Starting phenix.real_space_refine on Fri Feb 23 00:43:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c2l_30276/02_2024/7c2l_30276.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c2l_30276/02_2024/7c2l_30276.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c2l_30276/02_2024/7c2l_30276.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c2l_30276/02_2024/7c2l_30276.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c2l_30276/02_2024/7c2l_30276.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c2l_30276/02_2024/7c2l_30276.pdb" } resolution = 3.1 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= 0.004 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 158 5.16 5 C 22777 2.51 5 N 5872 2.21 5 O 7181 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 154": "OE1" <-> "OE2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A ARG 346": "NH1" <-> "NH2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A ARG 454": "NH1" <-> "NH2" Residue "A ARG 509": "NH1" <-> "NH2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A GLU 819": "OE1" <-> "OE2" Residue "A GLU 918": "OE1" <-> "OE2" Residue "A GLU 1092": "OE1" <-> "OE2" Residue "A ARG 1107": "NH1" <-> "NH2" Residue "A GLU 1111": "OE1" <-> "OE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 403": "NH1" <-> "NH2" Residue "B ARG 408": "NH1" <-> "NH2" Residue "B ARG 509": "NH1" <-> "NH2" Residue "B GLU 516": "OE1" <-> "OE2" Residue "B PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "B GLU 773": "OE1" <-> "OE2" Residue "B GLU 780": "OE1" <-> "OE2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B GLU 819": "OE1" <-> "OE2" Residue "B GLU 868": "OE1" <-> "OE2" Residue "B GLU 988": "OE1" <-> "OE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1072": "OE1" <-> "OE2" Residue "B GLU 1111": "OE1" <-> "OE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 154": "OE1" <-> "OE2" Residue "C ARG 158": "NH1" <-> "NH2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C ARG 214": "NH1" <-> "NH2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C ARG 346": "NH1" <-> "NH2" Residue "C ARG 403": "NH1" <-> "NH2" Residue "C ARG 408": "NH1" <-> "NH2" Residue "C GLU 465": "OE1" <-> "OE2" Residue "C ARG 509": "NH1" <-> "NH2" Residue "C PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 554": "OE1" <-> "OE2" Residue "C GLU 583": "OE1" <-> "OE2" Residue "C GLU 619": "OE1" <-> "OE2" Residue "C GLU 661": "OE1" <-> "OE2" Residue "C GLU 748": "OE1" <-> "OE2" Residue "C GLU 780": "OE1" <-> "OE2" Residue "C ARG 815": "NH1" <-> "NH2" Residue "C GLU 988": "OE1" <-> "OE2" Residue "C GLU 1031": "OE1" <-> "OE2" Residue "C GLU 1072": "OE1" <-> "OE2" Residue "C GLU 1092": "OE1" <-> "OE2" Residue "H GLU 1": "OE1" <-> "OE2" Residue "H GLU 54": "OE1" <-> "OE2" Residue "H GLU 57": "OE1" <-> "OE2" Residue "H PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 67": "NH1" <-> "NH2" Residue "H GLU 82": "OE1" <-> "OE2" Residue "H GLU 163": "OE1" <-> "OE2" Residue "L ARG 24": "NH1" <-> "NH2" Residue "L ARG 44": "NH1" <-> "NH2" Residue "L GLU 192": "OE1" <-> "OE2" Residue "I GLU 1": "OE1" <-> "OE2" Residue "I GLU 54": "OE1" <-> "OE2" Residue "I GLU 57": "OE1" <-> "OE2" Residue "I PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 67": "NH1" <-> "NH2" Residue "I GLU 82": "OE1" <-> "OE2" Residue "I GLU 163": "OE1" <-> "OE2" Residue "M ARG 24": "NH1" <-> "NH2" Residue "M ARG 44": "NH1" <-> "NH2" Residue "M GLU 192": "OE1" <-> "OE2" Residue "J GLU 1": "OE1" <-> "OE2" Residue "J GLU 54": "OE1" <-> "OE2" Residue "J GLU 57": "OE1" <-> "OE2" Residue "J PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 67": "NH1" <-> "NH2" Residue "J GLU 82": "OE1" <-> "OE2" Residue "J GLU 163": "OE1" <-> "OE2" Residue "N ARG 24": "NH1" <-> "NH2" Residue "N ARG 44": "NH1" <-> "NH2" Residue "N GLU 192": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 35988 Number of models: 1 Model: "" Number of chains: 41 Chain: "A" Number of atoms: 8064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1031, 8064 Classifications: {'peptide': 1031} Link IDs: {'PTRANS': 51, 'TRANS': 979} Chain breaks: 6 Chain: "B" Number of atoms: 8269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1055, 8269 Classifications: {'peptide': 1055} Link IDs: {'PTRANS': 51, 'TRANS': 1003} Chain breaks: 7 Chain: "C" Number of atoms: 8227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1049, 8227 Classifications: {'peptide': 1049} Link IDs: {'PTRANS': 52, 'TRANS': 996} Chain breaks: 6 Chain: "H" Number of atoms: 1706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1706 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 13, 'TRANS': 215} Chain: "L" Number of atoms: 1688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1688 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 13, 'TRANS': 205} Chain: "I" Number of atoms: 1706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1706 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 13, 'TRANS': 215} Chain: "M" Number of atoms: 1688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1688 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 13, 'TRANS': 205} Chain: "J" Number of atoms: 1706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1706 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 13, 'TRANS': 215} Chain: "N" Number of atoms: 1688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1688 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 13, 'TRANS': 205} Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "T" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "d" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 17.74, per 1000 atoms: 0.49 Number of scatterers: 35988 At special positions: 0 Unit cell: (229.357, 209.791, 228.27, 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 158 16.00 O 7181 8.00 N 5872 7.00 C 22777 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=1.86 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.14 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.00 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.11 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=1.98 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.00 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=1.86 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=1.92 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.02 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=1.99 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.76 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=1.86 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=1.91 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.08 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=1.82 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.01 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.18 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 155 " - pdb=" SG CYS H 211 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.13 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 199 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 155 " - pdb=" SG CYS I 211 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 93 " distance=2.13 Simple disulfide: pdb=" SG CYS M 139 " - pdb=" SG CYS M 199 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 155 " - pdb=" SG CYS J 211 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 93 " distance=2.13 Simple disulfide: pdb=" SG CYS N 139 " - pdb=" SG CYS N 199 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " NAG D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " NAG E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG K 1 " - " NAG K 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " NAG S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " NAG T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " NAG c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " NAG d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " NAG-ASN " NAG A1401 " - " ASN A 17 " " NAG A1402 " - " ASN A 61 " " NAG A1406 " - " ASN A 149 " " NAG A1414 " - " ASN A 331 " " NAG A1415 " - " ASN A 343 " " NAG A1416 " - " ASN A 603 " " NAG A1417 " - " ASN A 616 " " NAG A1418 " - " ASN A 657 " " NAG A1419 " - " ASN A 709 " " NAG B1401 " - " ASN B 17 " " NAG B1402 " - " ASN B 61 " " NAG B1406 " - " ASN B 149 " " NAG B1414 " - " ASN B 331 " " NAG B1415 " - " ASN B 343 " " NAG B1416 " - " ASN B 603 " " NAG B1417 " - " ASN B 616 " " NAG B1418 " - " ASN B 657 " " NAG C1401 " - " ASN C 17 " " NAG C1402 " - " ASN C 61 " " NAG C1406 " - " ASN C 149 " " NAG C1414 " - " ASN C 331 " " NAG C1415 " - " ASN C 343 " " NAG C1416 " - " ASN C 603 " " NAG C1417 " - " ASN C 616 " " NAG C1418 " - " ASN C 657 " " NAG D 1 " - " ASN A 122 " " NAG E 1 " - " ASN A 165 " " NAG F 1 " - " ASN A 234 " " NAG G 1 " - " ASN A 282 " " NAG K 1 " - " ASN A 717 " " NAG O 1 " - " ASN A 801 " " NAG P 1 " - " ASN A1074 " " NAG Q 1 " - " ASN A1098 " " NAG R 1 " - " ASN A1134 " " NAG S 1 " - " ASN B 122 " " NAG T 1 " - " ASN B 165 " " NAG U 1 " - " ASN B 234 " " NAG V 1 " - " ASN B 282 " " NAG W 1 " - " ASN B 709 " " NAG X 1 " - " ASN B 717 " " NAG Y 1 " - " ASN B 801 " " NAG Z 1 " - " ASN B1074 " " NAG a 1 " - " ASN B1098 " " NAG b 1 " - " ASN B1134 " " NAG c 1 " - " ASN C 122 " " NAG d 1 " - " ASN C 165 " " NAG e 1 " - " ASN C 234 " " NAG f 1 " - " ASN C 282 " " NAG g 1 " - " ASN C 709 " " NAG h 1 " - " ASN C 717 " " NAG i 1 " - " ASN C 801 " " NAG j 1 " - " ASN C1074 " " NAG k 1 " - " ASN C1098 " " NAG l 1 " - " ASN C1134 " Time building additional restraints: 14.66 Conformation dependent library (CDL) restraints added in 6.5 seconds 8846 Ramachandran restraints generated. 