Starting phenix.real_space_refine on Mon Mar 25 06:18:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pxa_13695/03_2024/7pxa_13695.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pxa_13695/03_2024/7pxa_13695.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pxa_13695/03_2024/7pxa_13695.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pxa_13695/03_2024/7pxa_13695.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pxa_13695/03_2024/7pxa_13695.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pxa_13695/03_2024/7pxa_13695.pdb" } resolution = 2.8 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= 0.005 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 112 5.16 5 C 29215 2.51 5 N 8271 2.21 5 O 9016 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 ARG 14": "NH1" <-> "NH2" Residue "0 PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ARG 26": "NH1" <-> "NH2" Residue "8 PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 382": "NH1" <-> "NH2" Residue "H TYR 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 432": "OE1" <-> "OE2" Residue "H ARG 488": "NH1" <-> "NH2" Residue "I PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 382": "NH1" <-> "NH2" Residue "J TYR 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 488": "NH1" <-> "NH2" Residue "K PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 488": "NH1" <-> "NH2" Residue "L GLU 512": "OE1" <-> "OE2" Residue "L ARG 515": "NH1" <-> "NH2" Residue "M TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 488": "NH1" <-> "NH2" Residue "M GLU 512": "OE1" <-> "OE2" Residue "N TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 382": "NH1" <-> "NH2" Residue "N TYR 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 488": "NH1" <-> "NH2" Residue "N PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 515": "NH1" <-> "NH2" Residue "O PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 173": "OE1" <-> "OE2" Residue "P TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 465": "NH1" <-> "NH2" Residue "P ARG 488": "NH1" <-> "NH2" Residue "P PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 512": "OE1" <-> "OE2" Residue "Q PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 357": "NH1" <-> "NH2" Residue "R TYR 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 488": "NH1" <-> "NH2" Residue "R GLU 512": "OE1" <-> "OE2" Residue "S TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 488": "NH1" <-> "NH2" Residue "S GLU 512": "OE1" <-> "OE2" Residue "T GLU 15": "OE1" <-> "OE2" Residue "T PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 97": "NH1" <-> "NH2" Residue "T TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 357": "NH1" <-> "NH2" Residue "U ARG 382": "NH1" <-> "NH2" Residue "U TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 488": "NH1" <-> "NH2" Residue "U PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 512": "OE1" <-> "OE2" Residue "U ARG 515": "NH1" <-> "NH2" Residue "V TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 488": "NH1" <-> "NH2" Residue "W TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 382": "NH1" <-> "NH2" Residue "W TYR 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 488": "NH1" <-> "NH2" Residue "W PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 76": "NH1" <-> "NH2" Residue "X TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 382": "NH1" <-> "NH2" Residue "Y ARG 488": "NH1" <-> "NH2" Residue "Y PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 382": "NH1" <-> "NH2" Residue "a ARG 388": "NH1" <-> "NH2" Residue "a ARG 488": "NH1" <-> "NH2" Residue "a PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 509": "NH1" <-> "NH2" Residue "b TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 382": "NH1" <-> "NH2" Residue "b TYR 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 488": "NH1" <-> "NH2" Residue "b PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 21": "NH1" <-> "NH2" Residue "f PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 46614 Number of models: 1 Model: "" Number of chains: 35 Chain: "0" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "1" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 42 Classifications: {'peptide': 5} Modifications used: {'COO': 1} Link IDs: {'TRANS': 4} Chain: "2" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "4" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "6" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "8" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 42 Classifications: {'peptide': 5} Modifications used: {'COO': 1} Link IDs: {'TRANS': 4} Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 42 Classifications: {'peptide': 5} Modifications used: {'COO': 1} Link IDs: {'TRANS': 4} Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'TRANS': 6} Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 42 Classifications: {'peptide': 5} Modifications used: {'COO': 1} Link IDs: {'TRANS': 4} Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'TRANS': 6} Chain: "F" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 50 Classifications: {'peptide': 6} Modifications used: {'COO': 1} Link IDs: {'TRANS': 5} Chain: "H" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1636 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1650 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 7, 'TRANS': 206} Chain breaks: 1 Chain: "J" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1640 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 215} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1668 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 7, 'TRANS': 209} Chain breaks: 1 Chain: "L" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1636 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1636 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1636 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "O" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "P" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1640 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 215} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "R" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1636 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1636 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1650 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 7, 'TRANS': 206} Chain breaks: 1 Chain: "U" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1715 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 226} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "V" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1640 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 215} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "W" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1715 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 226} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "X" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1650 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 7, 'TRANS': 206} Chain breaks: 1 Chain: "Y" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1640 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 215} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Z" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "a" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1640 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 215} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "b" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1640 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 215} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "d" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "f" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Time building chain proxies: 23.74, per 1000 atoms: 0.51 Number of scatterers: 46614 At special positions: 0 Unit cell: (136.864, 136.864, 174.746, 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 112 16.00 O 9016 8.00 N 8271 7.00 C 29215 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 17.71 Conformation dependent library (CDL) restraints added in 8.4 seconds 12178 Ramachandran restraints generated. 