366 " - pdb=" SG CYS B 419 " distance=2.04 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 511 " distance=2.04 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 474 " distance=2.03 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 576 " distance=2.00 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 635 " distance=2.03 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B 657 " distance=2.04 Simple disulfide: pdb=" SG CYS B 720 " - pdb=" SG CYS B 742 " distance=2.03 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 731 " distance=2.00 Simple disulfide: pdb=" SG CYS B 822 " - pdb=" SG CYS B 833 " distance=2.03 Simple disulfide: pdb=" SG CYS B1014 " - pdb=" SG CYS B1025 " distance=2.03 Simple disulfide: pdb=" SG CYS B1064 " - pdb=" SG CYS B1108 " distance=2.03 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 133 " distance=2.04 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 159 " distance=2.02 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 288 " distance=2.03 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 348 " distance=2.04 Simple disulfide: pdb=" SG CYS C 366 " - pdb=" SG CYS C 419 " distance=2.01 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 511 " distance=2.03 Simple disulfide: pdb=" SG CYS C 467 " - pdb=" SG CYS C 474 " distance=2.03 Simple disulfide: pdb=" SG CYS C 524 " - pdb=" SG CYS C 576 " distance=2.03 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 635 " distance=2.03 Simple disulfide: pdb=" SG CYS C 648 " - pdb=" SG CYS C 657 " distance=2.04 Simple disulfide: pdb=" SG CYS C 720 " - pdb=" SG CYS C 742 " distance=2.03 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 731 " distance=2.04 Simple disulfide: pdb=" SG CYS C 822 " - pdb=" SG CYS C 833 " distance=2.04 Simple disulfide: pdb=" SG CYS C1014 " - pdb=" SG CYS C1025 " distance=2.01 Simple disulfide: pdb=" SG CYS C1064 " - pdb=" SG CYS C1108 " distance=2.04 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 133 " distance=2.04 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 159 " distance=2.04 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 288 " distance=2.03 Simple disulfide: pdb=" SG CYS A 323 " - pdb=" SG CYS A 348 " distance=2.03 Simple disulfide: pdb=" SG CYS A 366 " - pdb=" SG CYS A 419 " distance=2.01 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 511 " distance=2.04 Simple disulfide: pdb=" SG CYS A 467 " - pdb=" SG CYS A 474 " distance=2.03 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 576 " distance=2.00 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 635 " distance=2.04 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A 657 " distance=2.03 Simple disulfide: pdb=" SG CYS A 720 " - pdb=" SG CYS A 742 " distance=2.03 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 731 " distance=2.03 Simple disulfide: pdb=" SG CYS A 822 " - pdb=" SG CYS A 833 " distance=2.03 Simple disulfide: pdb=" SG CYS A1014 " - pdb=" SG CYS A1025 " distance=2.02 Simple disulfide: pdb=" SG CYS A1064 " - pdb=" SG CYS A1108 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA G 3 " - " MAN G 4 " " BMA N 3 " - " MAN N 4 " " BMA O 3 " - " MAN O 4 " " BMA X 3 " - " MAN X 4 " " BMA a 3 " - " MAN a 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " 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 X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " NAG-ASN " NAG A1301 " - " ASN A 65 " " NAG B1308 " - " ASN B 589 " " NAG B1309 " - " ASN B 691 " " NAG B1314 " - " ASN B1056 " " NAG B1317 " - " ASN B1116 " " NAG C1307 " - " ASN C 589 " " NAG C1312 " - " ASN C 691 " " NAG D 1 " - " ASN B 602 " " NAG E 1 " - " ASN B 65 " " NAG F 1 " - " ASN B 269 " " NAG G 1 " - " ASN B 783 " " NAG H 1 " - " ASN B1080 " " NAG I 1 " - " ASN B 318 " " NAG J 1 " - " ASN B 699 " " NAG K 1 " - " ASN C 65 " " NAG L 1 " - " ASN C 227 " " NAG M 1 " - " ASN C 318 " " NAG N 1 " - " ASN C 602 " " NAG O 1 " - " ASN C 699 " " NAG P 1 " - " ASN C 783 " " NAG Q 1 " - " ASN C1056 " " NAG R 1 " - " ASN C1080 " " NAG S 1 " - " ASN C1116 " " NAG T 1 " - " ASN C 269 " " NAG U 1 " - " ASN A 269 " " NAG V 1 " - " ASN A 318 " " NAG W 1 " - " ASN A 589 " " NAG X 1 " - " ASN A 602 " " NAG Y 1 " - " ASN A 691 " " NAG Z 1 " - " ASN A 699 " " NAG a 1 " - " ASN A 783 " " NAG b 1 " - " ASN A1056 " " NAG c 1 " - " ASN A1080 " " NAG d 1 " - " ASN A1116 " Time building additional restraints: 10.53 Conformation dependent library (CDL) restraints added in 4.7 seconds 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6002 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 49 sheets defined 23.4% alpha, 32.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.70 Creating SS restraints... Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 324 through 328 Processing helix chain 'B' and resid 336 through 340 removed outlier: 3.631A pdb=" N TRP B 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 357 removed outlier: 3.606A pdb=" N TYR B 356 " --> pdb=" O TYR B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 377 removed outlier: 3.654A pdb=" N ASP B 376 " --> pdb=" O THR B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 395 removed outlier: 4.233A pdb=" N ARG B 395 " --> pdb=" O GLY B 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 391 through 395' Processing helix chain 'B' and resid 404 through 409 Processing helix chain 'B' and resid 488 through 491 removed outlier: 3.767A pdb=" N TYR B 491 " --> pdb=" O GLY B 488 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 488 through 491' Processing helix chain 'B' and resid 602 through 612 removed outlier: 3.900A pdb=" N VAL B 606 " --> pdb=" O ASN B 602 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS B 611 " --> pdb=" O SER B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 725 Processing helix chain 'B' and resid 728 through 736 removed outlier: 3.946A pdb=" N LEU B 734 " --> pdb=" O GLU B 730 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU B 736 " --> pdb=" O ALA B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 739 No H-bonds generated for 'chain 'B' and resid 737 through 739' Processing helix chain 'B' and resid 741 through 765 removed outlier: 3.557A pdb=" N LEU B 745 " --> pdb=" O PHE B 741 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN B 756 " --> pdb=" O ILE B 752 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ASP B 757 " --> pdb=" O ALA B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 785 through 787 No H-bonds generated for 'chain 'B' and resid 785 through 787' Processing helix chain 'B' and resid 798 through 806 Processing helix chain 'B' and resid 848 through 864 removed outlier: 3.502A pdb=" N ILE B 852 " --> pdb=" O THR B 848 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY B 862 " --> pdb=" O ALA B 858 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 872 removed outlier: 3.555A pdb=" N THR B 869 " --> pdb=" O ALA B 866 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLY B 871 " --> pdb=" O TRP B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 879 through 891 Processing helix chain 'B' and resid 895 through 900 Processing helix chain 'B' and resid 901 through 923 removed outlier: 3.757A pdb=" N ILE B 913 " --> pdb=" O PHE B 909 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER B 914 " --> pdb=" O ASN B 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 927 through 947 removed outlier: 4.296A pdb=" N VAL B 933 " --> pdb=" O LYS B 929 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL B 934 " --> pdb=" O LEU B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 966 removed outlier: 3.797A pdb=" N LEU B 966 " --> pdb=" O ILE B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 970 through 1016 removed outlier: 3.556A pdb=" N GLN B 984 " --> pdb=" O THR B 980 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR B 991 " --> pdb=" O GLN B 987 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA B 998 " --> pdb=" O LEU B 994 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N CYS B1014 " --> pdb=" O LYS B1010 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 291 removed outlier: 3.786A pdb=" N LEU C 286 " --> pdb=" O PRO C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 330 Processing helix chain 'C' and resid 352 through 357 Processing helix chain 'C' and resid 391 through 395 removed outlier: 3.949A pdb=" N ARG C 395 " --> pdb=" O GLY C 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 391 through 395' Processing helix chain 'C' and resid 403 through 408 removed outlier: 3.903A pdb=" N ASP C 407 " --> pdb=" O GLY C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 491 Processing helix chain 'C' and resid 602 through 612 Processing helix chain 'C' and resid 719 through 725 Processing helix chain 'C' and resid 728 through 737 removed outlier: 3.695A pdb=" N LEU C 734 " --> pdb=" O GLU C 730 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLN C 737 " --> pdb=" O ASN C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 765 removed outlier: 3.940A pdb=" N GLN C 744 " --> pdb=" O SER C 740 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU C 745 " --> pdb=" O PHE C 741 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN C 746 " --> pdb=" O CYS C 742 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP C 757 " --> pdb=" O ALA C 753 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR C 760 " --> pdb=" O GLN C 756 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE C 764 " --> pdb=" O THR C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 798 through 809 removed outlier: 3.727A pdb=" N ASN C 806 " --> pdb=" O ASP C 802 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS C 807 " --> pdb=" O LEU C 803 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL C 808 " --> pdb=" O LEU C 804 