4423 Oldfield, 0 Emsley, 4423 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8362 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 79 sheets defined 17.4% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.69 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 removed outlier: 4.417A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASN A 343 " --> pdb=" O GLY A 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 338 through 343' Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.652A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.992A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.650A pdb=" N GLN A 409 " --> pdb=" O GLU A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 removed outlier: 4.017A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.956A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.571A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 removed outlier: 3.534A pdb=" N PHE A 823 " --> pdb=" O GLU A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 878 Processing helix chain 'A' and resid 879 through 884 removed outlier: 3.773A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 891 removed outlier: 4.114A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 removed outlier: 3.509A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY A 908 " --> pdb=" O TYR A 904 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.313A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.566A pdb=" N ASN A 925 " --> pdb=" O LYS A 921 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.566A pdb=" N ASP A 950 " --> pdb=" O GLY A 946 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.910A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1026 removed outlier: 4.073A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA A1025 " --> pdb=" O SER A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1026 through 1033 removed outlier: 3.584A pdb=" N SER A1030 " --> pdb=" O ALA A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.615A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.662A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 removed outlier: 3.732A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.572A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.716A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.598A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLN B 774 " --> pdb=" O ILE B 770 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 815 removed outlier: 3.612A pdb=" N LYS B 814 " --> pdb=" O LYS B 811 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG B 815 " --> pdb=" O PRO B 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 811 through 815' Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 882 removed outlier: 3.568A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 removed outlier: 3.567A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.697A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 removed outlier: 3.549A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 964 removed outlier: 3.913A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 965 through 968 removed outlier: 3.640A pdb=" N SER B 968 " --> pdb=" O GLN B 965 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 965 through 968' Processing helix chain 'B' and resid 985 through 1034 removed outlier: 3.603A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR B 998 " --> pdb=" O ASP B 994 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA B1016 " --> pdb=" O LEU B1012 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.575A pdb=" N GLU C 298 " --> pdb=" O ASP C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.597A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 385 through 389 removed outlier: 4.023A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 409 removed outlier: 4.028A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 502 through 505 removed outlier: 3.660A pdb=" N TYR C 505 " --> pdb=" O GLY C 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 502 through 505' Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 753 removed outlier: 3.504A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 754 through 757 removed outlier: 3.584A pdb=" N GLY C 757 " --> pdb=" O LEU C 754 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 754 through 757' Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.539A pdb=" N GLY C 769 " --> pdb=" O ARG C 765 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 823 Processing helix chain 'C' and resid 866 through 879 Processing helix chain 'C' and resid 879 through 884 removed outlier: 3.747A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.664A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 910 removed outlier: 3.588A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.506A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.729A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER C 939 " --> pdb=" O GLN C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.931A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 983 removed outlier: 3.521A pdb=" N ARG C 983 " --> pdb=" O ASP C 979 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1031 removed outlier: 3.689A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY C 999 " --> pdb=" O ARG C 995 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA C1020 " --> pdb=" O ALA C1016 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA C1026 " --> pdb=" O ALA C1022 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 61 through 65 Processing helix chain 'L' and resid 187 through 193 removed outlier: 3.894A pdb=" N GLU L 192 " --> pdb=" O LYS L 188 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LYS L 193 " --> pdb=" O ALA L 189 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 30 No H-bonds generated for 'chain 'I' and resid 28 through 30' Processing helix chain 'I' and resid 61 through 65 Processing helix chain 'M' and resid 187 through 193 removed outlier: 3.894A pdb=" N GLU M 192 " --> pdb=" O LYS M 188 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LYS M 193 " --> pdb=" O ALA M 189 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 30 No H-bonds generated for 'chain 'J' and resid 28 through 30' Processing helix chain 'J' and resid 61 through 65 Processing helix chain 'N' and resid 187 through 193 removed outlier: 3.893A pdb=" N GLU N 192 " --> pdb=" O LYS N 188 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LYS N 193 " --> pdb=" O ALA N 189 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 37 removed outlier: 6.786A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 8.830A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.397A pdb=" N THR A 274 " --> pdb=" O CYS A 291 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 69 through 70 Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 101 through 104 removed outlier: 6.593A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 116 through 120 removed outlier: 3.653A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 116 through 120 removed outlier: 3.653A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.105A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA A 609 " --> pdb=" O ILE A 598 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.770A pdb=" N VAL A 433 " --> pdb=" O LYS A 378 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 453 removed outlier: 3.696A pdb=" N TYR A 453 " --> pdb=" O GLN A 493 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLN A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 539 through 543 removed outlier: 3.505A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU A 583 " --> pdb=" O ASP A 578 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 664 through 667 removed outlier: 6.562A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER A 673 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE A 693 " --> pdb=" O SER A 673 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.514A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.790A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.013A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.776A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 36 through 37 removed outlier: 6.786A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 8.830A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 69 through 70 Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC3, first strand: chain 'B' and resid 101 through 104 removed outlier: 6.593A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 116 through 120 removed outlier: 3.653A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 116 through 120 removed outlier: 3.653A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 275 through 279 removed outlier: 3.860A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 309 through 319 removed outlier: 5.892A pdb=" N LYS B 310 " --> pdb=" O GLY B 601 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N GLY B 601 " --> pdb=" O LYS B 310 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.515A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AD1, first strand: chain 'B' and resid 539 through 543 removed outlier: 3.829A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.096A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.648A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 701 through 704 removed outlier: 7.000A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.591A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.591A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.575A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD8, first strand: chain 'C' and resid 36 through 37 removed outlier: 6.786A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 8.831A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.408A pdb=" N THR C 274 " --> pdb=" O CYS C 291 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 69 through 70 Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE3, first strand: chain 'C' and resid 101 through 104 removed outlier: 6.592A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 