6089 Oldfield, 0 Emsley, 6089 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11210 Finding SS restraints... Secondary structure from input PDB file: 207 helices and 70 sheets defined 46.5% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.31 Creating SS restraints... Processing helix chain '0' and resid 8 through 26 Processing helix chain '0' and resid 67 through 89 removed outlier: 3.909A pdb=" N ASN 0 73 " --> pdb=" O ASN 0 69 " (cutoff:3.500A) Processing helix chain '0' and resid 95 through 114 Processing helix chain '0' and resid 159 through 171 removed outlier: 4.530A pdb=" N ILE 0 163 " --> pdb=" O THR 0 159 " (cutoff:3.500A) Processing helix chain '0' and resid 176 through 190 removed outlier: 3.511A pdb=" N ALA 0 190 " --> pdb=" O ALA 0 186 " (cutoff:3.500A) Processing helix chain '0' and resid 227 through 234 Processing helix chain '2' and resid 9 through 26 Processing helix chain '2' and resid 67 through 89 removed outlier: 4.386A pdb=" N ASN 2 73 " --> pdb=" O ASN 2 69 " (cutoff:3.500A) Processing helix chain '2' and resid 90 through 94 Processing helix chain '2' and resid 95 through 114 Processing helix chain '2' and resid 159 through 171 removed outlier: 4.535A pdb=" N ILE 2 163 " --> pdb=" O THR 2 159 " (cutoff:3.500A) Processing helix chain '2' and resid 176 through 190 Processing helix chain '2' and resid 226 through 234 removed outlier: 3.592A pdb=" N LEU 2 230 " --> pdb=" O THR 2 226 " (cutoff:3.500A) Processing helix chain '4' and resid 9 through 26 Processing helix chain '4' and resid 67 through 89 removed outlier: 3.753A pdb=" N ASN 4 73 " --> pdb=" O ASN 4 69 " (cutoff:3.500A) Processing helix chain '4' and resid 95 through 114 Processing helix chain '4' and resid 159 through 171 removed outlier: 4.546A pdb=" N ILE 4 163 " --> pdb=" O THR 4 159 " (cutoff:3.500A) Processing helix chain '4' and resid 176 through 190 removed outlier: 3.633A pdb=" N ALA 4 190 " --> pdb=" O ALA 4 186 " (cutoff:3.500A) Processing helix chain '4' and resid 204 through 206 No H-bonds generated for 'chain '4' and resid 204 through 206' Processing helix chain '4' and resid 227 through 234 Processing helix chain '6' and resid 9 through 26 Processing helix chain '6' and resid 67 through 89 removed outlier: 3.764A pdb=" N ASN 6 73 " --> pdb=" O ASN 6 69 " (cutoff:3.500A) Processing helix chain '6' and resid 95 through 114 Processing helix chain '6' and resid 159 through 171 removed outlier: 4.569A pdb=" N ILE 6 163 " --> pdb=" O THR 6 159 " (cutoff:3.500A) Processing helix chain '6' and resid 176 through 190 Processing helix chain '6' and resid 227 through 234 Processing helix chain '8' and resid 9 through 26 Processing helix chain '8' and resid 67 through 89 removed outlier: 3.836A pdb=" N ASN 8 73 " --> pdb=" O ASN 8 69 " (cutoff:3.500A) Processing helix chain '8' and resid 95 through 114 Processing helix chain '8' and resid 159 through 171 removed outlier: 4.452A pdb=" N ILE 8 163 " --> pdb=" O THR 8 159 " (cutoff:3.500A) Processing helix chain '8' and resid 176 through 190 Processing helix chain '8' and resid 227 through 234 Processing helix chain 'H' and resid 348 through 371 Processing helix chain 'H' and resid 375 through 390 Processing helix chain 'H' and resid 390 through 395 Processing helix chain 'H' and resid 413 through 416 Processing helix chain 'H' and resid 442 through 454 removed outlier: 3.692A pdb=" N LYS H 452 " --> pdb=" O SER H 448 " (cutoff:3.500A) Processing helix chain 'H' and resid 455 through 457 No H-bonds generated for 'chain 'H' and resid 455 through 457' Processing helix chain 'H' and resid 459 through 478 Processing helix chain 'H' and resid 506 through 522 removed outlier: 3.660A pdb=" N ILE H 510 " --> pdb=" O PRO H 506 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 26 Processing helix chain 'I' and resid 67 through 89 removed outlier: 3.709A pdb=" N ASN I 73 " --> pdb=" O ASN I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 90 through 94 Processing helix chain 'I' and resid 95 through 114 removed outlier: 3.504A pdb=" N LEU I 99 " --> pdb=" O THR I 95 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 171 removed outlier: 4.505A pdb=" N ILE I 163 " --> pdb=" O THR I 159 " (cutoff:3.500A) Processing helix chain 