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR C 809 " --> pdb=" O PHE C 805 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 864 Processing helix chain 'C' and resid 868 through 873 removed outlier: 3.771A pdb=" N ALA C 872 " --> pdb=" O TRP C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 879 through 890 Processing helix chain 'C' and resid 895 through 901 Processing helix chain 'C' and resid 903 through 923 removed outlier: 3.694A pdb=" N PHE C 909 " --> pdb=" O ILE C 905 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN C 910 " --> pdb=" O ALA C 906 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N SER C 914 " --> pdb=" O ASN C 910 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR C 923 " --> pdb=" O SER C 919 " (cutoff:3.500A) Processing helix chain 'C' and resid 927 through 947 removed outlier: 3.624A pdb=" N VAL C 933 " --> pdb=" O LYS C 929 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL C 934 " --> pdb=" O LEU C 930 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN C 937 " --> pdb=" O VAL C 933 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA C 940 " --> pdb=" O GLN C 936 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN C 947 " --> pdb=" O THR C 943 " (cutoff:3.500A) Processing helix chain 'C' and resid 959 through 964 Processing helix chain 'C' and resid 967 through 1014 removed outlier: 3.527A pdb=" N SER C 985 " --> pdb=" O GLY C 981 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ARG C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 324 through 329 Processing helix chain 'A' and resid 336 through 340 removed outlier: 3.579A pdb=" N ALA A 339 " --> pdb=" O SER A 336 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N TRP A 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 336 through 340' Processing helix chain 'A' and resid 352 through 357 removed outlier: 4.353A pdb=" N ASN A 357 " --> pdb=" O SER A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 377 removed outlier: 3.890A pdb=" N ASP A 376 " --> pdb=" O THR A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 409 Processing helix chain 'A' and resid 425 through 430 Processing helix chain 'A' and resid 488 through 492 removed outlier: 3.764A pdb=" N TYR A 491 " --> pdb=" O GLY A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 612 removed outlier: 3.737A pdb=" N ALA A 609 " --> pdb=" O ASP A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 725 Processing helix chain 'A' and resid 729 through 736 removed outlier: 3.980A pdb=" N LEU A 736 " --> pdb=" O ALA A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 764 removed outlier: 4.044A pdb=" N THR A 760 " --> pdb=" O GLN A 756 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG A 761 " --> pdb=" O ASP A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 805 Processing helix chain 'A' and resid 848 through 867 removed outlier: 3.891A pdb=" N THR A 865 " --> pdb=" O SER A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 871 removed outlier: 4.247A pdb=" N GLY A 871 " --> pdb=" O TRP A 868 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 868 through 871' Processing helix chain 'A' and resid 879 through 891 removed outlier: 3.557A pdb=" N ARG A 887 " --> pdb=" O GLN A 883 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A 891 " --> pdb=" O ARG A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 901 removed outlier: 3.505A pdb=" N TYR A 899 " --> pdb=" O GLN A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 922 Processing helix chain 'A' and resid 927 through 947 removed outlier: 3.716A pdb=" N ASN A 937 " --> pdb=" O VAL A 933 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A 941 " --> pdb=" O ASN A 937 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS A 946 " --> pdb=" O ASN A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 964 removed outlier: 3.688A pdb=" N ILE A 962 " --> pdb=" O VAL A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 1013 removed outlier: 3.556A pdb=" N VAL A 973 " --> pdb=" O PRO A 969 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR A 980 " --> pdb=" O ASP A 976 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET A1011 " --> pdb=" O ALA A1007 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 31 through 34 removed outlier: 8.731A pdb=" N ASN B 65 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N TYR B 256 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR B 67 " --> pdb=" O VAL B 254 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA B 250 " --> pdb=" O THR B 71 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ALA B 251 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR B 92 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA B 90 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS B 180 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU B 194 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LYS B 221 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL B 196 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N TYR B 200 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N THR B 215 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N VAL B 40 " --> pdb=" O LEU B 216 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 47 removed outlier: 6.215A pdb=" N PHE B 47 " --> pdb=" O ARG A 553 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ASP A 560 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY A 534 " --> pdb=" O PHE A 527 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL A 313 " --> pdb=" O ASN A 528 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 51 through 59 removed outlier: 3.628A pdb=" N THR B 51 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASP B 274 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 80 through 82 removed outlier: 3.640A pdb=" N GLY B 104 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLY B 100 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N THR B 236 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL B 98 " --> pdb=" O THR B 236 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ARG B 99 " --> pdb=" O ASN B 118 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE B 161 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ASN B 129 " --> pdb=" O CYS B 159 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N CYS B 159 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N GLU B 131 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 9.069A pdb=" N PHE B 157 " --> pdb=" O GLU B 131 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N CYS B 133 " --> pdb=" O ASN B 155 " (cutoff:3.500A) removed outlier: 10.870A pdb=" N ASN B 155 " --> pdb=" O CYS B 133 " (cutoff:3.500A) removed outlier: 11.397A pdb=" N ASN B 135 " --> pdb=" O PHE B 153 " (cutoff:3.500A) removed outlier: 8.653A pdb=" N PHE B 153 " --> pdb=" O ASN B 135 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N HIS B 149 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N SER B 141 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N GLN B 147 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 80 through 82 removed outlier: 14.117A pdb=" N PHE B 231 " --> pdb=" O PHE B 130 " (cutoff:3.500A) removed outlier: 13.710A pdb=" N LEU B 132 " --> pdb=" O PHE B 231 " (cutoff:3.500A) removed outlier: 13.166A pdb=" N ALA B 233 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 10.558A pdb=" N ASP B 134 " --> pdb=" O ALA B 233 " (cutoff:3.500A) removed outlier: 10.221A pdb=" N LEU B 235 " --> pdb=" O ASP B 134 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ALA B 237 " --> pdb=" O PRO B 136 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N PHE B 138 " --> pdb=" O ALA B 237 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N SER B 239 " --> pdb=" O PHE B 138 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N VAL B 140 " --> pdb=" O SER B 239 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE B 161 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ASN B 129 " --> pdb=" O CYS B 159 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N CYS B 159 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N GLU B 131 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 9.069A pdb=" N PHE B 157 " --> pdb=" O GLU B 131 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N CYS B 133 " --> pdb=" O ASN B 155 " (cutoff:3.500A) removed outlier: 10.870A pdb=" N ASN B 155 " --> pdb=" O CYS B 133 " (cutoff:3.500A) removed outlier: 11.397A pdb=" N ASN B 135 " --> pdb=" O PHE B 153 " (cutoff:3.500A) removed outlier: 8.653A pdb=" N PHE B 153 " --> pdb=" O ASN B 135 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N HIS B 149 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N SER B 141 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N GLN B 147 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 615 through 616 removed outlier: 4.577A pdb=" N VAL B 581 " --> pdb=" O THR B 302 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ASN B 304 " --> pdb=" O GLY B 579 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N GLY B 579 " --> pdb=" O ASN B 304 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY B 580 " --> pdb=" O GLN B 599 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 312 through 315 removed outlier: 6.449A pdb=" N VAL B 313 " --> pdb=" O ASN B 528 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ASP B 560 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER B 561 " --> pdb=" O GLY B 552 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N PHE B 551 " --> pdb=" O PHE C 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 341 through 345 removed outlier: 3.729A pdb=" N LYS B 343 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU B 502 " --> pdb=" O ASN B 381 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR B 