116 through 120 removed outlier: 3.653A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 116 through 120 removed outlier: 3.653A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.270A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE8, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'C' and resid 542 through 543 Processing sheet with id=AF2, first strand: chain 'C' and resid 551 through 554 removed outlier: 3.510A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.636A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.704A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.704A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF7, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.971A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AF9, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.739A pdb=" N THR H 122 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER H 99 " --> pdb=" O SER H 33 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER H 33 " --> pdb=" O SER H 99 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.739A pdb=" N THR H 122 " --> pdb=" O TYR H 94 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'H' and resid 136 through 137 removed outlier: 4.040A pdb=" N VAL H 196 " --> pdb=" O HIS H 179 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N HIS H 179 " --> pdb=" O VAL H 196 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'H' and resid 209 through 215 removed outlier: 4.596A pdb=" N TYR H 209 " --> pdb=" O VAL H 226 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 19 through 23 removed outlier: 3.882A pdb=" N PHE L 76 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N THR L 77 " --> pdb=" O SER L 70 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 41 through 43 removed outlier: 3.651A pdb=" N GLY L 89 " --> pdb=" O VAL L 109 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 119 through 123 removed outlier: 3.937A pdb=" N PHE L 123 " --> pdb=" O VAL L 138 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL L 138 " --> pdb=" O PHE L 123 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N VAL L 137 " --> pdb=" O LEU L 184 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU L 184 " --> pdb=" O VAL L 137 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N CYS L 139 " --> pdb=" O SER L 182 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N SER L 182 " --> pdb=" O CYS L 139 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'L' and resid 151 through 153 removed outlier: 3.625A pdb=" N GLN L 152 " --> pdb=" O GLU L 200 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS L 212 " --> pdb=" O CYS L 199 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'I' and resid 3 through 5 Processing sheet with id=AG9, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.739A pdb=" N THR I 122 " --> pdb=" O TYR I 94 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER I 99 " --> pdb=" O SER I 33 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER I 33 " --> pdb=" O SER I 99 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.739A pdb=" N THR I 122 " --> pdb=" O TYR I 94 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'I' and resid 136 through 137 removed outlier: 4.040A pdb=" N VAL I 196 " --> pdb=" O HIS I 179 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N HIS I 179 " --> pdb=" O VAL I 196 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'I' and resid 209 through 215 removed outlier: 4.597A pdb=" N TYR I 209 " --> pdb=" O VAL I 226 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'M' and resid 19 through 23 removed outlier: 3.881A pdb=" N PHE M 76 " --> pdb=" O CYS M 23 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N THR M 77 " --> pdb=" O SER M 70 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'M' and resid 41 through 43 removed outlier: 3.652A pdb=" N GLY M 89 " --> pdb=" O VAL M 109 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'M' and resid 119 through 123 removed outlier: 3.938A pdb=" N PHE M 123 " --> pdb=" O VAL M 138 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL M 138 " --> pdb=" O PHE M 123 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N VAL M 137 " --> pdb=" O LEU M 184 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU M 184 " --> pdb=" O VAL M 137 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N CYS M 139 " --> pdb=" O SER M 182 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N SER M 182 " --> pdb=" O CYS M 139 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'M' and resid 151 through 153 removed outlier: 3.625A pdb=" N GLN M 152 " --> pdb=" O GLU M 200 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS M 212 " --> pdb=" O CYS M 199 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'J' and resid 3 through 5 Processing sheet with id=AH9, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.739A pdb=" N THR J 122 " --> pdb=" O TYR J 94 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER J 99 " --> pdb=" O SER J 33 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER J 33 " --> pdb=" O SER J 99 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TRP J 36 " --> pdb=" O MET J 48 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.739A pdb=" N THR J 122 " --> pdb=" O TYR J 94 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'J' and resid 136 through 137 removed outlier: 4.040A pdb=" N VAL J 196 " --> pdb=" O HIS J 179 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N HIS J 179 " --> pdb=" O VAL J 196 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'J' and resid 209 through 215 removed outlier: 4.596A pdb=" N TYR J 209 " --> pdb=" O VAL J 226 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'N' and resid 19 through 23 removed outlier: 3.881A pdb=" N PHE N 76 " --> pdb=" O CYS N 23 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N THR N 77 " --> pdb=" O SER N 70 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'N' and resid 41 through 43 removed outlier: 3.652A pdb=" N GLY N 89 " --> pdb=" O VAL N 109 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'N' and resid 119 through 123 removed outlier: 3.938A pdb=" N PHE N 123 " --> pdb=" O VAL N 138 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL N 138 " --> pdb=" O PHE N 123 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N VAL N 137 " --> pdb=" O LEU N 184 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU N 184 " --> pdb=" O VAL N 137 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N CYS N 139 " --> pdb=" O SER N 182 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N SER N 182 " --> pdb=" O CYS N 139 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'N' and resid 151 through 153 removed outlier: 3.624A pdb=" N GLN N 152 " --> pdb=" O GLU N 200 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS N 212 " --> pdb=" O CYS N 199 " (cutoff:3.500A) 1084 hydrogen bonds defined for protein. 2868 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: 17.78 Time building geometry restraints manager: 15.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 10525 1.33 - 1.46: 10139 1.46 - 1.59: 15910 1.59 - 1.73: 0 1.73 - 1.86: 209 Bond restraints: 36783 Sorted by residual: bond pdb=" C ALA A 520 " pdb=" N PRO A 521 " ideal model delta sigma weight residual 1.331 1.390 -0.059 1.20e-02 6.94e+03 2.42e+01 bond pdb=" C LEU B 425 " pdb=" N PRO B 426 " ideal model delta sigma weight residual 1.330 1.390 -0.060 1.22e-02 6.72e+03 2.42e+01 bond pdb=" C GLU I 227 " pdb=" N PRO I 228 " ideal model delta sigma weight residual 1.331 1.390 -0.059 1.27e-02 6.20e+03 2.16e+01 bond pdb=" C GLN C 498 " pdb=" N PRO C 499 " ideal model delta sigma weight residual 1.331 1.390 -0.059 1.27e-02 6.20e+03 2.16e+01 bond pdb=" C GLU J 227 " pdb=" N PRO J 228 " ideal model delta sigma weight residual 1.331 1.390 -0.059 1.27e-02 6.20e+03 2.13e+01 ... (remaining 36778 not shown) Histogram of bond angle deviations from ideal: 97.60 - 105.82: 941 105.82 - 114.03: 21353 114.03 - 122.25: 21325 122.25 - 130.46: 6281 130.46 - 138.68: 149 Bond angle restraints: 50049 Sorted by residual: angle pdb=" N SER J 145 " pdb=" CA SER J 145 " pdb=" C SER J 145 " ideal model delta sigma weight residual 111.36 102.86 8.50 1.09e+00 8.42e-01 6.08e+01 angle pdb=" N SER H 145 " pdb=" CA SER H 145 " pdb=" C SER H 145 " ideal model delta sigma weight residual 111.36 102.87 8.49 1.09e+00 8.42e-01 6.06e+01 angle pdb=" N SER I 145 " pdb=" CA SER I 145 " pdb=" C SER I 145 " ideal model delta sigma weight residual 111.36 102.88 8.48 1.09e+00 8.42e-01 6.05e+01 angle pdb=" CA GLN A1142 " pdb=" C GLN A1142 " pdb=" N PRO A1143 " ideal model delta sigma weight residual 120.58 115.66 4.92 7.40e-01 1.83e+00 4.42e+01 angle pdb=" N THR B 274 " pdb=" CA THR B 274 " pdb=" C THR B 274 " ideal model delta sigma weight residual 108.32 97.60 10.72 1.64e+00 3.72e-01 4.27e+01 ... (remaining 50044 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.71: 20691 20.71 - 41.41: 1875 41.41 - 62.12: 457 62.12 - 82.82: 64 82.82 - 103.53: 31 Dihedral angle restraints: 23118 sinusoidal: 10107 harmonic: 13011 Sorted by residual: dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual 93.00 14.92 78.08 1 1.00e+01 1.00e-02 7.62e+01 dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual 93.00 167.35 -74.35 1 1.00e+01 1.00e-02 7.01e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -157.54 71.54 1 1.00e+01 1.00e-02 6.56e+01 ... (remaining 23115 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.267: 5893 0.267 - 0.535: 34 0.535 - 0.802: 2 0.802 - 1.069: 7 1.069 - 1.336: 4 Chirality restraints: 5940 Sorted by residual: chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.74 -0.66 2.00e-02 2.50e+03 1.10e+03 chirality pdb=" C1 NAG C1401 " pdb=" ND2 ASN C 17 " pdb=" C2 NAG C1401 " pdb=" O5 NAG C1401 " both_signs ideal model delta sigma weight residual