'I' and resid 176 through 190 removed outlier: 3.590A pdb=" N ALA I 190 " --> pdb=" O ALA I 186 " (cutoff:3.500A) Processing helix chain 'I' and resid 204 through 208 removed outlier: 3.801A pdb=" N LEU I 208 " --> pdb=" O VAL I 205 " (cutoff:3.500A) Processing helix chain 'I' and resid 227 through 234 Processing helix chain 'J' and resid 348 through 371 Processing helix chain 'J' and resid 375 through 390 Processing helix chain 'J' and resid 390 through 395 Processing helix chain 'J' and resid 413 through 416 Processing helix chain 'J' and resid 442 through 454 removed outlier: 3.539A pdb=" N LYS J 452 " --> pdb=" O SER J 448 " (cutoff:3.500A) Processing helix chain 'J' and resid 455 through 457 No H-bonds generated for 'chain 'J' and resid 455 through 457' Processing helix chain 'J' and resid 459 through 478 Processing helix chain 'J' and resid 506 through 522 removed outlier: 3.584A pdb=" N ILE J 510 " --> pdb=" O PRO J 506 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 26 Processing helix chain 'K' and resid 67 through 89 removed outlier: 3.767A pdb=" N ASN K 73 " --> pdb=" O ASN K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 94 Processing helix chain 'K' and resid 95 through 114 removed outlier: 3.501A pdb=" N LEU K 99 " --> pdb=" O THR K 95 " (cutoff:3.500A) Processing helix chain 'K' and resid 159 through 171 removed outlier: 4.583A pdb=" N ILE K 163 " --> pdb=" O THR K 159 " (cutoff:3.500A) Processing helix chain 'K' and resid 176 through 192 removed outlier: 3.670A pdb=" N GLY K 191 " --> pdb=" O ALA K 187 " (cutoff:3.500A) Processing helix chain 'K' and resid 204 through 206 No H-bonds generated for 'chain 'K' and resid 204 through 206' Processing helix chain 'K' and resid 227 through 234 Processing helix chain 'L' and resid 348 through 371 Processing helix chain 'L' and resid 375 through 390 Processing helix chain 'L' and resid 390 through 396 removed outlier: 3.500A pdb=" N GLN L 396 " --> pdb=" O ALA L 392 " (cutoff:3.500A) Processing helix chain 'L' and resid 413 through 416 Processing helix chain 'L' and resid 442 through 454 removed outlier: 3.648A pdb=" N LYS L 452 " --> pdb=" O SER L 448 " (cutoff:3.500A) Processing helix chain 'L' and resid 455 through 457 No H-bonds generated for 'chain 'L' and resid 455 through 457' Processing helix chain 'L' and resid 459 through 478 Processing helix chain 'L' and resid 506 through 522 removed outlier: 3.607A pdb=" N ILE L 510 " --> pdb=" O PRO L 506 " (cutoff:3.500A) Processing helix chain 'M' and resid 348 through 371 Processing helix chain 'M' and resid 375 through 390 Processing helix chain 'M' and resid 390 through 395 Processing helix chain 'M' and resid 413 through 416 Processing helix chain 'M' and resid 442 through 454 removed outlier: 3.547A pdb=" N LYS M 452 " --> pdb=" O SER M 448 " (cutoff:3.500A) Processing helix chain 'M' and resid 455 through 457 No H-bonds generated for 'chain 'M' and resid 455 through 457' Processing helix chain 'M' and resid 459 through 478 Processing helix chain 'M' and resid 506 through 522 removed outlier: 3.623A pdb=" N ILE M 510 " --> pdb=" O PRO M 506 " (cutoff:3.500A) Processing helix chain 'N' and resid 348 through 371 Processing helix chain 'N' and resid 375 through 390 Processing helix chain 'N' and resid 390 through 395 Processing helix chain 'N' and resid 413 through 416 Processing helix chain 'N' and resid 442 through 454 removed outlier: 3.574A pdb=" N LYS N 452 " --> pdb=" O SER N 448 " (cutoff:3.500A) Processing helix chain 'N' and resid 455 through 457 No H-bonds generated for 'chain 'N' and resid 455 through 457' Processing helix chain 'N' and resid 459 through 478 Processing helix chain 'N' and resid 506 through 521 removed outlier: 3.588A pdb=" N ILE N 510 " --> pdb=" O PRO N 506 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 26 Processing helix chain 'O' and resid 67 through 89 removed outlier: 3.731A pdb=" N ASN O 73 " --> pdb=" O ASN O 69 " (cutoff:3.500A) Processing helix chain 'O' and resid 90 through 94 Processing helix chain 'O' and resid 95 through 114 Processing helix chain 'O' and resid 159 through 171 removed