383 " --> pdb=" O SER B 500 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER B 500 " --> pdb=" O TYR B 383 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL B 498 " --> pdb=" O ASP B 385 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL B 497 " --> pdb=" O LEU B 421 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU B 421 " --> pdb=" O VAL B 497 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 348 through 349 removed outlier: 6.776A pdb=" N CYS B 348 " --> pdb=" O CYS B 511 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 439 through 441 Processing sheet with id=AB2, first strand: chain 'B' and resid 640 through 646 removed outlier: 4.938A pdb=" N THR B 678 " --> pdb=" O VAL B 642 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N THR B 644 " --> pdb=" O THR B 678 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR B 677 " --> pdb=" O CYS B 657 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE B 656 " --> pdb=" O ILE B 652 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 683 through 685 removed outlier: 6.283A pdb=" N ALA B 683 " --> pdb=" O MET C 770 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 693 through 700 removed outlier: 6.809A pdb=" N THR B 693 " --> pdb=" O THR B1058 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N THR B1058 " --> pdb=" O THR B 693 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ALA B 695 " --> pdb=" O ASN B1056 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ASN B1056 " --> pdb=" O ALA B 695 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N GLU B1054 " --> pdb=" O PRO B 697 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N PHE B1077 " --> pdb=" O ALA B1060 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 703 through 709 removed outlier: 3.640A pdb=" N SER B 703 " --> pdb=" O THR B1048 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA B1038 " --> pdb=" O GLY B1041 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N MET B1032 " --> pdb=" O VAL B1047 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N TYR B1049 " --> pdb=" O HIS B1030 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N HIS B1030 " --> pdb=" O TYR B1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 716 through 718 Processing sheet with id=AB7, first strand: chain 'B' and resid 769 through 771 Processing sheet with id=AB8, first strand: chain 'B' and resid 778 through 779 Processing sheet with id=AB9, first strand: chain 'B' and resid 1102 through 1107 removed outlier: 3.603A pdb=" N SER B1105 " --> pdb=" O ALA B1069 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ALA B1069 " --> pdb=" O SER B1105 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 31 through 34 removed outlier: 3.536A pdb=" N THR C 31 " --> pdb=" O GLY C 68 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N ASN C 65 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N TYR C 256 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA C 251 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N HIS C 181 " --> pdb=" O GLU C 93 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LYS C 180 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LEU C 194 " --> pdb=" O LYS C 221 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LYS C 221 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL C 196 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N TYR C 200 " --> pdb=" O THR C 215 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N THR C 215 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N VAL C 40 " --> pdb=" O LEU C 216 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 52 through 59 removed outlier: 7.516A pdb=" N THR C 261 " --> pdb=" O ASP C 277 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ASP C 277 " --> pdb=" O THR C 261 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N MET C 263 " --> pdb=" O ALA C 275 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ALA C 275 " --> pdb=" O MET C 263 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LYS C 265 " --> pdb=" O THR C 273 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 81 through 82 removed outlier: 3.598A pdb=" N ARG C 232 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR C 236 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL C 98 " --> pdb=" O THR C 236 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ARG C 99 " --> pdb=" O ASN C 118 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL C 123 " --> pdb=" O TYR C 163 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N TYR C 163 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ILE C 125 " --> pdb=" O PHE C 161 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N PHE C 161 " --> pdb=" O ILE C 125 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N ALA C 127 " --> pdb=" O CYS C 159 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N CYS C 159 " --> pdb=" O ALA C 127 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE C 157 " --> pdb=" O ASN C 129 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU C 131 " --> pdb=" O ASN C 155 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ASN C 155 " --> pdb=" O GLU C 131 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N CYS C 133 " --> pdb=" O PHE C 153 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N PHE C 153 " --> pdb=" O CYS C 133 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ASN C 135 " --> pdb=" O MET C 151 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N MET C 151 " --> pdb=" O ASN C 135 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N PHE C 137 " --> pdb=" O HIS C 149 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N HIS C 149 " --> pdb=" O PHE C 137 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ALA C 139 " --> pdb=" O GLN C 147 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N GLN C 147 " --> pdb=" O ALA C 139 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 81 through 82 removed outlier: 12.679A pdb=" N PHE C 231 " --> pdb=" O PHE C 130 " (cutoff:3.500A) removed outlier: 12.465A pdb=" N LEU C 132 " --> pdb=" O PHE C 231 " (cutoff:3.500A) removed outlier: 12.362A pdb=" N ALA C 233 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 9.370A pdb=" N ASP C 134 " --> pdb=" O ALA C 233 " (cutoff:3.500A) removed outlier: 9.272A pdb=" N LEU C 235 " --> pdb=" O ASP C 134 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA C 237 " --> pdb=" O PRO C 136 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N PHE C 138 " --> pdb=" O ALA C 237 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N SER C 239 " --> pdb=" O PHE C 138 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL C 140 " --> pdb=" O SER C 239 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL C 123 " --> pdb=" O TYR C 163 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N TYR C 163 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ILE C 125 " --> pdb=" O PHE C 161 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N PHE C 161 " --> pdb=" O ILE C 125 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N ALA C 127 " --> pdb=" O CYS C 159 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N CYS C 159 " --> pdb=" O ALA C 127 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE C 157 " --> pdb=" O ASN C 129 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU C 131 " --> pdb=" O ASN C 155 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ASN C 155 " --> pdb=" O GLU C 131 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N CYS C 133 " --> pdb=" O PHE C 153 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N PHE C 153 " --> pdb=" O CYS C 133 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ASN C 135 " --> pdb=" O MET C 151 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N MET C 151 " --> pdb=" O ASN C 135 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N PHE C 137 " --> pdb=" O HIS C 149 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N HIS C 149 " --> pdb=" O PHE C 137 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ALA C 139 " --> pdb=" O GLN C 147 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N GLN C 147 " --> pdb=" O ALA C 139 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 615 through 616 removed outlier: 4.019A pdb=" N VAL C 581 " --> pdb=" O THR C 302 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ASN C 304 " --> pdb=" O GLY C 579 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N GLY C 579 " --> pdb=" O ASN C 304 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLY C 580 " --> pdb=" O GLN C 599 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 312 through 314 removed outlier: 6.591A pdb=" N VAL C 313 " --> pdb=" O ASN C 528 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY C 534 " --> pdb=" O PHE C 527 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ASP C 560 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N SER C 561 " --> pdb=" O GLY C 552 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N PHE C 551 " --> pdb=" O PHE A 47 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 344 through 345 removed outlier: 3.699A pdb=" N VAL C 382 " --> pdb=" O ILE C 345 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 385 through 390 removed outlier: 3.529A pdb=" N PHE C 387 " --> pdb=" O VAL C 496 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 439 through 441 Processing sheet with id=AD1, first strand: chain 'C' and resid 640 through 646 removed outlier: 6.245A pdb=" N GLU C 640 " --> pdb=" O ALA C 676 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N THR C 678 " --> pdb=" O GLU C 640 " (cutoff:3.500A) removed outlier: 8.878A pdb=" N VAL C 642 " --> pdb=" O THR C 678 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE C 656 " --> pdb=" O ILE C 652 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 