False -2.40 -1.06 -1.34 2.00e-01 2.50e+01 4.46e+01 chirality pdb=" C1 NAG B1401 " pdb=" ND2 ASN B 17 " pdb=" C2 NAG B1401 " pdb=" O5 NAG B1401 " both_signs ideal model delta sigma weight residual False -2.40 -1.06 -1.34 2.00e-01 2.50e+01 4.46e+01 ... (remaining 5937 not shown) Planarity restraints: 6392 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 801 " 0.144 2.00e-02 2.50e+03 2.03e-01 5.13e+02 pdb=" CG ASN A 801 " -0.062 2.00e-02 2.50e+03 pdb=" OD1 ASN A 801 " 0.039 2.00e-02 2.50e+03 pdb=" ND2 ASN A 801 " -0.354 2.00e-02 2.50e+03 pdb=" C1 NAG O 1 " 0.232 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 17 " -0.032 2.00e-02 2.50e+03 1.90e-01 4.53e+02 pdb=" CG ASN A 17 " 0.051 2.00e-02 2.50e+03 pdb=" OD1 ASN A 17 " -0.138 2.00e-02 2.50e+03 pdb=" ND2 ASN A 17 " 0.335 2.00e-02 2.50e+03 pdb=" C1 NAG A1401 " -0.216 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 17 " -0.032 2.00e-02 2.50e+03 1.90e-01 4.53e+02 pdb=" CG ASN B 17 " 0.051 2.00e-02 2.50e+03 pdb=" OD1 ASN B 17 " -0.138 2.00e-02 2.50e+03 pdb=" ND2 ASN B 17 " 0.334 2.00e-02 2.50e+03 pdb=" C1 NAG B1401 " -0.216 2.00e-02 2.50e+03 ... (remaining 6389 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.50: 511 2.50 - 3.10: 25874 3.10 - 3.70: 51910 3.70 - 4.30: 74353 4.30 - 4.90: 124828 Nonbonded interactions: 277476 Sorted by model distance: nonbonded pdb=" O VAL L 210 " pdb=" OG1 THR L 211 " model vdw 1.905 2.440 nonbonded pdb=" O VAL M 210 " pdb=" OG1 THR M 211 " model vdw 1.905 2.440 nonbonded pdb=" O VAL N 210 " pdb=" OG1 THR N 211 " model vdw 1.905 2.440 nonbonded pdb=" O ASP B 427 " pdb=" O ASP B 428 " model vdw 1.925 3.040 nonbonded pdb=" O SER M 10 " pdb=" OG SER M 11 " model vdw 1.930 2.440 ... (remaining 277471 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 441 or resid 449 or resid 451 through 452 or re \ sid 454 through 498 or resid 503 through 620 or resid 641 through 827 or resid 8 \ 53 through 1146 or resid 1401 through 1418)) selection = (chain 'B' and (resid 14 through 441 or resid 449 or resid 451 through 452 or re \ sid 454 or resid 491 through 620 or resid 641 through 675 or resid 690 through 1 \ 146 or resid 1401 through 1418)) selection = (chain 'C' and (resid 14 through 441 or resid 451 or resid 453 or resid 455 or r \ esid 457 or resid 491 through 498 or resid 503 through 827 or resid 853 through \ 1146 or resid 1401 through 1418)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'S' selection = chain 'T' selection = chain 'c' selection = chain 'd' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'K' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.660 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: 0.030 Extract box with map and model: 7.420 Check model and map are aligned: 0.510 Set scattering table: 0.300 Process input model: 95.860 Find NCS groups from input model: 3.110 Set up NCS constraints: 0.660 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 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 : 0.011 0.090 36783 Z= 0.728 Angle : 1.237 13.678 50049 Z= 0.695 Chirality : 0.085 1.336 5940 Planarity : 0.009 0.177 6338 Dihedral : 16.708 103.530 14603 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 38.60 Ramachandran Plot: Outliers : 4.39 % Allowed : 13.18 % Favored : 82.43 % Rotamer: Outliers : 6.37 % Allowed : 12.36 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.85 (0.10), residues: 4423 helix: -4.36 (0.10), residues: 623 sheet: -2.02 (0.15), residues: 1124 loop : -3.67 (0.09), residues: 2676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP B 886 HIS 0.019 0.003 HIS B 245 PHE 0.027 0.003 PHE B 238 TYR 0.027 0.002 TYR A1067 ARG 0.017 0.001 ARG A1107 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8846 Ramachandran restraints generated. 4423 Oldfield, 0 Emsley, 4423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8846 Ramachandran restraints generated. 4423 Oldfield, 0 Emsley, 4423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 3907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 249 poor density : 412 time to evaluate : 4.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 VAL cc_start: 0.6604 (m) cc_final: 0.6381 (m) REVERT: A 811 LYS cc_start: 0.5624 (OUTLIER) cc_final: 0.5324 (ttmm) REVERT: B 22 THR cc_start: 0.3373 (OUTLIER) cc_final: 0.2247 (t) REVERT: B 44 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.7716 (mtt90) REVERT: B 173 GLN cc_start: 0.7375 (mm-40) cc_final: 0.7169 (tm-30) REVERT: B 457 ARG cc_start: 0.3247 (OUTLIER) cc_final: 0.2757 (mmp80) REVERT: B 508 TYR cc_start: 0.7434 (m-80) cc_final: 0.7058 (m-80) REVERT: B 1142 GLN cc_start: 0.7935 (OUTLIER) cc_final: 0.7467 (tp-100) REVERT: B 1146 ASP cc_start: 0.6329 (OUTLIER) cc_final: 0.5639 (m-30) REVERT: C 418 ILE cc_start: 0.9122 (mt) cc_final: 0.8868 (tt) REVERT: C 720 ILE cc_start: 0.8917 (OUTLIER) cc_final: 0.8688 (pt) REVERT: H 144 LYS cc_start: 0.3397 (mtmm) cc_final: 0.2913 (pttt) REVERT: L 12 PRO cc_start: 0.3224 (Cg_exo) cc_final: 0.2968 (Cg_endo) REVERT: I 57 GLU cc_start: 0.3524 (OUTLIER) cc_final: 0.2881 (pm20) REVERT: I 179 HIS cc_start: 0.1767 (OUTLIER) cc_final: 0.0091 (m170) REVERT: M 130 LEU cc_start: 0.1780 (mt) cc_final: 0.1321 (mm) REVERT: M 141 LEU cc_start: 0.3022 (mt) cc_final: 0.2803 (tp) REVERT: M 192 GLU cc_start: 0.2077 (OUTLIER) cc_final: 0.1363 (pt0) REVERT: J 18 VAL cc_start: -0.0933 (p) cc_final: -0.1321 (p) REVERT: J 185 LEU cc_start: 0.3015 (mt) cc_final: 0.2654 (tp) REVERT: N 9 LEU cc_start: 0.0707 (OUTLIER) cc_final: 0.0103 (mt) REVERT: N 112 LYS cc_start: 0.5135 (OUTLIER) cc_final: 0.4700 (tmtt) REVERT: N 192 GLU cc_start: 0.1154 (OUTLIER) cc_final: 0.0857 (mt-10) outliers start: 249 outliers final: 71 residues processed: 627 average time/residue: 0.5034 time to fit residues: 508.9296 Evaluate side-chains 307 residues out of total 3907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 223 time to evaluate : 4.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 300 LYS Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 424 LYS Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1142 GLN Chi-restraints excluded: chain B residue 1146 ASP Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 59 MET Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain H residue 169 TRP Chi-restraints excluded: chain H residue 179 HIS Chi-restraints excluded: chain L residue 99 PHE Chi-restraints excluded: chain L residue 105 GLN Chi-restraints excluded: chain L residue 144 PHE Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 195 LYS Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 130 SER Chi-restraints excluded: chain I residue 169 TRP Chi-restraints excluded: chain I residue 179 HIS Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 192 GLU Chi-restraints excluded: chain J residue 169 TRP Chi-restraints excluded: chain N residue 9 LEU Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain N residue 97 THR Chi-restraints excluded: chain N residue 99 PHE Chi-restraints excluded: chain N residue 112 LYS Chi-restraints excluded: chain N residue 144 PHE Chi-restraints excluded: chain N residue 192 GLU Chi-restraints excluded: chain N residue 195 LYS Chi-restraints excluded: chain N residue 203 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 372 optimal weight: 50.0000 chunk 334 optimal weight: 20.0000 chunk 185 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 225 optimal weight: 6.9990 chunk 178 optimal weight: 0.9980 chunk 345 optimal weight: 5.9990 chunk 133 optimal weight: 10.0000 chunk 210 optimal weight: 0.0970 chunk 257 optimal weight: 7.9990 chunk 400 optimal weight: 10.0000 overall best weight: 3.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN A 334 ASN A 414 GLN A 506 GLN A 542 ASN A 644 GLN A 658 ASN A 751 ASN A 755 GLN A 764 ASN A 804 GLN A 914 ASN A 969 ASN A 978 ASN A1142 GLN B 14 GLN B 52 GLN B 121 ASN B 188 ASN B 271 GLN B 360 ASN B 487 ASN B 498 GLN B 506 GLN B 544 ASN B 607 GLN B 644 GLN B 762 GLN B 926 GLN B 957 GLN B1054 GLN B1101 HIS B1113 GLN C 121 ASN C 188 ASN C 321 GLN C 370 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C 914 ASN C 919 ASN C 955 ASN C1010 GLN C1101 HIS ** H 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 42 GLN L 43 GLN L 105 GLN L 160 GLN ** I 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 42 GLN M 43 GLN M 105 GLN M 160 GLN M 204 GLN ** J 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 6 GLN N 42 GLN N 43 GLN N 157 ASN N 160 GLN Total number of N/Q/H flips: 58 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 36783 Z= 0.354 Angle : 0.881 13.018 50049 Z= 0.436 Chirality : 0.055 0.600 5940 Planarity : 0.007 0.079 6338 Dihedral : 10.812 85.278 6825 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 1.18 % Allowed : 10.60 % Favored : 88.22 % Rotamer: Outliers : 5.07 % Allowed : 16.61 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -3.74 (0.11), residues: 4423 helix: -2.17 (0.17), residues: 665 sheet: -1.36 (0.16), residues: 1034 loop : -3.21 (0.10), residues: 2724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 47 HIS 0.019 0.002 HIS M 203 PHE 0.032 0.002 PHE M 144 TYR 0.024 0.002 TYR C1067 ARG 0.005 0.001 ARG A1107 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8846 Ramachandran restraints generated. 4423 Oldfield, 0 Emsley, 4423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8846 Ramachandran restraints generated. 4423 Oldfield, 0 Emsley, 4423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 3907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 255 time to evaluate : 3.