outlier: 4.315A pdb=" N ILE O 163 " --> pdb=" O THR O 159 " (cutoff:3.500A) Processing helix chain 'O' and resid 176 through 190 Processing helix chain 'O' and resid 227 through 234 Processing helix chain 'P' and resid 348 through 371 Processing helix chain 'P' and resid 375 through 390 Processing helix chain 'P' and resid 390 through 396 Processing helix chain 'P' and resid 413 through 416 Processing helix chain 'P' and resid 442 through 454 removed outlier: 3.668A pdb=" N LYS P 452 " --> pdb=" O SER P 448 " (cutoff:3.500A) Processing helix chain 'P' and resid 455 through 457 No H-bonds generated for 'chain 'P' and resid 455 through 457' Processing helix chain 'P' and resid 459 through 478 Processing helix chain 'P' and resid 506 through 523 removed outlier: 3.635A pdb=" N ILE P 510 " --> pdb=" O PRO P 506 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY P 523 " --> pdb=" O GLU P 519 " (cutoff:3.500A) Processing helix chain 'Q' and resid 9 through 27 removed outlier: 3.657A pdb=" N ALA Q 27 " --> pdb=" O GLY Q 23 " (cutoff:3.500A) Processing helix chain 'Q' and resid 67 through 89 removed outlier: 3.714A pdb=" N ASN Q 73 " --> pdb=" O ASN Q 69 " (cutoff:3.500A) Processing helix chain 'Q' and resid 90 through 94 Processing helix chain 'Q' and resid 95 through 114 removed outlier: 3.541A pdb=" N LEU Q 99 " --> pdb=" O THR Q 95 " (cutoff:3.500A) Processing helix chain 'Q' and resid 159 through 171 removed outlier: 4.402A pdb=" N ILE Q 163 " --> pdb=" O THR Q 159 " (cutoff:3.500A) Processing helix chain 'Q' and resid 176 through 190 Processing helix chain 'Q' and resid 227 through 234 Processing helix chain 'R' and resid 348 through 371 Processing helix chain 'R' and resid 375 through 390 Processing helix chain 'R' and resid 390 through 396 Processing helix chain 'R' and resid 413 through 416 Processing helix chain 'R' and resid 442 through 454 removed outlier: 3.673A pdb=" N LYS R 452 " --> pdb=" O SER R 448 " (cutoff:3.500A) Processing helix chain 'R' and resid 455 through 457 No H-bonds generated for 'chain 'R' and resid 455 through 457' Processing helix chain 'R' and resid 459 through 478 Processing helix chain 'R' and resid 506 through 521 removed outlier: 3.639A pdb=" N ILE R 510 " --> pdb=" O PRO R 506 " (cutoff:3.500A) Processing helix chain 'S' and resid 348 through 371 Processing helix chain 'S' and resid 375 through 390 Processing helix chain 'S' and resid 390 through 395 Processing helix chain 'S' and resid 413 through 416 Processing helix chain 'S' and resid 442 through 454 removed outlier: 3.595A pdb=" N LYS S 452 " --> pdb=" O SER S 448 " (cutoff:3.500A) Processing helix chain 'S' and resid 455 through 457 No H-bonds generated for 'chain 'S' and resid 455 through 457' Processing helix chain 'S' and resid 459 through 478 Processing helix chain 'S' and resid 506 through 522 removed outlier: 3.679A pdb=" N ILE S 510 " --> pdb=" O PRO S 506 " (cutoff:3.500A) Processing helix chain 'T' and resid 9 through 26 Processing helix chain 'T' and resid 67 through 89 removed outlier: 3.864A pdb=" N ASN T 73 " --> pdb=" O ASN T 69 " (cutoff:3.500A) Processing helix chain 'T' and resid 90 through 94 Processing helix chain 'T' and resid 95 through 114 removed outlier: 3.523A pdb=" N LEU T 99 " --> pdb=" O THR T 95 " (cutoff:3.500A) Processing helix chain 'T' and resid 160 through 171 Processing helix chain 'T' and resid 176 through 190 removed outlier: 3.506A pdb=" N ALA T 190 " --> pdb=" O ALA T 186 " (cutoff:3.500A) Processing helix chain 'T' and resid 204 through 206 No H-bonds generated for 'chain 'T' and resid 204 through 206' Processing helix chain 'T' and resid 227 through 234 Processing helix chain 'U' and resid 348 through 371 Processing helix chain 'U' and resid 375 through 390 Processing helix chain 'U' and resid 390 through 396 Processing helix chain 'U' and resid 413 through 416 Processing helix chain 'U' and resid 442 through 454 removed outlier: 3.526A pdb=" N LYS U 452 " --> pdb=" O SER U 448 " (cutoff:3.500A) Processing helix chain 'U' and resid 455 through 457 No H-bonds generated for 'chain 'U' and resid 455 through 457' Processing helix