683 through 685 removed outlier: 5.630A pdb=" N ALA C 683 " --> pdb=" O MET A 770 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'C' and resid 693 through 710 removed outlier: 6.725A pdb=" N THR C 693 " --> pdb=" O THR C1058 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N THR C1058 " --> pdb=" O THR C 693 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ALA C 695 " --> pdb=" O ASN C1056 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASN C1056 " --> pdb=" O ALA C 695 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLU C1054 " --> pdb=" O PRO C 697 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N GLY C1041 " --> pdb=" O ALA C1037 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N ALA C1037 " --> pdb=" O GLY C1041 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL C1043 " --> pdb=" O PRO C1035 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU C1045 " --> pdb=" O SER C1033 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N SER C1033 " --> pdb=" O LEU C1045 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL C1047 " --> pdb=" O LEU C1031 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 693 through 710 removed outlier: 6.725A pdb=" N THR C 693 " --> pdb=" O THR C1058 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N THR C1058 " --> pdb=" O THR C 693 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ALA C 695 " --> pdb=" O ASN C1056 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASN C1056 " --> pdb=" O ALA C 695 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLU C1054 " --> pdb=" O PRO C 697 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 716 through 718 Processing sheet with id=AD6, first strand: chain 'C' and resid 778 through 779 Processing sheet with id=AD7, first strand: chain 'C' and resid 821 through 823 removed outlier: 3.537A pdb=" N GLU C 821 " --> pdb=" O ALA C 834 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA C 834 " --> pdb=" O GLU C 821 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 1102 through 1107 removed outlier: 5.164A pdb=" N ALA C1069 " --> pdb=" O SER C1105 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 31 through 34 removed outlier: 3.764A pdb=" N ALA A 251 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA A 90 " --> pdb=" O PHE A 253 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LYS A 180 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N LEU A 194 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N LYS A 221 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N VAL A 196 " --> pdb=" O ILE A 219 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 51 through 59 removed outlier: 3.592A pdb=" N THR A 51 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASP A 274 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 81 through 82 removed outlier: 12.571A pdb=" N LEU A 132 " --> pdb=" O PHE A 231 " (cutoff:3.500A) removed outlier: 12.612A pdb=" N ALA A 233 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 9.884A pdb=" N ASP A 134 " --> pdb=" O ALA A 233 " (cutoff:3.500A) removed outlier: 9.879A pdb=" N LEU A 235 " --> pdb=" O ASP A 134 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ALA A 237 " --> pdb=" O PRO A 136 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N PHE A 138 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N SER A 239 " --> pdb=" O PHE A 138 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N VAL A 140 " --> pdb=" O SER A 239 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ASN A 135 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ILE A 152 " --> pdb=" O ASN A 135 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N PHE A 137 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N THR A 150 " --> pdb=" O PHE A 137 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ALA A 139 " --> pdb=" O THR A 148 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 81 through 82 Processing sheet with id=AE4, first strand: chain 'A' and resid 615 through 616 removed outlier: 4.438A pdb=" N VAL A 581 " --> pdb=" O THR A 302 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ASN A 304 " --> pdb=" O GLY A 579 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N GLY A 579 " --> pdb=" O ASN A 304 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY A 580 " --> pdb=" O GLN A 599 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 344 through 345 removed outlier: 3.574A pdb=" N VAL A 382 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 421 " --> pdb=" O VAL A 497 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LEU A 499 " --> pdb=" O CYS A 419 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N CYS A 419 " --> pdb=" O LEU A 499 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 348 through 349 removed outlier: 6.557A pdb=" N CYS A 348 " --> pdb=" O CYS A 511 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'A' and resid 439 through 441 Processing sheet with id=AE8, first strand: chain 'A' and resid 640 through 641 removed outlier: 6.140A pdb=" N GLU A 640 " --> pdb=" O ALA A 676 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N THR A 678 " --> pdb=" O GLU A 640 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR A 677 " --> pdb=" O CYS A 657 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'A' and resid 693 through 710 removed outlier: 6.577A pdb=" N THR A 693 " --> pdb=" O THR A1058 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N THR A1058 " --> pdb=" O THR A 693 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ALA A 695 " --> pdb=" O ASN A1056 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ASN A1056 " --> pdb=" O ALA A 695 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N GLU A1054 " --> pdb=" O PRO A 697 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU A 707 " --> pdb=" O PHE A1044 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'A' and resid 1029 through 1033 removed outlier: 6.904A pdb=" N VAL A1047 " --> pdb=" O LEU A1031 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N SER A1033 " --> pdb=" O LEU A1045 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N LEU A1045 " --> pdb=" O SER A1033 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR A1058 " --> pdb=" O PHE A1079 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A1060 " --> pdb=" O PHE A1077 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N PHE A1077 " --> pdb=" O ALA A1060 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'A' and resid 716 through 718 Processing sheet with id=AF3, first strand: chain 'A' and resid 778 through 779 Processing sheet with id=AF4, first strand: chain 'A' and resid 1102 through 1107 removed outlier: 4.782A pdb=" N VAL A1104 " --> pdb=" O PHE A1071 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N PHE A1071 " --> pdb=" O VAL A1104 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLY A1106 " --> pdb=" O ALA A1069 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N HIS A1065 " --> pdb=" O LYS A1068 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ALA A1062 " --> pdb=" O ILE A1115 " (cutoff:3.500A) 925 hydrogen bonds defined for protein. 2562 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.47 Time building geometry restraints manager: 11.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8118 1.34 - 1.47: 7104 1.47 - 1.59: 11201 1.59 - 1.72: 0 1.72 - 1.85: 186 Bond restraints: 26609 Sorted by residual: bond pdb=" C1 MAN X 4 " pdb=" O5 MAN X 4 " ideal model delta sigma weight residual 1.399 1.470 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" C TYR C1070 " pdb=" N PHE C1071 " ideal model delta sigma weight residual 1.331 1.261 0.070 2.07e-02 2.33e+03 1.13e+01 bond pdb=" C1 MAN X 4 " pdb=" C2 MAN X 4 " ideal model delta sigma weight residual 1.526 1.593 -0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" C ILE A 573 " pdb=" N SER A 574 " ideal model delta sigma weight residual 1.327 1.270 0.057 1.71e-02 3.42e+03 1.11e+01 bond pdb=" C5 BMA N 3 " pdb=" O5 BMA N 3 " ideal model delta sigma weight residual 1.417 1.481 -0.064 2.00e-02 2.50e+03 1.02e+01 ... (remaining 26604 not shown) Histogram of bond angle deviations from ideal: 97.07 - 104.51: 488 104.51 - 111.94: 12925 111.94 - 119.38: 9012 119.38 - 126.81: 13506 126.81 - 134.24: 273 Bond angle restraints: 36204 Sorted by residual: angle pdb=" C PHE B 83 " pdb=" N LYS B 84 " pdb=" CA LYS B 84 " ideal model delta sigma weight residual 121.54 132.76 -11.22 1.91e+00 2.74e-01 3.45e+01 angle pdb=" C GLN C 908 " pdb=" N PHE C 909 " pdb=" CA PHE C 909 " ideal model delta sigma weight residual 122.06 112.43 9.63 1.86e+00 2.89e-01 2.68e+01 angle pdb=" C PHE C 83 " pdb=" N LYS C 84 " pdb=" CA LYS C 84 " ideal model delta sigma weight residual 121.54 131.34 -9.80 1.91e+00 2.74e-01 2.63e+01 angle pdb=" C ILE A 72 " pdb=" N ASN A 73 " pdb=" CA ASN A 73 " ideal model delta sigma weight residual 120.82 127.95 -7.13 1.50e+00 4.44e-01 2.26e+01 angle pdb=" C THR B 106 " pdb=" N MET B 107 " pdb=" CA MET B 107 " ideal model delta sigma weight residual 121.54 130.21 -8.67 1.91e+00 2.74e-01 2.06e+01 ... (remaining 36199 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.87: 16235 23.87 - 47.74: 392 47.74 - 71.61: 67 71.61 - 95.48: 42 95.48 - 119.36: 30 Dihedral angle restraints: 16766 sinusoidal: 7435 harmonic: 9331 Sorted by residual: dihedral pdb=" CB CYS B1014 " pdb=" SG CYS B1014 " pdb=" SG CYS B1025 " pdb=" CB CYS B1025 " ideal model delta sinusoidal sigma weight residual -86.00 -173.13 87.13 1 1.00e+01 1.00e-02 9.12e+01 dihedral pdb=" CA PHE A 83 " pdb=" C PHE A 83 " pdb=" N LYS A 84 " pdb=" CA LYS A 84 " ideal model delta harmonic sigma weight residual -180.00 -133.37 -46.63 0 5.00e+00 4.00e-02 8.70e+01 dihedral pdb=" CA SER A 35 " pdb=" C SER A 35 " pdb=" N SER