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 HIS cc_start: 0.7152 (OUTLIER) cc_final: 0.5862 (t-90) REVERT: A 148 ASN cc_start: 0.6676 (m110) cc_final: 0.6376 (t0) REVERT: A 353 TRP cc_start: 0.3306 (OUTLIER) cc_final: 0.2876 (p90) REVERT: A 495 TYR cc_start: 0.4519 (OUTLIER) cc_final: 0.3105 (m-80) REVERT: B 121 ASN cc_start: 0.7500 (OUTLIER) cc_final: 0.7013 (t0) REVERT: B 173 GLN cc_start: 0.7643 (mm-40) cc_final: 0.7303 (tm-30) REVERT: B 558 LYS cc_start: 0.7658 (pttt) cc_final: 0.7349 (mmtt) REVERT: C 40 ASP cc_start: 0.7967 (OUTLIER) cc_final: 0.7668 (p0) REVERT: C 595 VAL cc_start: 0.9343 (OUTLIER) cc_final: 0.9081 (t) REVERT: C 873 TYR cc_start: 0.9231 (OUTLIER) cc_final: 0.8294 (m-80) REVERT: H 169 TRP cc_start: -0.2499 (OUTLIER) cc_final: -0.3313 (t-100) REVERT: H 226 VAL cc_start: 0.1559 (OUTLIER) cc_final: 0.1345 (m) REVERT: I 115 MET cc_start: 0.4637 (mpp) cc_final: 0.4269 (mpp) REVERT: M 130 LEU cc_start: 0.1561 (mt) cc_final: 0.1257 (mm) REVERT: M 144 PHE cc_start: 0.0142 (OUTLIER) cc_final: -0.0137 (t80) REVERT: M 192 GLU cc_start: 0.1887 (OUTLIER) cc_final: 0.1402 (pt0) REVERT: J 18 VAL cc_start: -0.0958 (p) cc_final: -0.1228 (p) REVERT: J 111 TYR cc_start: 0.4353 (m-80) cc_final: 0.4004 (m-80) REVERT: N 4 MET cc_start: 0.3276 (OUTLIER) cc_final: 0.2977 (ptm) REVERT: N 201 VAL cc_start: 0.0857 (m) cc_final: 0.0620 (p) outliers start: 198 outliers final: 97 residues processed: 430 average time/residue: 0.4155 time to fit residues: 309.1606 Evaluate side-chains 319 residues out of total 3907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 210 time to evaluate : 4.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 424 LYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 107 ASP Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 142 SER Chi-restraints excluded: chain H residue 169 TRP Chi-restraints excluded: chain H residue 226 VAL Chi-restraints excluded: chain L residue 15 LEU Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 144 PHE Chi-restraints excluded: chain L residue 179 SER Chi-restraints excluded: chain L residue 195 LYS Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 169 TRP Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 68 SER Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 144 PHE Chi-restraints excluded: chain M residue 192 GLU Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 55 ASP Chi-restraints excluded: chain J residue 146 THR Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain N residue 97 THR Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain N residue 144 PHE Chi-restraints excluded: chain N residue 192 GLU Chi-restraints excluded: chain N residue 203 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 222 optimal weight: 10.0000 chunk 124 optimal weight: 7.9990 chunk 333 optimal weight: 3.9990 chunk 272 optimal weight: 3.9990 chunk 110 optimal weight: 8.9990 chunk 401 optimal weight: 8.9990 chunk 433 optimal weight: 9.9990 chunk 357 optimal weight: 5.9990 chunk 397 optimal weight: 10.0000 chunk 136 optimal weight: 20.0000 chunk 321 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS A 148 ASN A 954 GLN A 965 GLN A1071 GLN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN B 655 HIS ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C 935 GLN ** H 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 160 GLN ** I 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 6 GLN ** N 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.082 36783 Z= 0.525 Angle : 0.878 16.311 50049 Z= 0.431 Chirality : 0.056 0.653 5940 Planarity : 0.006 0.089 6338 Dihedral : 10.004 65.551 6741 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.79 % Allowed : 11.98 % Favored : 87.23 % Rotamer: Outliers : 5.84 % Allowed : 18.15 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -3.35 (0.11), residues: 4423 helix: -1.13 (0.19), residues: 661 sheet: -1.26 (0.15), residues: 1126 loop : -3.13 (0.10), residues: 2636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP J 169 HIS 0.017 0.002 HIS A 69 PHE 0.024 0.002 PHE A 58 TYR 0.026 0.002 TYR C1067 ARG 0.011 0.001 ARG C 457 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8846 Ramachandran restraints generated. 4423 Oldfield, 0 Emsley, 4423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8846 Ramachandran restraints generated. 4423 Oldfield, 0 Emsley, 4423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 3907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 225 time to evaluate : 3.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 HIS cc_start: 0.7070 (OUTLIER) cc_final: 0.5664 (t-90) REVERT: A 269 TYR cc_start: 0.8611 (m-80) cc_final: 0.8391 (m-80) REVERT: A 353 TRP cc_start: 0.3477 (OUTLIER) cc_final: 0.3106 (p90) REVERT: A 495 TYR cc_start: 0.4416 (OUTLIER) cc_final: 0.2662 (m-10) REVERT: B 40 ASP cc_start: 0.8604 (OUTLIER) cc_final: 0.8372 (m-30) REVERT: B 41 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8437 (mmtp) REVERT: B 173 GLN cc_start: 0.7722 (mm-40) cc_final: 0.7000 (tm-30) REVERT: B 558 LYS cc_start: 0.7940 (pttt) cc_final: 0.7470 (mmtt) REVERT: B 699 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.8601 (mp) REVERT: C 18 LEU cc_start: 0.4442 (OUTLIER) cc_final: 0.4197 (pp) REVERT: C 506 GLN cc_start: 0.8015 (pt0) cc_final: 0.7626 (pt0) REVERT: C 873 TYR cc_start: 0.9287 (OUTLIER) cc_final: 0.8444 (m-80) REVERT: H 115 MET cc_start: 0.3678 (mmt) cc_final: 0.2964 (tpp) REVERT: H 169 TRP cc_start: -0.2668 (OUTLIER) cc_final: -0.3396 (t-100) REVERT: H 226 VAL cc_start: 0.1175 (OUTLIER) cc_final: 0.0942 (p) REVERT: I 57 GLU cc_start: 0.3236 (OUTLIER) cc_final: 0.3018 (pm20) REVERT: I 115 MET cc_start: 0.4281 (mpp) cc_final: 0.4021 (mpp) REVERT: M 130 LEU cc_start: 0.1843 (mt) cc_final: 0.1593 (mm) REVERT: M 144 PHE cc_start: 0.0017 (OUTLIER) cc_final: -0.0265 (t80) REVERT: M 155 VAL cc_start: -0.0521 (OUTLIER) cc_final: -0.1014 (p) REVERT: M 192 GLU cc_start: 0.2351 (OUTLIER) cc_final: 0.1891 (pt0) REVERT: J 18 VAL cc_start: -0.0411 (p) cc_final: -0.0730 (p) REVERT: J 53 PRO cc_start: 0.5741 (Cg_exo) cc_final: 0.5514 (Cg_endo) REVERT: J 111 TYR cc_start: 0.4566 (m-80) cc_final: 0.4087 (m-80) REVERT: N 4 MET cc_start: 0.3106 (OUTLIER) cc_final: 0.2801 (ptm) outliers start: 228 outliers final: 151 residues processed: 423 average time/residue: 0.4096 time to fit residues: 301.7642 Evaluate side-chains 367 residues out of total 3907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 201 time to evaluate : 3.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 424 LYS Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 107 ASP Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 169 TRP Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 226 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 15 LEU Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 144 PHE Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain L residue 195 LYS Chi-restraints excluded: chain I residue 34 MET Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 169 TRP Chi-restraints excluded: chain I residue 170 ASN Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 226 VAL Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 68 SER Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 144 PHE Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain M residue 185 THR Chi-restraints excluded: chain M residue 192 GLU Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 55 ASP Chi-restraints excluded: chain J residue 110 ASP Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain J residue 226 VAL Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain N residue 97 THR Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 192 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 396 optimal weight: 9.9990 chunk 301 optimal weight: 0.6980 chunk 208 optimal weight: 20.0000 chunk 44 optimal weight: 40.0000 chunk 191 optimal weight: 2.9990 chunk 269 optimal weight: 4.9990 chunk 402 optimal weight: 20.0000 chunk 426 optimal weight: 0.7980 chunk 210 optimal weight: 7.9990 chunk 381 optimal weight: 30.0000 chunk 114 optimal weight: 7.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 872 GLN A1071 GLN B 207 HIS B 762 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 ASN C 422 ASN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN H 219 ASN ** I 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 6 GLN N 42 GLN ** N 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 171 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 36783 Z= 0.325 Angle : 0.767 15.172 50049 Z= 0.373 Chirality : 0.050 0.529 5940 Planarity : 0.005 0.085 6338 Dihedral : 9.165 65.849 6720 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.68 % Allowed : 10.17 % Favored : 89.15 % Rotamer: Outliers : 5.17 % Allowed : 20.19 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.98 (0.12), residues: 4423 helix: -0.52 (0.20), residues: 665 sheet: -1.16 (0.15), residues: 1148 loop : -2.91 (0.11), residues: 2610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP J 118 HIS 0.013 0.001 HIS A 69 PHE 0.021 0.002 PHE A 168 TYR 0.027 0.002 TYR B 453 ARG 0.008 0.000 ARG C 457 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8846 Ramachandran restraints generated. 4423 Oldfield, 0 Emsley, 4423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8846 Ramachandran restraints generated. 4423 Oldfield, 0 Emsley, 4423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 3907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 218 time to evaluate : 4.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 HIS cc_start: 0.6774 (OUTLIER) cc_final: 0.5927 (t-90) REVERT: A 79 PHE cc_start: 0.7169 (t80) cc_final: 0.6623 (t80) REVERT: A 495 TYR cc_start: 0.4324 (OUTLIER) cc_final: 0.2547 (m-10) REVERT: B 40 ASP cc_start: 0.8430 (OUTLIER) cc_final: 0.8162 (m-30) REVERT: B 41 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8456 (mmtp) REVERT: B 558 LYS cc_start: 0.7904 (pttt) cc_final: 0.7482 (mmtt) REVERT: B 699 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8912 (mt) REVERT: C 506 GLN cc_start: 0.7918 (pt0) cc_final: 0.7520 (pt0) REVERT: C 569 ILE cc_start: 0.6400 (OUTLIER) cc_final: 0.6174 (mp) REVERT: C 855 PHE cc_start: 0.6650 (OUTLIER) cc_final: 0.6313 (m-10) REVERT: C 873 TYR cc_start: 0.9252 (OUTLIER) cc_final: 0.8278 (m-80) REVERT: H 156 LEU cc_start: 0.0908 (tp) cc_final: 0.0495 (pp) REVERT: H 169 TRP cc_start: -0.2741 (OUTLIER) cc_final: -0.3412 (t-100) REVERT: H 198 THR cc_start: 0.0088 (OUTLIER) cc_final: -0.0112 (m) REVERT: I 48 MET cc_start: 0.3190 (pmm) cc_final: 0.2986 (pmm) REVERT: I 70 MET cc_start: 0.3407 (tpp) cc_final: 0.2851 (tpp) REVERT: M 130 LEU cc_start: 0.1562 (mt) cc_final: 0.1343 (mm) REVERT: M 144 PHE cc_start: 0.0074 (OUTLIER) cc_final: -0.0259 (t80) REVERT: M 192 GLU cc_start: 0.2359 (OUTLIER) cc_final: 0.1850 (pt0) REVERT: J 18 VAL cc_start: -0.0412 (p) cc_final: -0.0722 (p) outliers start: 202 outliers final: 129 residues processed: 400 average time/residue: 0.3987 time to fit residues: 278.2127 Evaluate side-chains 335 residues out of total 3907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 194 time to evaluate : 3.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 107 ASP Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 169 TRP Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 15 LEU Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 144 PHE Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 226 VAL Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 68 SER Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 144 PHE Chi-restraints excluded: chain M residue 192 GLU Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 96 CYS Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain N residue 192 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 355 optimal weight: 2.9990 chunk 241 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 317 optimal weight: 4.9990 chunk 175 optimal weight: 7.9990 chunk 363 optimal weight: 30.0000 chunk 294 optimal weight: 0.1980 chunk 0 optimal weight: 20.0000 chunk 217 optimal weight: 10.0000 chunk 382 optimal weight: 20.0000 chunk 107 optimal weight: 5.9990 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN A 69 HIS ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN ** L 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 6 GLN ** N 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 36783 Z= 0.307 Angle : 0.750 14.343 50049 Z= 0.364 Chirality : 0.049 0.487 5940 Planarity : 0.005 0.079 6338 Dihedral : 8.815 67.480 6709 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.66 % Allowed : 10.29 % Favored : 89.06 % Rotamer: Outliers : 5.43 % Allowed : 20.63 % Favored : 73.94 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.82 (0.12), residues: 4423 helix: -0.21 (0.21), residues: 666 sheet: -1.13 (0.15), residues: 1159 loop : -2.82 (0.11), residues: 2598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP J 118 HIS 0.006 0.001 HIS M 203 PHE 0.021 0.002 PHE N 144 TYR 0.025 0.001 TYR H 160 ARG 0.008 0.000 ARG C 457 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8846 Ramachandran restraints generated. 4423 Oldfield, 0 Emsley, 4423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8846 Ramachandran restraints generated. 4423 Oldfield, 0 Emsley, 4423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 3907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 209 time to evaluate : 3.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 PHE cc_start: 0.7118 (t80) cc_final: 0.6844 (t80) REVERT: A 495 TYR cc_start: 0.4165 (OUTLIER) cc_final: 0.2658 (m-10) REVERT: A 814 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8317 (mtmm) REVERT: B 40 ASP cc_start: 0.8390 (OUTLIER) cc_final: 0.8119 (m-30) REVERT: B 78 ARG cc_start: 0.5428 (OUTLIER) cc_final: 0.4922 (mmp80) REVERT: B 493 GLN cc_start: 0.7326 (tm-30) cc_final: 0.7116 (tm-30) REVERT: B 558 LYS cc_start: 0.7846 (pttt) cc_final: 0.7537 (mmtt) REVERT: B 699 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8967 (mt) REVERT: C 396 TYR cc_start: 0.7799 (m-80) cc_final: 0.6567 (m-80) REVERT: C 516 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7133 (mt-10) REVERT: C 569 ILE cc_start: 0.6429 (OUTLIER) cc_final: 0.6191 (mp) REVERT: C 873 TYR cc_start: 0.9250 (OUTLIER) cc_final: 0.8302 (m-80) REVERT: H 156 LEU cc_start: 0.1079 (tp) cc_final: 0.0669 (pp) REVERT: H 169 TRP cc_start: -0.2807 (OUTLIER) cc_final: -0.3418 (t-100) REVERT: H 226 VAL cc_start: 0.1228 (OUTLIER) cc_final: 0.0987 (p) REVERT: L 144 PHE cc_start: 0.2731 (OUTLIER) cc_final: 0.2334 (t80) REVERT: I 48 MET cc_start: 0.3245 (pmm) cc_final: 0.3040 (pmm) REVERT: M 144 PHE cc_start: 0.0145 (OUTLIER) cc_final: -0.0199 (t80) REVERT: M 155 VAL cc_start: -0.1449 (OUTLIER) cc_final: -0.1656 (p) REVERT: J 111 TYR cc_start: 0.4739 (m-80) cc_final: 0.4329 (m-80) REVERT: J 226 VAL cc_start: 0.0749 (OUTLIER) cc_final: 0.0499 (p) outliers start: 212 outliers final: 154 residues processed: 405 average time/residue: 0.4132 time to fit residues: 291.8529 Evaluate side-chains 357 residues out of total 3907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 190 time to evaluate : 4.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 107 ASP Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 146 THR Chi-restraints excluded: chain H residue 169 TRP Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 226 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 15 LEU Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 144 PHE Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 107 ASP Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 24 ARG Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 68 SER Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 144 PHE Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 96 CYS Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain J residue 226 VAL Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain N residue 192 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 143 optimal weight: 9.9990 chunk 383 optimal weight: 20.0000 chunk 84 optimal weight: 0.6980 chunk 250 optimal weight: 20.0000 chunk 105 optimal weight: 8.9990 chunk 426 optimal weight: 9.9990 chunk 354 optimal weight: 7.9990 chunk 197 optimal weight: 3.9990 chunk 35 optimal weight: 30.0000 chunk 141 optimal weight: 20.0000 chunk 224 optimal weight: 0.0870 overall best weight: 4.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 506 GLN ** L 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 219 ASN ** M 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 6 GLN ** N 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.3930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 36783 Z= 0.383 Angle : 0.777 14.135 50049 Z= 0.376 Chirality : 0.051 0.469 5940 Planarity : 0.005 0.081 6338 Dihedral : 8.733 68.220 6703 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.52 % Allowed : 10.78 % Favored : 88.70 % Rotamer: Outliers : 5.78 % Allowed : 20.91 % Favored : 73.30 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.77 (0.12), residues: 4423 helix: -0.16 (0.21), residues: 660 sheet: -1.07 (0.15), residues: 1163 loop : -2.80 (0.11), residues: 2600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP J 118 HIS 0.006 0.001 HIS A1064 PHE 0.033 0.002 PHE N 99 TYR 0.022 0.002 TYR C1067 ARG 0.008 0.001 ARG C 457 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8846 Ramachandran restraints generated. 4423 Oldfield, 0 Emsley, 4423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8846 Ramachandran restraints generated. 4423 Oldfield, 0 Emsley, 4423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 3907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 205 time to evaluate : 3.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 PHE cc_start: 0.7162 (t80) cc_final: 0.6903 (t80) REVERT: A 495 TYR cc_start: 0.4037 (OUTLIER) cc_final: 0.2573 (m-10) REVERT: A 619 GLU cc_start: 0.6694 (OUTLIER) cc_final: 0.6398 (pt0) REVERT: A 814 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8407 (mtmm) REVERT: B 40 ASP cc_start: 0.8473 (OUTLIER) cc_final: 0.8249 (m-30) REVERT: B 41 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8379 (mmtp) REVERT: B 78 ARG cc_start: 0.5378 (OUTLIER) cc_final: 0.4882 (mmp80) REVERT: B 188 ASN cc_start: 0.6566 (m-40) cc_final: 0.6080 (t0) REVERT: B 558 LYS cc_start: 0.7797 (pttt) cc_final: 0.7485 (mmtt) REVERT: B 699 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8740 (mp) REVERT: C 396 TYR cc_start: 0.7799 (m-80) cc_final: 0.6469 (m-80) REVERT: C 516 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7203 (mt-10) REVERT: C 569 ILE cc_start: 0.6548 (OUTLIER) cc_final: 0.6317 (mp) REVERT: C 820 ASP cc_start: 0.8424 (OUTLIER) cc_final: 0.8207 (m-30) REVERT: C 873 TYR cc_start: 0.9255 (OUTLIER) cc_final: 0.8419 (m-80) REVERT: H 115 MET cc_start: 0.3313 (tpp) cc_final: 0.2221 (tpt) REVERT: H 156 LEU cc_start: 0.0996 (tp) cc_final: 0.0586 (pp) REVERT: H 169 TRP cc_start: -0.2814 (OUTLIER) cc_final: -0.3466 (t-100) REVERT: H 226 VAL cc_start: 0.1200 (OUTLIER) cc_final: 0.0921 (p) REVERT: L 144 PHE cc_start: 0.2520 (OUTLIER) cc_final: 0.2277 (t80) REVERT: I 169 TRP cc_start: -0.1601 (OUTLIER) cc_final: -0.2245 (t-100) REVERT: M 144 PHE cc_start: 0.0280 (OUTLIER) cc_final: -0.0077 (t80) REVERT: M 155 VAL cc_start: -0.1232 (OUTLIER) cc_final: -0.1459 (p) REVERT: J 226 VAL cc_start: 0.0620 (OUTLIER) cc_final: 0.0324 (p) outliers start: 226 outliers final: 164 residues processed: 412 average time/residue: 0.4437 time to fit residues: 320.8563 Evaluate side-chains 368 residues out of total 3907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 187 time to evaluate : 3.