A 36 " pdb=" CA SER A 36 " ideal model delta harmonic sigma weight residual -180.00 -134.27 -45.73 0 5.00e+00 4.00e-02 8.36e+01 ... (remaining 16763 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 4099 0.122 - 0.243: 181 0.243 - 0.365: 19 0.365 - 0.486: 1 0.486 - 0.608: 2 Chirality restraints: 4302 Sorted by residual: chirality pdb=" C1 NAG Y 1 " pdb=" ND2 ASN A 691 " pdb=" C2 NAG Y 1 " pdb=" O5 NAG Y 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.23e+00 chirality pdb=" C1 NAG S 1 " pdb=" ND2 ASN C1116 " pdb=" C2 NAG S 1 " pdb=" O5 NAG S 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.83 -0.57 2.00e-01 2.50e+01 8.23e+00 chirality pdb=" C1 NAG a 1 " pdb=" ND2 ASN A 783 " pdb=" C2 NAG a 1 " pdb=" O5 NAG a 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.30e+00 ... (remaining 4299 not shown) Planarity restraints: 4609 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 83 " 0.020 2.00e-02 2.50e+03 4.06e-02 1.65e+01 pdb=" C PHE A 83 " -0.070 2.00e-02 2.50e+03 pdb=" O PHE A 83 " 0.026 2.00e-02 2.50e+03 pdb=" N LYS A 84 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 968 " -0.056 5.00e-02 4.00e+02 8.30e-02 1.10e+01 pdb=" N PRO B 969 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO B 969 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 969 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER C 380 " -0.016 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" C SER C 380 " 0.055 2.00e-02 2.50e+03 pdb=" O SER C 380 " -0.021 2.00e-02 2.50e+03 pdb=" N ASN C 381 " -0.019 2.00e-02 2.50e+03 ... (remaining 4606 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3580 2.75 - 3.28: 24044 3.28 - 3.82: 43698 3.82 - 4.36: 50954 4.36 - 4.90: 85587 Nonbonded interactions: 207863 Sorted by model distance: nonbonded pdb=" O GLY B 77 " pdb=" OH TYR B 252 " model vdw 2.208 2.440 nonbonded pdb=" O PHE B1071 " pdb=" OG1 THR B1102 " model vdw 2.224 2.440 nonbonded pdb=" OE1 GLN A 947 " pdb=" OG SER A 985 " model vdw 2.231 2.440 nonbonded pdb=" O GLY C 77 " pdb=" OH TYR C 252 " model vdw 2.235 2.440 nonbonded pdb=" OH TYR C 41 " pdb=" O LEU C 58 " model vdw 2.249 2.440 ... (remaining 207858 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 18 through 662 or resid 672 through 823 or resid 832 throu \ gh 1120 or resid 1308)) selection = (chain 'C' and (resid 18 through 662 or resid 672 through 823 or resid 832 throu \ gh 1120 or resid 1307)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = 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 'Y' selection = chain 'b' selection = chain 'c' selection = chain 'd' } ncs_group { reference = chain 'F' selection = chain 'J' selection = chain 'Z' } ncs_group { reference = chain 'G' selection = chain 'N' selection = chain 'O' selection = chain 'X' 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.450 Check model and map are aligned: 0.350 Set scattering table: 0.210 Process input model: 71.690 Find NCS groups from input model: 1.960 Set up NCS constraints: 0.370 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:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 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 : 0.010 0.115 26609 Z= 0.650 Angle : 1.118 13.902 36204 Z= 0.592 Chirality : 0.064 0.608 4302 Planarity : 0.007 0.083 4575 Dihedral : 12.927 119.356 10629 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.80 % Favored : 93.17 % Rotamer: Outliers : 0.18 % Allowed : 1.12 % Favored : 98.70 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.73 (0.12), residues: 3161 helix: -3.72 (0.12), residues: 648 sheet: -1.17 (0.20), residues: 606 loop : -2.57 (0.12), residues: 1907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.004 TRP C 340 HIS 0.018 0.004 HIS A 641 PHE 0.043 0.005 PHE B 22 TYR 0.043 0.004 TYR B1029 ARG 0.020 0.001 ARG C 453 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 370 time to evaluate : 2.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 71 THR cc_start: 0.5041 (m) cc_final: 0.4605 (t) REVERT: B 103 PHE cc_start: 0.8578 (m-80) cc_final: 0.8282 (m-10) REVERT: B 107 MET cc_start: 0.4623 (mmt) cc_final: 0.3682 (mmt) REVERT: B 155 ASN cc_start: 0.8350 (m-40) cc_final: 0.7951 (m110) REVERT: B 194 LEU cc_start: 0.8287 (tp) cc_final: 0.7781 (tt) REVERT: B 1099 THR cc_start: 0.8326 (p) cc_final: 0.8113 (t) REVERT: C 50 ASP cc_start: 0.8092 (t0) cc_final: 0.7685 (t0) REVERT: C 407 ASP cc_start: 0.6412 (m-30) cc_final: 0.5356 (p0) REVERT: C 709 MET cc_start: 0.8384 (mtm) cc_final: 0.8115 (mmm) REVERT: C 884 MET cc_start: 0.8343 (mmm) cc_final: 0.8025 (mmm) REVERT: C 886 TYR cc_start: 0.7351 (t80) cc_final: 0.7058 (t80) REVERT: A 87 ILE cc_start: 0.9046 (pt) cc_final: 0.8389 (mm) REVERT: A 606 VAL cc_start: 0.8793 (t) cc_final: 0.8488 (t) REVERT: A 939 GLN cc_start: 0.7863 (mt0) cc_final: 0.7611 (tm-30) outliers start: 5 outliers final: 0 residues processed: 375 average time/residue: 0.4226 time to fit residues: 243.8288 Evaluate side-chains 178 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 2.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 2.9990 chunk 241 optimal weight: 0.0970 chunk 133 optimal weight: 8.9990 chunk 82 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 128 optimal weight: 7.9990 chunk 249 optimal weight: 5.9990 chunk 96 optimal weight: 0.7980 chunk 151 optimal weight: 0.0970 chunk 185 optimal weight: 0.8980 chunk 288 optimal weight: 0.8980 overall best weight: 0.5576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 ASN B 214 ASN B 599 GLN B 641 HIS B 759 ASN B 907 ASN B 993 GLN B1088 GLN C 29 ASN C 122 ASN C 201 GLN C 396 GLN C 445 HIS C 530 ASN ** C 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 746 ASN ** C 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 838 ASN ** C 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 937 ASN C 993 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 ASN A 227 ASN A 661 HIS A 733 ASN ** A 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 889 ASN ** A 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1030 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26609 Z= 0.179 Angle : 0.675 11.306 36204 Z= 0.353 Chirality : 0.047 0.279 4302 Planarity : 0.005 0.066 4575 Dihedral : 11.508 87.293 4965 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.26 % Allowed : 7.02 % Favored : 91.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.41 (0.13), residues: 3161 helix: -1.29 (0.17), residues: 669 sheet: -0.79 (0.20), residues: 620 loop : -2.08 (0.13), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 423 HIS 0.003 0.001 HIS C 70 PHE 0.021 0.002 PHE B 325 TYR 0.021 0.002 TYR A 163 ARG 0.020 0.001 ARG C 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 253 time to evaluate : 2.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 ILE cc_start: 0.6648 (OUTLIER) cc_final: 0.6152 (mp) REVERT: B 83 PHE cc_start: 0.6409 (t80) cc_final: 0.6121 (t80) REVERT: B 87 ILE cc_start: 0.8542 (tt) cc_final: 0.7910 (mm) REVERT: B 103 PHE cc_start: 0.8573 (m-80) cc_final: 0.8173 (m-10) REVERT: B 107 MET cc_start: 0.4575 (mmt) cc_final: 0.4323 (mmt) REVERT: B 155 ASN cc_start: 0.8181 (m-40) cc_final: 0.7769 (m110) REVERT: B 231 PHE cc_start: 0.7669 (OUTLIER) cc_final: 0.7236 (p90) REVERT: B 1099 THR cc_start: 0.8237 (p) cc_final: 0.7969 (t) REVERT: C 50 ASP cc_start: 0.7999 (t0) cc_final: 0.7615 (t0) REVERT: C 274 ASP cc_start: 0.7449 (OUTLIER) cc_final: 0.7196 (m-30) REVERT: C 407 ASP cc_start: 0.6407 (m-30) cc_final: 0.5440 (p0) REVERT: C 707 GLU cc_start: 0.6986 (pt0) cc_final: 0.6766 (pt0) REVERT: C 886 TYR cc_start: 0.7202 (t80) cc_final: 0.6986 (t80) REVERT: A 37 MET cc_start: 0.7870 (mtm) cc_final: 0.7419 (mpp) REVERT: A 107 MET cc_start: 0.3950 (mmt) cc_final: 0.3681 (mmt) REVERT: A 150 THR cc_start: 0.0351 (OUTLIER) cc_final: -0.0004 (t) REVERT: A 151 MET cc_start: 0.5065 (mmm) cc_final: 0.3938 (mtp) outliers start: 35 outliers final: 13 residues processed: 277 average time/residue: 0.3737 time to fit residues: 169.8618 Evaluate side-chains 192 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 175 time to evaluate : 2.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 207 ARG Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 757 ASP Chi-restraints excluded: chain B residue 896 ASN Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 800 ILE Chi-restraints excluded: chain A residue 869 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 160 optimal weight: 6.9990 chunk 89 optimal weight: 0.9990 chunk 240 optimal weight: 10.0000 chunk 196 optimal weight: 9.9990 chunk 79 optimal weight: 3.9990 chunk 289 optimal weight: 10.0000 chunk 312 optimal weight: 5.9990 chunk 257 optimal weight: 50.0000 chunk 286 optimal weight: 8.9990 chunk 98 optimal weight: 7.9990 chunk 232 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 599 GLN B 627 ASN B 759 ASN B 896 ASN B 907 ASN ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 546 GLN ** C 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN C 902 GLN C1005 ASN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN ** A 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A 935 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 26609 Z= 0.369 Angle : 0.753 9.817 36204 Z= 0.388 Chirality : 0.048 0.286 4302 Planarity : 0.005 0.058 4575 Dihedral : 10.184 78.956 4965 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 2.27 % Allowed : 8.89 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.14 (0.14), residues: 3161 helix: -0.44 (0.19), residues: 656 sheet: -0.91 (0.20), residues: 621 loop : -2.05 (0.13), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 423 HIS 0.007 0.002 HIS C1040 PHE 0.025 0.002 PHE C 83 TYR 0.019 0.002 TYR B 855 ARG 0.006 0.001 ARG C 453 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 170 time to evaluate : 2.