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 107 ASP Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 146 THR Chi-restraints excluded: chain H residue 169 TRP Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 226 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 144 PHE Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 107 ASP Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 169 TRP Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 53 ILE Chi-restraints excluded: chain M residue 68 SER Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 144 PHE Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 96 CYS Chi-restraints excluded: chain J residue 107 ASP Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 145 SER Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain J residue 226 VAL Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 192 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 411 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 243 optimal weight: 6.9990 chunk 311 optimal weight: 1.9990 chunk 241 optimal weight: 7.9990 chunk 359 optimal weight: 0.0000 chunk 238 optimal weight: 7.9990 chunk 425 optimal weight: 4.9990 chunk 266 optimal weight: 6.9990 chunk 259 optimal weight: 9.9990 chunk 196 optimal weight: 0.9990 overall best weight: 1.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN B 81 ASN B 239 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN H 39 GLN L 42 GLN ** L 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 6 GLN ** N 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 36783 Z= 0.214 Angle : 0.721 16.142 50049 Z= 0.346 Chirality : 0.048 0.446 5940 Planarity : 0.005 0.079 6338 Dihedral : 8.325 68.377 6702 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.56 % Favored : 90.01 % Rotamer: Outliers : 4.27 % Allowed : 22.42 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.47 (0.12), residues: 4423 helix: 0.26 (0.21), residues: 657 sheet: -0.87 (0.15), residues: 1166 loop : -2.66 (0.11), residues: 2600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 258 HIS 0.004 0.001 HIS B 245 PHE 0.018 0.001 PHE N 144 TYR 0.021 0.001 TYR C 170 ARG 0.013 0.000 ARG C 457 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8846 Ramachandran restraints generated. 4423 Oldfield, 0 Emsley, 4423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8846 Ramachandran restraints generated. 4423 Oldfield, 0 Emsley, 4423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 3907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 205 time to evaluate : 4.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 PHE cc_start: 0.7115 (t80) cc_final: 0.6887 (t80) REVERT: A 220 PHE cc_start: 0.6984 (OUTLIER) cc_final: 0.6493 (t80) REVERT: A 495 TYR cc_start: 0.4182 (OUTLIER) cc_final: 0.2696 (m-10) REVERT: A 619 GLU cc_start: 0.6479 (OUTLIER) cc_final: 0.6197 (pt0) REVERT: A 814 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8356 (mtmm) REVERT: B 40 ASP cc_start: 0.8303 (OUTLIER) cc_final: 0.8087 (m-30) REVERT: B 78 ARG cc_start: 0.5348 (OUTLIER) cc_final: 0.4813 (mmp80) REVERT: B 188 ASN cc_start: 0.6545 (m-40) cc_final: 0.6007 (t0) REVERT: B 558 LYS cc_start: 0.7690 (pttt) cc_final: 0.7311 (mmtt) REVERT: B 699 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8879 (mt) REVERT: B 988 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7672 (mp0) REVERT: C 396 TYR cc_start: 0.7824 (m-80) cc_final: 0.6551 (m-80) REVERT: C 516 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7269 (mt-10) REVERT: C 569 ILE cc_start: 0.6522 (OUTLIER) cc_final: 0.6298 (mp) REVERT: C 873 TYR cc_start: 0.9224 (OUTLIER) cc_final: 0.8249 (m-80) REVERT: H 80 TYR cc_start: 0.4880 (m-80) cc_final: 0.4490 (m-10) REVERT: H 115 MET cc_start: 0.3218 (tpp) cc_final: 0.2016 (tpt) REVERT: H 169 TRP cc_start: -0.2852 (OUTLIER) cc_final: -0.3508 (t-100) REVERT: H 226 VAL cc_start: 0.1239 (OUTLIER) cc_final: 0.1016 (p) REVERT: L 7 SER cc_start: 0.3496 (OUTLIER) cc_final: 0.3119 (m) REVERT: L 144 PHE cc_start: 0.3259 (OUTLIER) cc_final: 0.2468 (t80) REVERT: I 169 TRP cc_start: -0.1368 (OUTLIER) cc_final: -0.2072 (t-100) REVERT: I 190 LEU cc_start: 0.3431 (tp) cc_final: 0.3220 (pp) REVERT: M 144 PHE cc_start: 0.0372 (OUTLIER) cc_final: -0.0014 (t80) REVERT: M 155 VAL cc_start: -0.0911 (OUTLIER) cc_final: -0.1325 (p) REVERT: J 111 TYR cc_start: 0.4237 (m-80) cc_final: 0.3573 (m-80) REVERT: J 226 VAL cc_start: 0.0591 (OUTLIER) cc_final: 0.0313 (p) outliers start: 167 outliers final: 117 residues processed: 357 average time/residue: 0.4331 time to fit residues: 266.2919 Evaluate side-chains 331 residues out of total 3907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 196 time to evaluate : 3.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 107 ASP Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 169 TRP Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 226 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 144 PHE Chi-restraints excluded: chain I residue 107 ASP Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 169 TRP Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 53 ILE Chi-restraints excluded: chain M residue 144 PHE Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain J residue 96 CYS Chi-restraints excluded: chain J residue 107 ASP Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain J residue 226 VAL Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 192 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 262 optimal weight: 6.9990 chunk 169 optimal weight: 1.9990 chunk 253 optimal weight: 20.0000 chunk 128 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 chunk 82 optimal weight: 0.1980 chunk 270 optimal weight: 0.8980 chunk 289 optimal weight: 3.9990 chunk 210 optimal weight: 7.9990 chunk 39 optimal weight: 0.9980 chunk 334 optimal weight: 30.0000 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN L 42 GLN ** L 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 6 GLN ** N 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 160 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.4246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 36783 Z= 0.204 Angle : 0.700 15.777 50049 Z= 0.335 Chirality : 0.047 0.462 5940 Planarity : 0.005 0.077 6338 Dihedral : 8.040 69.623 6701 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.41 % Allowed : 9.63 % Favored : 89.96 % Rotamer: Outliers : 4.15 % Allowed : 22.93 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.28 (0.12), residues: 4423 helix: 0.48 (0.21), residues: 657 sheet: -0.70 (0.15), residues: 1175 loop : -2.59 (0.11), residues: 2591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 258 HIS 0.004 0.001 HIS M 203 PHE 0.023 0.001 PHE B 238 TYR 0.022 0.001 TYR B 453 ARG 0.010 0.000 ARG C 457 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8846 Ramachandran restraints generated. 4423 Oldfield, 0 Emsley, 4423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8846 Ramachandran restraints generated. 4423 Oldfield, 0 Emsley, 4423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 3907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 200 time to evaluate : 3.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 HIS cc_start: 0.6384 (OUTLIER) cc_final: 0.5859 (t70) REVERT: A 79 PHE cc_start: 0.7110 (t80) cc_final: 0.6864 (t80) REVERT: A 220 PHE cc_start: 0.7099 (OUTLIER) cc_final: 0.6670 (t80) REVERT: A 619 GLU cc_start: 0.5885 (OUTLIER) cc_final: 0.5663 (pt0) REVERT: A 814 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8394 (mtmm) REVERT: B 40 ASP cc_start: 0.8214 (OUTLIER) cc_final: 0.7932 (m-30) REVERT: B 44 ARG cc_start: 0.7670 (OUTLIER) cc_final: 0.7186 (mtt-85) REVERT: B 78 ARG cc_start: 0.5314 (OUTLIER) cc_final: 0.4765 (mmp80) REVERT: B 188 ASN cc_start: 0.6521 (m-40) cc_final: 0.6003 (t0) REVERT: B 699 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8927 (mt) REVERT: B 988 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7660 (mp0) REVERT: C 396 TYR cc_start: 0.7803 (m-80) cc_final: 0.6469 (m-80) REVERT: C 457 ARG cc_start: 0.6403 (mpt90) cc_final: 0.6062 (mpp-170) REVERT: C 516 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7202 (mt-10) REVERT: C 569 ILE cc_start: 0.6610 (OUTLIER) cc_final: 0.6390 (mp) REVERT: C 873 TYR cc_start: 0.9215 (OUTLIER) cc_final: 0.8268 (m-80) REVERT: H 80 TYR cc_start: 0.4724 (m-80) cc_final: 0.4413 (m-10) REVERT: H 115 MET cc_start: 0.3264 (tpp) cc_final: 0.2173 (tpt) REVERT: H 169 TRP cc_start: -0.2996 (OUTLIER) cc_final: -0.3606 (t-100) REVERT: H 226 VAL cc_start: 0.1176 (OUTLIER) cc_final: 0.0976 (p) REVERT: L 7 SER cc_start: 0.3680 (OUTLIER) cc_final: 0.3108 (m) REVERT: L 144 PHE cc_start: 0.3323 (OUTLIER) cc_final: 0.2606 (t80) REVERT: I 190 LEU cc_start: 0.3387 (tp) cc_final: 0.3138 (pp) REVERT: M 144 PHE cc_start: 0.0365 (OUTLIER) cc_final: -0.0034 (t80) REVERT: M 155 VAL cc_start: -0.1374 (OUTLIER) cc_final: -0.1720 (p) REVERT: J 48 MET cc_start: 0.3074 (pmm) cc_final: 0.2634 (pmm) REVERT: J 111 TYR cc_start: 0.4137 (m-80) cc_final: 0.3522 (m-80) REVERT: J 169 TRP cc_start: -0.0880 (OUTLIER) cc_final: -0.1699 (m-90) REVERT: J 226 VAL cc_start: 0.0549 (OUTLIER) cc_final: 0.0217 (p) outliers start: 162 outliers final: 121 residues processed: 346 average time/residue: 0.4179 time to fit residues: 251.0648 Evaluate side-chains 330 residues out of total 3907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 190 time to evaluate : 4.