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 ILE cc_start: 0.6531 (OUTLIER) cc_final: 0.6017 (mp) REVERT: B 87 ILE cc_start: 0.8763 (tt) cc_final: 0.8156 (mm) REVERT: B 103 PHE cc_start: 0.8570 (m-80) cc_final: 0.8216 (m-10) REVERT: B 107 MET cc_start: 0.4703 (mmt) cc_final: 0.4249 (mmt) REVERT: B 151 MET cc_start: 0.3891 (mpp) cc_final: 0.3544 (ppp) REVERT: B 155 ASN cc_start: 0.8231 (m-40) cc_final: 0.7846 (m110) REVERT: B 231 PHE cc_start: 0.7944 (OUTLIER) cc_final: 0.7209 (p90) REVERT: B 805 PHE cc_start: 0.8406 (OUTLIER) cc_final: 0.8059 (t80) REVERT: B 1099 THR cc_start: 0.8533 (p) cc_final: 0.8261 (t) REVERT: C 50 ASP cc_start: 0.8101 (t0) cc_final: 0.7655 (t0) REVERT: C 407 ASP cc_start: 0.6541 (m-30) cc_final: 0.5532 (p0) REVERT: C 884 MET cc_start: 0.8102 (mmm) cc_final: 0.7849 (mmm) REVERT: C 886 TYR cc_start: 0.7490 (t80) cc_final: 0.7250 (t80) REVERT: A 37 MET cc_start: 0.8011 (mtm) cc_final: 0.7482 (mpp) outliers start: 63 outliers final: 36 residues processed: 219 average time/residue: 0.3216 time to fit residues: 119.3663 Evaluate side-chains 187 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 148 time to evaluate : 2.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 207 ARG Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 805 PHE Chi-restraints excluded: chain B residue 849 ASP Chi-restraints excluded: chain B residue 896 ASN Chi-restraints excluded: chain B residue 1032 MET Chi-restraints excluded: chain B residue 1085 PHE Chi-restraints excluded: chain B residue 1090 ASN Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 731 CYS Chi-restraints excluded: chain C residue 763 VAL Chi-restraints excluded: chain C residue 841 THR Chi-restraints excluded: chain C residue 1019 SER Chi-restraints excluded: chain C residue 1033 SER Chi-restraints excluded: chain C residue 1098 THR Chi-restraints excluded: chain C residue 1107 ASN Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 800 ILE Chi-restraints excluded: chain A residue 838 ASN Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 1110 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 285 optimal weight: 1.9990 chunk 217 optimal weight: 0.0070 chunk 150 optimal weight: 9.9990 chunk 32 optimal weight: 0.0270 chunk 138 optimal weight: 0.1980 chunk 194 optimal weight: 0.6980 chunk 290 optimal weight: 2.9990 chunk 307 optimal weight: 0.8980 chunk 151 optimal weight: 0.9990 chunk 275 optimal weight: 7.9990 chunk 82 optimal weight: 10.0000 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 907 ASN C 158 ASN C 546 GLN ** C 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 661 HIS ** C 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1036 GLN A 632 GLN A 786 GLN ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN ** A 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 26609 Z= 0.157 Angle : 0.601 10.481 36204 Z= 0.309 Chirality : 0.046 0.275 4302 Planarity : 0.004 0.059 4575 Dihedral : 8.238 58.813 4965 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 1.33 % Allowed : 10.58 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: -1.64 (0.14), residues: 3161 helix: 0.31 (0.20), residues: 659 sheet: -0.61 (0.20), residues: 614 loop : -1.85 (0.13), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 423 HIS 0.003 0.001 HIS B 70 PHE 0.020 0.001 PHE A 360 TYR 0.022 0.001 TYR A 886 ARG 0.006 0.000 ARG B1001 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 192 time to evaluate : 2.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 19 CYS cc_start: 0.4419 (OUTLIER) cc_final: 0.4141 (m) REVERT: B 37 MET cc_start: 0.8311 (mmm) cc_final: 0.8071 (mmm) REVERT: B 81 ILE cc_start: 0.6454 (OUTLIER) cc_final: 0.6026 (mp) REVERT: B 87 ILE cc_start: 0.8613 (tt) cc_final: 0.8011 (mm) REVERT: B 103 PHE cc_start: 0.8474 (m-80) cc_final: 0.8119 (m-10) REVERT: B 151 MET cc_start: 0.4073 (mpp) cc_final: 0.3788 (ppp) REVERT: B 155 ASN cc_start: 0.8173 (m-40) cc_final: 0.7788 (m110) REVERT: B 231 PHE cc_start: 0.7731 (OUTLIER) cc_final: 0.7180 (p90) REVERT: B 600 ASP cc_start: 0.6656 (t70) cc_final: 0.6123 (t70) REVERT: B 805 PHE cc_start: 0.8345 (OUTLIER) cc_final: 0.7943 (t80) REVERT: B 927 LEU cc_start: 0.7658 (mm) cc_final: 0.7091 (mm) REVERT: B 1099 THR cc_start: 0.8248 (p) cc_final: 0.8000 (t) REVERT: C 407 ASP cc_start: 0.6564 (m-30) cc_final: 0.5579 (p0) REVERT: C 851 MET cc_start: 0.8860 (mtt) cc_final: 0.8531 (mtm) REVERT: C 886 TYR cc_start: 0.7256 (t80) cc_final: 0.6995 (t80) REVERT: A 37 MET cc_start: 0.8046 (mtm) cc_final: 0.7616 (mpp) REVERT: A 151 MET cc_start: 0.5156 (mmm) cc_final: 0.3989 (tmm) REVERT: A 182 LEU cc_start: 0.8460 (pp) cc_final: 0.8238 (tp) REVERT: A 197 TYR cc_start: 0.6887 (m-10) cc_final: 0.6493 (m-10) REVERT: A 413 PRO cc_start: 0.5200 (Cg_endo) cc_final: 0.4973 (Cg_exo) outliers start: 37 outliers final: 13 residues processed: 215 average time/residue: 0.3145 time to fit residues: 114.5173 Evaluate side-chains 173 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 156 time to evaluate : 2.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain B residue 207 ARG Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 805 PHE Chi-restraints excluded: chain B residue 896 ASN Chi-restraints excluded: chain B residue 1085 PHE Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 731 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 255 optimal weight: 10.0000 chunk 174 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 228 optimal weight: 10.0000 chunk 126 optimal weight: 0.0970 chunk 262 optimal weight: 10.0000 chunk 212 optimal weight: 40.0000 chunk 0 optimal weight: 40.0000 chunk 156 optimal weight: 8.9990 chunk 275 optimal weight: 8.9990 chunk 77 optimal weight: 10.0000 overall best weight: 4.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 746 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 896 ASN B1090 ASN C 118 ASN ** C 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 GLN A 627 ASN ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 26609 Z= 0.298 Angle : 0.670 10.195 36204 Z= 0.342 Chirality : 0.047 0.278 4302 Planarity : 0.004 0.054 4575 Dihedral : 7.659 56.049 4965 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 2.20 % Allowed : 11.62 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: -1.68 (0.14), residues: 3161 helix: 0.37 (0.20), residues: 659 sheet: -0.75 (0.21), residues: 602 loop : -1.86 (0.13), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 423 HIS 0.005 0.001 HIS C1040 PHE 0.022 0.002 PHE C 83 TYR 0.017 0.002 TYR A 300 ARG 0.006 0.001 ARG B1001 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 155 time to evaluate : 3.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 ILE cc_start: 0.6524 (OUTLIER) cc_final: 0.6078 (mp) REVERT: B 87 ILE cc_start: 0.8734 (tt) cc_final: 0.8130 (mm) REVERT: B 103 PHE cc_start: 0.8617 (m-80) cc_final: 0.8356 (m-10) REVERT: B 107 MET cc_start: 0.4605 (mmt) cc_final: 0.4256 (mmt) REVERT: B 151 MET cc_start: 0.4231 (mpp) cc_final: 0.3734 (ppp) REVERT: B 155 ASN cc_start: 0.8256 (m-40) cc_final: 0.7867 (m110) REVERT: B 231 PHE cc_start: 0.7928 (OUTLIER) cc_final: 0.7197 (p90) REVERT: B 600 ASP cc_start: 0.6890 (t70) cc_final: 0.6360 (t70) REVERT: B 805 PHE cc_start: 0.8431 (OUTLIER) cc_final: 0.8056 (t80) REVERT: B 1099 THR cc_start: 0.8372 (p) cc_final: 0.8094 (t) REVERT: C 407 ASP cc_start: 0.6587 (m-30) cc_final: 0.5570 (p0) REVERT: C 417 MET cc_start: 0.2534 (tpt) cc_final: -0.1817 (ptm) REVERT: C 851 MET cc_start: 0.8915 (mtt) cc_final: 0.8577 (mtm) REVERT: C 886 TYR cc_start: 0.7559 (t80) cc_final: 0.7281 (t80) REVERT: A 37 MET cc_start: 0.7872 (mtm) cc_final: 0.7567 (mpp) REVERT: A 151 MET cc_start: 0.4986 (mmm) cc_final: 0.3536 (tmm) REVERT: A 197 TYR cc_start: 0.7312 (m-10) cc_final: 0.6778 (m-10) REVERT: A 799 PHE cc_start: 0.8629 (OUTLIER) cc_final: 0.8157 (t80) outliers start: 61 outliers final: 32 residues processed: 205 average time/residue: 0.3216 time to fit residues: 112.5958 Evaluate side-chains 186 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 150 time to evaluate : 2.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 207 ARG Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 805 PHE Chi-restraints excluded: chain B residue 849 ASP Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 896 ASN Chi-restraints excluded: chain B residue 1085 PHE Chi-restraints excluded: chain B residue 1105 SER Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 841 THR Chi-restraints excluded: chain C residue 991 THR Chi-restraints excluded: chain C residue 1033 SER Chi-restraints excluded: chain C residue 1086 ILE Chi-restraints excluded: chain C residue 1107 ASN Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 975 ILE Chi-restraints excluded: chain A residue 1103 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 103 optimal weight: 6.9990 chunk 276 optimal weight: 9.9990 chunk 60 optimal weight: 0.8980 chunk 180 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 307 optimal weight: 1.9990 chunk 255 optimal weight: 6.9990 chunk 142 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 101 optimal weight: 5.9990 chunk 161 optimal weight: 8.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 550 GLN ** B 746 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 759 ASN C 301 GLN C 599 GLN ** C 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 135 ASN ** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN A 896 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 26609 Z= 0.219 Angle : 0.599 10.245 36204 Z= 0.308 Chirality : 0.045 0.272 4302 Planarity : 0.004 0.054 4575 Dihedral : 6.986 53.172 4965 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 1.87 % Allowed : 12.74 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: -1.58 (0.14), residues: 3161 helix: 0.62 (0.21), residues: 659 sheet: -0.66 (0.21), residues: 620 loop : -1.88 (0.13), residues: 1882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 423 HIS 0.004 0.001 HIS A 641 PHE 0.022 0.001 PHE C 83 TYR 0.015 0.001 TYR C 300 ARG 0.006 0.000 ARG B1001 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 159 time to evaluate : 2.