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 107 ASP Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 169 TRP Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 226 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 144 PHE Chi-restraints excluded: chain I residue 107 ASP Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 53 ILE Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 144 PHE Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain J residue 96 CYS Chi-restraints excluded: chain J residue 107 ASP Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain J residue 169 TRP Chi-restraints excluded: chain J residue 226 VAL Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 192 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 386 optimal weight: 20.0000 chunk 407 optimal weight: 10.0000 chunk 371 optimal weight: 0.0870 chunk 396 optimal weight: 50.0000 chunk 238 optimal weight: 10.0000 chunk 172 optimal weight: 0.5980 chunk 311 optimal weight: 4.9990 chunk 121 optimal weight: 9.9990 chunk 357 optimal weight: 8.9990 chunk 374 optimal weight: 6.9990 chunk 394 optimal weight: 30.0000 overall best weight: 4.3364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 613 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 179 HIS ** M 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 6 GLN ** N 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.4354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 36783 Z= 0.381 Angle : 0.768 16.281 50049 Z= 0.370 Chirality : 0.051 0.497 5940 Planarity : 0.005 0.078 6338 Dihedral : 8.300 70.612 6691 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.41 % Allowed : 11.01 % Favored : 88.58 % Rotamer: Outliers : 4.30 % Allowed : 22.91 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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 (0.12), residues: 4423 helix: 0.19 (0.21), residues: 651 sheet: -0.74 (0.15), residues: 1203 loop : -2.65 (0.11), residues: 2569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 258 HIS 0.006 0.001 HIS B1064 PHE 0.020 0.002 PHE C 456 TYR 0.024 0.002 TYR B 453 ARG 0.008 0.001 ARG C 457 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8846 Ramachandran restraints generated. 4423 Oldfield, 0 Emsley, 4423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8846 Ramachandran restraints generated. 4423 Oldfield, 0 Emsley, 4423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 197 time to evaluate : 4.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 HIS cc_start: 0.6565 (OUTLIER) cc_final: 0.6080 (t70) REVERT: A 79 PHE cc_start: 0.7165 (t80) cc_final: 0.6918 (t80) REVERT: A 220 PHE cc_start: 0.7229 (OUTLIER) cc_final: 0.6879 (t80) REVERT: A 619 GLU cc_start: 0.5771 (OUTLIER) cc_final: 0.5571 (pt0) REVERT: A 814 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8515 (mtmm) REVERT: B 40 ASP cc_start: 0.8317 (OUTLIER) cc_final: 0.8093 (m-30) REVERT: B 44 ARG cc_start: 0.7692 (OUTLIER) cc_final: 0.7215 (mtt-85) REVERT: B 78 ARG cc_start: 0.5429 (OUTLIER) cc_final: 0.4851 (mmp80) REVERT: B 188 ASN cc_start: 0.6589 (m-40) cc_final: 0.6063 (t0) REVERT: B 699 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.8617 (mp) REVERT: B 988 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7658 (mp0) REVERT: C 177 MET cc_start: 0.6789 (mmm) cc_final: 0.6418 (tmm) REVERT: C 190 ARG cc_start: 0.7430 (OUTLIER) cc_final: 0.7180 (mtt-85) REVERT: C 569 ILE cc_start: 0.6546 (OUTLIER) cc_final: 0.6307 (mp) REVERT: C 873 TYR cc_start: 0.9259 (OUTLIER) cc_final: 0.8428 (m-80) REVERT: H 80 TYR cc_start: 0.5141 (m-80) cc_final: 0.4704 (m-10) REVERT: L 7 SER cc_start: 0.3489 (OUTLIER) cc_final: 0.2768 (m) REVERT: M 144 PHE cc_start: 0.0481 (OUTLIER) cc_final: 0.0031 (t80) REVERT: M 155 VAL cc_start: -0.1794 (OUTLIER) cc_final: -0.2066 (p) REVERT: J 48 MET cc_start: 0.2757 (pmm) cc_final: 0.2511 (pmm) REVERT: J 111 TYR cc_start: 0.4441 (m-80) cc_final: 0.3875 (m-80) REVERT: J 169 TRP cc_start: -0.0883 (OUTLIER) cc_final: -0.1688 (m-90) REVERT: J 226 VAL cc_start: 0.0919 (OUTLIER) cc_final: 0.0483 (p) outliers start: 168 outliers final: 136 residues processed: 347 average time/residue: 0.4273 time to fit residues: 257.1021 Evaluate side-chains 339 residues out of total 3907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 186 time to evaluate : 3.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 506 GLN Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 107 ASP Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 169 TRP Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 144 PHE Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 53 ILE Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 144 PHE Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain J residue 96 CYS Chi-restraints excluded: chain J residue 107 ASP Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain J residue 169 TRP Chi-restraints excluded: chain J residue 226 VAL Chi-restraints excluded: chain N residue 47 GLN Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 192 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 260 optimal weight: 3.9990 chunk 418 optimal weight: 0.0040 chunk 255 optimal weight: 10.0000 chunk 198 optimal weight: 0.8980 chunk 291 optimal weight: 2.9990 chunk 439 optimal weight: 10.0000 chunk 404 optimal weight: 20.0000 chunk 349 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 chunk 270 optimal weight: 0.7980 chunk 214 optimal weight: 8.9990 overall best weight: 1.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.4504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 36783 Z= 0.205 Angle : 0.695 16.753 50049 Z= 0.333 Chirality : 0.047 0.480 5940 Planarity : 0.005 0.074 6338 Dihedral : 7.889 70.343 6690 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.41 % Allowed : 9.13 % Favored : 90.46 % Rotamer: Outliers : 3.63 % Allowed : 23.75 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.12 (0.12), residues: 4423 helix: 0.51 (0.21), residues: 656 sheet: -0.56 (0.15), residues: 1170 loop : -2.47 (0.11), residues: 2597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP A 258 HIS 0.004 0.001 HIS N 203 PHE 0.018 0.001 PHE N 144 TYR 0.021 0.001 TYR L 54 ARG 0.005 0.000 ARG B 403 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8846 Ramachandran restraints generated. 4423 Oldfield, 0 Emsley, 4423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8846 Ramachandran restraints generated. 4423 Oldfield, 0 Emsley, 4423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 187 time to evaluate : 4.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 PHE cc_start: 0.7216 (t80) cc_final: 0.6957 (t80) REVERT: A 220 PHE cc_start: 0.7043 (OUTLIER) cc_final: 0.6728 (t80) REVERT: A 619 GLU cc_start: 0.5593 (OUTLIER) cc_final: 0.5357 (pt0) REVERT: B 40 ASP cc_start: 0.8184 (OUTLIER) cc_final: 0.7932 (m-30) REVERT: B 44 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.7161 (mtt-85) REVERT: B 78 ARG cc_start: 0.5227 (OUTLIER) cc_final: 0.4644 (mmp80) REVERT: B 188 ASN cc_start: 0.6548 (m-40) cc_final: 0.6076 (t0) REVERT: B 988 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7675 (mp0) REVERT: C 177 MET cc_start: 0.6691 (mmm) cc_final: 0.6130 (tmm) REVERT: C 242 LEU cc_start: 0.6558 (mm) cc_final: 0.6259 (mm) REVERT: C 396 TYR cc_start: 0.7510 (m-80) cc_final: 0.6868 (m-80) REVERT: C 569 ILE cc_start: 0.6582 (OUTLIER) cc_final: 0.6361 (mp) REVERT: C 873 TYR cc_start: 0.9221 (OUTLIER) cc_final: 0.8340 (m-80) REVERT: H 80 TYR cc_start: 0.4958 (m-80) cc_final: 0.4567 (m-10) REVERT: H 115 MET cc_start: 0.3510 (tpp) cc_final: 0.2466 (tpt) REVERT: M 144 PHE cc_start: 0.0414 (OUTLIER) cc_final: -0.0037 (t80) REVERT: J 48 MET cc_start: 0.2900 (pmm) cc_final: 0.2614 (pmm) REVERT: J 111 TYR cc_start: 0.4218 (m-80) cc_final: 0.3612 (m-80) REVERT: J 169 TRP cc_start: -0.0975 (OUTLIER) cc_final: -0.1755 (m-90) REVERT: J 226 VAL cc_start: 0.0051 (OUTLIER) cc_final: -0.0277 (p) REVERT: N 6 GLN cc_start: 0.2680 (OUTLIER) cc_final: 0.2047 (mt0) outliers start: 142 outliers final: 121 residues processed: 315 average time/residue: 0.4264 time to fit residues: 235.1225 Evaluate side-chains 316 residues out of total 3907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 183 time to evaluate : 4.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 107 ASP Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 169 TRP Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 144 PHE Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 53 ILE Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 144 PHE Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain J residue 96 CYS Chi-restraints excluded: chain J residue 107 ASP Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 145 SER Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain J residue 169 TRP Chi-restraints excluded: chain J residue 226 VAL Chi-restraints excluded: chain N residue 6 GLN Chi-restraints excluded: chain N residue 47 GLN Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 192 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 277 optimal weight: 1.9990 chunk 372 optimal weight: 0.0070 chunk 107 optimal weight: 7.9990 chunk 322 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 350 optimal weight: 7.9990 chunk 146 optimal weight: 9.9990 chunk 359 optimal weight: 8.9990 chunk 44 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 overall best weight: 3.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 GLN ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 6 GLN ** N 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.178472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.140711 restraints weight = 70157.637| |-----------------------------------------------------------------------------| r_work (start): 0.3917 rms_B_bonded: 3.39 r_work: 0.3167 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.4537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 36783 Z= 0.287 Angle : 0.715 16.988 50049 Z= 0.344 Chirality : 0.048 0.500 5940 Planarity : 0.005 0.075 6338 Dihedral : 7.902 70.598 6686 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.99 % Favored : 89.65 % Rotamer: Outliers : 3.94 % Allowed : 23.45 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.16 (0.12), residues: 4423 helix: 0.51 (0.21), residues: 651 sheet: -0.55 (0.15), residues: 1204 loop : -2.53 (0.11), residues: 2568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 258 HIS 0.004 0.001 HIS A1064 PHE 0.030 0.002 PHE B 106 TYR 0.021 0.001 TYR C 170 ARG 0.006 0.000 ARG C 190 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8496.01 seconds wall clock time: 154 minutes 59.52 seconds (9299.52 seconds total)