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 ILE cc_start: 0.6514 (OUTLIER) cc_final: 0.6122 (mp) REVERT: B 87 ILE cc_start: 0.8695 (tt) cc_final: 0.8111 (mm) REVERT: B 103 PHE cc_start: 0.8632 (m-80) cc_final: 0.8426 (m-10) REVERT: B 107 MET cc_start: 0.4630 (mmt) cc_final: 0.4287 (mmt) REVERT: B 151 MET cc_start: 0.4100 (mpp) cc_final: 0.3578 (ppp) REVERT: B 155 ASN cc_start: 0.8203 (m-40) cc_final: 0.7852 (m110) REVERT: B 231 PHE cc_start: 0.7935 (OUTLIER) cc_final: 0.7181 (p90) REVERT: B 600 ASP cc_start: 0.6920 (t70) cc_final: 0.6373 (t70) REVERT: B 805 PHE cc_start: 0.8406 (OUTLIER) cc_final: 0.8023 (t80) REVERT: B 1099 THR cc_start: 0.8298 (p) cc_final: 0.8025 (t) REVERT: C 407 ASP cc_start: 0.6413 (m-30) cc_final: 0.5413 (p0) REVERT: C 417 MET cc_start: 0.2599 (tpt) cc_final: -0.1913 (ptm) REVERT: C 758 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7742 (ttt180) REVERT: C 851 MET cc_start: 0.8926 (mtt) cc_final: 0.8555 (mtm) REVERT: A 37 MET cc_start: 0.7879 (mtm) cc_final: 0.7353 (mpp) REVERT: A 151 MET cc_start: 0.5297 (mmm) cc_final: 0.3923 (tmm) REVERT: A 197 TYR cc_start: 0.7315 (m-10) cc_final: 0.6828 (m-10) REVERT: A 799 PHE cc_start: 0.8654 (OUTLIER) cc_final: 0.8208 (t80) outliers start: 52 outliers final: 32 residues processed: 197 average time/residue: 0.3160 time to fit residues: 106.5185 Evaluate side-chains 191 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 154 time to evaluate : 2.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain B residue 207 ARG Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 805 PHE Chi-restraints excluded: chain B residue 849 ASP Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 896 ASN Chi-restraints excluded: chain B residue 967 ASP Chi-restraints excluded: chain B residue 1085 PHE Chi-restraints excluded: chain B residue 1090 ASN Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 758 ARG Chi-restraints excluded: chain C residue 909 PHE Chi-restraints excluded: chain C residue 991 THR Chi-restraints excluded: chain C residue 1033 SER Chi-restraints excluded: chain C residue 1086 ILE Chi-restraints excluded: chain C residue 1107 ASN Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 733 ASN Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 975 ILE Chi-restraints excluded: chain A residue 1103 PHE Chi-restraints excluded: chain A residue 1110 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 296 optimal weight: 5.9990 chunk 34 optimal weight: 30.0000 chunk 175 optimal weight: 0.7980 chunk 224 optimal weight: 8.9990 chunk 174 optimal weight: 4.9990 chunk 259 optimal weight: 30.0000 chunk 171 optimal weight: 4.9990 chunk 306 optimal weight: 7.9990 chunk 191 optimal weight: 1.9990 chunk 186 optimal weight: 8.9990 chunk 141 optimal weight: 20.0000 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 546 GLN ** B 746 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 896 ASN B 907 ASN ** B1065 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 GLN C 599 GLN ** C 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1065 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN A 935 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 26609 Z= 0.277 Angle : 0.634 9.073 36204 Z= 0.324 Chirality : 0.046 0.263 4302 Planarity : 0.004 0.059 4575 Dihedral : 6.855 57.671 4965 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 2.45 % Allowed : 12.92 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.60 (0.15), residues: 3161 helix: 0.58 (0.20), residues: 659 sheet: -0.72 (0.21), residues: 616 loop : -1.87 (0.14), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 423 HIS 0.005 0.001 HIS A 641 PHE 0.023 0.002 PHE C 83 TYR 0.015 0.001 TYR B 855 ARG 0.008 0.001 ARG B1001 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 164 time to evaluate : 2.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 ILE cc_start: 0.6580 (OUTLIER) cc_final: 0.6189 (mp) REVERT: B 87 ILE cc_start: 0.8758 (tt) cc_final: 0.8127 (mm) REVERT: B 107 MET cc_start: 0.4681 (mmt) cc_final: 0.4127 (mmt) REVERT: B 151 MET cc_start: 0.4270 (mpp) cc_final: 0.3715 (ppp) REVERT: B 155 ASN cc_start: 0.8268 (m-40) cc_final: 0.7947 (m110) REVERT: B 194 LEU cc_start: 0.8355 (tp) cc_final: 0.8014 (tp) REVERT: B 231 PHE cc_start: 0.8030 (OUTLIER) cc_final: 0.7243 (p90) REVERT: B 545 PHE cc_start: 0.8633 (OUTLIER) cc_final: 0.8426 (m-10) REVERT: B 600 ASP cc_start: 0.7001 (t70) cc_final: 0.6444 (t70) REVERT: B 805 PHE cc_start: 0.8350 (OUTLIER) cc_final: 0.8000 (t80) REVERT: B 868 TRP cc_start: 0.4796 (p-90) cc_final: 0.3112 (p-90) REVERT: B 1099 THR cc_start: 0.8392 (p) cc_final: 0.8111 (t) REVERT: C 262 PHE cc_start: 0.8760 (OUTLIER) cc_final: 0.8509 (m-80) REVERT: C 407 ASP cc_start: 0.6517 (m-30) cc_final: 0.5419 (p0) REVERT: C 417 MET cc_start: 0.2502 (tpt) cc_final: -0.1924 (ptm) REVERT: C 758 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7828 (ttt180) REVERT: C 851 MET cc_start: 0.8956 (mtt) cc_final: 0.8583 (mtm) REVERT: A 37 MET cc_start: 0.7853 (mtm) cc_final: 0.7235 (mpp) REVERT: A 151 MET cc_start: 0.5687 (mmm) cc_final: 0.4148 (tmm) REVERT: A 197 TYR cc_start: 0.7407 (m-10) cc_final: 0.7147 (m-10) REVERT: A 799 PHE cc_start: 0.8649 (OUTLIER) cc_final: 0.8277 (t80) REVERT: A 865 THR cc_start: 0.8325 (OUTLIER) cc_final: 0.8066 (m) REVERT: A 970 GLU cc_start: 0.7661 (tm-30) cc_final: 0.7294 (tp30) outliers start: 68 outliers final: 41 residues processed: 217 average time/residue: 0.3154 time to fit residues: 117.0269 Evaluate side-chains 200 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 151 time to evaluate : 2.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain B residue 207 ARG Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 545 PHE Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 805 PHE Chi-restraints excluded: chain B residue 849 ASP Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 896 ASN Chi-restraints excluded: chain B residue 1085 PHE Chi-restraints excluded: chain B residue 1090 ASN Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 758 ARG Chi-restraints excluded: chain C residue 841 THR Chi-restraints excluded: chain C residue 909 PHE Chi-restraints excluded: chain C residue 991 THR Chi-restraints excluded: chain C residue 1033 SER Chi-restraints excluded: chain C residue 1086 ILE Chi-restraints excluded: chain C residue 1107 ASN Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 733 ASN Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 999 GLU Chi-restraints excluded: chain A residue 1103 PHE Chi-restraints excluded: chain A residue 1110 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 189 optimal weight: 6.9990 chunk 122 optimal weight: 10.0000 chunk 183 optimal weight: 10.0000 chunk 92 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 194 optimal weight: 10.0000 chunk 208 optimal weight: 0.9980 chunk 151 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 240 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 896 ASN ** B1065 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 GLN C 599 GLN ** C 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1095 GLN A 201 GLN A 744 GLN ** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26609 Z= 0.182 Angle : 0.581 9.520 36204 Z= 0.298 Chirality : 0.044 0.265 4302 Planarity : 0.004 0.063 4575 Dihedral : 6.532 55.156 4965 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 2.05 % Allowed : 13.35 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: -1.44 (0.15), residues: 3161 helix: 0.87 (0.21), residues: 653 sheet: -0.59 (0.21), residues: 615 loop : -1.84 (0.14), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 423 HIS 0.004 0.001 HIS A 641 PHE 0.021 0.001 PHE C 83 TYR 0.016 0.001 TYR C 886 ARG 0.007 0.000 ARG B1001 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 161 time to evaluate : 2.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 ILE cc_start: 0.6496 (OUTLIER) cc_final: 0.6150 (mp) REVERT: B 87 ILE cc_start: 0.8723 (tt) cc_final: 0.8102 (mm) REVERT: B 107 MET cc_start: 0.4542 (mmt) cc_final: 0.3994 (mmt) REVERT: B 151 MET cc_start: 0.4211 (mpp) cc_final: 0.3711 (ppp) REVERT: B 155 ASN cc_start: 0.8169 (m-40) cc_final: 0.7838 (m110) REVERT: B 231 PHE cc_start: 0.8034 (OUTLIER) cc_final: 0.7222 (p90) REVERT: B 600 ASP cc_start: 0.6892 (t70) cc_final: 0.6292 (t70) REVERT: B 805 PHE cc_start: 0.8309 (OUTLIER) cc_final: 0.7964 (t80) REVERT: B 1099 THR cc_start: 0.8380 (p) cc_final: 0.8117 (t) REVERT: C 179 PHE cc_start: 0.4818 (m-10) cc_final: 0.4418 (m-10) REVERT: C 262 PHE cc_start: 0.8734 (OUTLIER) cc_final: 0.8472 (m-80) REVERT: C 407 ASP cc_start: 0.6618 (m-30) cc_final: 0.5540 (p0) REVERT: C 417 MET cc_start: 0.2738 (tpt) cc_final: -0.1669 (ptm) REVERT: C 758 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7736 (ttt180) REVERT: C 851 MET cc_start: 0.8929 (mtt) cc_final: 0.8542 (mtm) REVERT: A 37 MET cc_start: 0.7822 (mtm) cc_final: 0.7304 (mpp) REVERT: A 151 MET cc_start: 0.5706 (mmm) cc_final: 0.4222 (tmm) REVERT: A 197 TYR cc_start: 0.7358 (m-10) cc_final: 0.7113 (m-10) REVERT: A 799 PHE cc_start: 0.8632 (OUTLIER) cc_final: 0.8228 (t80) REVERT: A 865 THR cc_start: 0.8278 (OUTLIER) cc_final: 0.8016 (m) outliers start: 57 outliers final: 39 residues processed: 206 average time/residue: 0.3166 time to fit residues: 111.0061 Evaluate side-chains 202 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 156 time to evaluate : 2.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain B residue 207 ARG Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 805 PHE Chi-restraints excluded: chain B residue 849 ASP Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 967 ASP Chi-restraints excluded: chain B residue 1085 PHE Chi-restraints excluded: chain B residue 1090 ASN Chi-restraints excluded: chain C residue 89 PHE Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 758 ARG Chi-restraints excluded: chain C residue 841 THR Chi-restraints excluded: chain C residue 909 PHE Chi-restraints excluded: chain C residue 943 THR Chi-restraints excluded: chain C residue 1000 ILE Chi-restraints excluded: chain C residue 1033 SER Chi-restraints excluded: chain C residue 1086 ILE Chi-restraints excluded: chain C residue 1107 ASN Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 733 ASN Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 999 GLU Chi-restraints excluded: chain A residue 1103 PHE Chi-restraints excluded: chain A residue 1110 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 278 optimal weight: 4.9990 chunk 293 optimal weight: 0.1980 chunk 267 optimal weight: 1.9990 chunk 285 optimal weight: 0.0000 chunk 171 optimal weight: 5.9990 chunk 124 optimal weight: 0.5980 chunk 224 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 chunk 258 optimal weight: 0.0040 chunk 270 optimal weight: 4.9990 chunk 284 optimal weight: 0.8980 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 627 ASN C 396 GLN ** C 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1095 GLN A 158 ASN A 766 GLN A 895 GLN ** A 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 931 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.4227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 26609 Z= 0.133 Angle : 0.556 12.252 36204 Z= 0.284 Chirality : 0.044 0.261 4302 Planarity : 0.004 0.061 4575 Dihedral : 5.806 51.619 4965 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 1.62 % Allowed : 14.14 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: -1.22 (0.15), residues: 3161 helix: 1.18 (0.21), residues: 650 sheet: -0.53 (0.21), residues: 628 loop : -1.71 (0.14), residues: 1883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 423 HIS 0.003 0.000 HIS C1065 PHE 0.046 0.001 PHE B 83 TYR 0.025 0.001 TYR C 886 ARG 0.004 0.000 ARG A 761 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 189 time to evaluate : 3.149 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 81 ILE cc_start: 0.6674 (OUTLIER) cc_final: 0.6320 (mp) REVERT: B 107 MET cc_start: 0.4071 (mmt) cc_final: 0.3629 (mmt) REVERT: B 151 MET cc_start: 0.3939 (mpp) cc_final: 0.3536 (ppp) REVERT: B 231 PHE cc_start: 0.7838 (OUTLIER) cc_final: 0.7186 (p90) REVERT: B 805 PHE cc_start: 0.8385 (OUTLIER) cc_final: 0.8046 (t80) REVERT: B 1099 THR cc_start: 0.8344 (p) cc_final: 0.8113 (t) REVERT: C 22 PHE cc_start: 0.2126 (OUTLIER) cc_final: 0.1912 (t80) REVERT: C 50 ASP cc_start: 0.7987 (t0) cc_final: 0.7628 (t70) REVERT: C 179 PHE cc_start: 0.4248 (m-10) cc_final: 0.3787 (m-10) REVERT: C 262 PHE cc_start: 0.8717 (OUTLIER) cc_final: 0.8408 (m-80) REVERT: C 407 ASP cc_start: 0.6693 (m-30) cc_final: 0.5700 (p0) REVERT: C 417 MET cc_start: 0.2418 (tpt) cc_final: -0.1403 (ptm) REVERT: C 758 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.7671 (ttt180) REVERT: C 851 MET cc_start: 0.8877 (mtt) cc_final: 0.8649 (mtm) REVERT: A 37 MET cc_start: 0.7850 (mtm) cc_final: 0.7432 (mpp) REVERT: A 151 MET cc_start: 0.5420 (mmm) cc_final: 0.3946 (tmm) REVERT: A 741 PHE cc_start: 0.6219 (OUTLIER) cc_final: 0.5934 (p90) REVERT: A 799 PHE cc_start: 0.8542 (OUTLIER) cc_final: 0.8144 (t80) outliers start: 45 outliers final: 24 residues processed: 222 average time/residue: 0.3342 time to fit residues: 123.9109 Evaluate side-chains 192 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 160 time to evaluate : 2.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain B residue 207 ARG Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 805 PHE Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 1085 PHE Chi-restraints excluded: chain C residue 22 PHE Chi-restraints excluded: chain C residue 89 PHE Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 758 ARG Chi-restraints excluded: chain C residue 909 PHE Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 741 PHE Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 987 GLN Chi-restraints excluded: chain A residue 999 GLU Chi-restraints excluded: chain A residue 1103 PHE Chi-restraints excluded: chain A residue 1110 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 187 optimal weight: 4.9990 chunk 302 optimal weight: 6.9990 chunk 184 optimal weight: 3.9990 chunk 143 optimal weight: 5.9990 chunk 209 optimal weight: 10.0000 chunk 316 optimal weight: 0.9980 chunk 291 optimal weight: 3.9990 chunk 252 optimal weight: 20.0000 chunk 26 optimal weight: 2.9990 chunk 194 optimal weight: 10.0000 chunk 154 optimal weight: 0.0040 overall best weight: 2.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1095 GLN ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.114 26609 Z= 0.214 Angle : 0.600 10.527 36204 Z= 0.305 Chirality : 0.044 0.273 4302 Planarity : 0.004 0.064 4575 Dihedral : 5.876 52.827 4965 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 1.48 % Allowed : 14.83 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.23 (0.15), residues: 3161 helix: 1.19 (0.21), residues: 651 sheet: -0.53 (0.20), residues: 659 loop : -1.75 (0.14), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 868 HIS 0.003 0.001 HIS A 641 PHE 0.034 0.001 PHE B 83 TYR 0.029 0.001 TYR A 383 ARG 0.011 0.000 ARG A1073 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 157 time to evaluate : 2.695 Fit side-chains revert: symmetry clash REVERT: B 81 ILE cc_start: 0.6629 (mm) cc_final: 0.6330 (mp) REVERT: B 107 MET cc_start: 0.4405 (mmt) cc_final: 0.3880 (mmt) REVERT: B 151 MET cc_start: 0.3992 (mpp) cc_final: 0.3600 (ppp) REVERT: B 155 ASN cc_start: 0.8198 (m-40) cc_final: 0.7848 (m110) REVERT: B 231 PHE cc_start: 0.7921 (OUTLIER) cc_final: 0.7225 (p90) REVERT: B 545 PHE cc_start: 0.8688 (OUTLIER) cc_final: 0.8453 (m-10) REVERT: B 600 ASP cc_start: 0.6893 (t70) cc_final: 0.6104 (t70) REVERT: B 805 PHE cc_start: 0.8430 (OUTLIER) cc_final: 0.8087 (t80) REVERT: B 1099 THR cc_start: 0.8377 (p) cc_final: 0.8136 (t) REVERT: C 22 PHE cc_start: 0.2261 (OUTLIER) cc_final: 0.1872 (t80) REVERT: C 50 ASP cc_start: 0.8047 (t0) cc_final: 0.7817 (t70) REVERT: C 262 PHE cc_start: 0.8717 (OUTLIER) cc_final: 0.8449 (m-80) REVERT: C 407 ASP cc_start: 0.6458 (m-30) cc_final: 0.5448 (p0) REVERT: C 417 MET cc_start: 0.2620 (tpt) cc_final: -0.1457 (ptm) REVERT: C 758 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7689 (ttt180) REVERT: C 851 MET cc_start: 0.8958 (mtt) cc_final: 0.8714 (mtm) REVERT: A 37 MET cc_start: 0.7768 (mtm) cc_final: 0.7311 (mpp) REVERT: A 151 MET cc_start: 0.5313 (mmm) cc_final: 0.3755 (tmm) REVERT: A 799 PHE cc_start: 0.8549 (OUTLIER) cc_final: 0.8211 (t80) REVERT: A 869 THR cc_start: 0.7896 (p) cc_final: 0.7645 (t) outliers start: 41 outliers final: 27 residues processed: 189 average time/residue: 0.3200 time to fit residues: 103.4224 Evaluate side-chains 188 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 154 time to evaluate : 3.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 207 ARG Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 545 PHE Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 805 PHE Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 967 ASP Chi-restraints excluded: chain B residue 1085 PHE Chi-restraints excluded: chain B residue 1090 ASN Chi-restraints excluded: chain C residue 22 PHE Chi-restraints excluded: chain C residue 89 PHE Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 758 ARG Chi-restraints excluded: chain C residue 909 PHE Chi-restraints excluded: chain C residue 915 GLN Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 999 GLU Chi-restraints excluded: chain A residue 1110 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 200 optimal weight: 1.9990 chunk 268 optimal weight: 9.9990 chunk 77 optimal weight: 10.0000 chunk 232 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 252 optimal weight: 30.0000 chunk 105 optimal weight: 4.9990 chunk 259 optimal weight: 8.9990 chunk 31 optimal weight: 20.0000 chunk 46 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 135 ASN ** B1065 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 GLN C 396 GLN C 599 GLN ** C 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 746 ASN ** C 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1065 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1095 GLN ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.115397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.089264 restraints weight = 107119.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.088624 restraints weight = 74301.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.088576 restraints weight = 62735.358| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.4408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 26609 Z= 0.283 Angle : 0.658 9.828 36204 Z= 0.336 Chirality : 0.046 0.246 4302 Planarity : 0.004 0.063 4575 Dihedral : 6.487 59.043 4965 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 1.62 % Allowed : 14.83 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.42 (0.15), residues: 3161 helix: 0.83 (0.21), residues: 649 sheet: -0.50 (0.21), residues: 577 loop : -1.80 (0.13), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 101 HIS 0.005 0.001 HIS A 641 PHE 0.036 0.002 PHE B 83 TYR 0.019 0.002 TYR C 886 ARG 0.007 0.001 ARG A1073 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4308.70 seconds wall clock time: 79 minutes 50.69 seconds (4790.69 seconds total)