chain 'U' and resid 459 through 478 Processing helix chain 'U' and resid 506 through 528 removed outlier: 3.680A pdb=" N ILE U 510 " --> pdb=" O PRO U 506 " (cutoff:3.500A) Processing helix chain 'V' and resid 348 through 371 Processing helix chain 'V' and resid 375 through 395 removed outlier: 4.668A pdb=" N ALA V 392 " --> pdb=" O ARG V 388 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N ALA V 393 " --> pdb=" O GLY V 389 " (cutoff:3.500A) Processing helix chain 'V' and resid 413 through 416 Processing helix chain 'V' and resid 442 through 454 removed outlier: 3.646A pdb=" N LYS V 452 " --> pdb=" O SER V 448 " (cutoff:3.500A) Processing helix chain 'V' and resid 455 through 457 No H-bonds generated for 'chain 'V' and resid 455 through 457' Processing helix chain 'V' and resid 459 through 478 Processing helix chain 'V' and resid 506 through 523 removed outlier: 3.620A pdb=" N ILE V 510 " --> pdb=" O PRO V 506 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY V 523 " --> pdb=" O GLU V 519 " (cutoff:3.500A) Processing helix chain 'W' and resid 348 through 371 Processing helix chain 'W' and resid 375 through 390 Processing helix chain 'W' and resid 390 through 395 Processing helix chain 'W' and resid 413 through 416 Processing helix chain 'W' and resid 442 through 454 Processing helix chain 'W' and resid 455 through 457 No H-bonds generated for 'chain 'W' and resid 455 through 457' Processing helix chain 'W' and resid 459 through 478 Processing helix chain 'W' and resid 506 through 528 removed outlier: 3.674A pdb=" N ILE W 510 " --> pdb=" O PRO W 506 " (cutoff:3.500A) Processing helix chain 'X' and resid 9 through 26 Processing helix chain 'X' and resid 67 through 89 removed outlier: 3.872A pdb=" N ASN X 73 " --> pdb=" O ASN X 69 " (cutoff:3.500A) Processing helix chain 'X' and resid 90 through 94 Processing helix chain 'X' and resid 95 through 114 removed outlier: 3.523A pdb=" N LEU X 99 " --> pdb=" O THR X 95 " (cutoff:3.500A) Processing helix chain 'X' and resid 159 through 171 removed outlier: 4.311A pdb=" N ILE X 163 " --> pdb=" O THR X 159 " (cutoff:3.500A) Processing helix chain 'X' and resid 176 through 190 Processing helix chain 'X' and resid 227 through 234 Processing helix chain 'Y' and resid 348 through 371 Processing helix chain 'Y' and resid 375 through 390 Processing helix chain 'Y' and resid 390 through 397 Processing helix chain 'Y' and resid 413 through 416 Processing helix chain 'Y' and resid 442 through 454 Processing helix chain 'Y' and resid 455 through 457 No H-bonds generated for 'chain 'Y' and resid 455 through 457' Processing helix chain 'Y' and resid 459 through 478 Processing helix chain 'Y' and resid 506 through 523 removed outlier: 3.628A pdb=" N ILE Y 510 " --> pdb=" O PRO Y 506 " (cutoff:3.500A) Processing helix chain 'Z' and resid 9 through 27 removed outlier: 4.245A pdb=" N MET Z 13 " --> pdb=" O PRO Z 9 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG Z 14 " --> pdb=" O GLU Z 10 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA Z 27 " --> pdb=" O GLY Z 23 " (cutoff:3.500A) Processing helix chain 'Z' and resid 67 through 89 removed outlier: 3.815A pdb=" N ASN Z 73 " --> pdb=" O ASN Z 69 " (cutoff:3.500A) Processing helix chain 'Z' and resid 90 through 94 Processing helix chain 'Z' and resid 95 through 114 Processing helix chain 'Z' and resid 160 through 171 Processing helix chain 'Z' and resid 176 through 190 Processing helix chain 'Z' and resid 227 through 234 Processing helix chain 'a' and resid 348 through 371 Processing helix chain 'a' and resid 375 through 390 Processing helix chain 'a' and resid 390 through 396 removed outlier: 3.589A pdb=" N GLN a 396 " --> pdb=" O ALA a 392 " (cutoff:3.500A) Processing helix chain 'a' and resid 413 through 416 Processing helix chain 'a' and resid 442 through 454 removed outlier: 3.522A pdb=" N LYS a 452 " --> pdb=" O SER a 448 " (cutoff:3.500A) Processing helix chain 'a' and resid 455 through 457 No H-bonds generated for 'chain 'a' and resid 455 through 457' Processing helix chain 'a' and resid 459 through 478 Processing helix chain 'a' and resid 506 through 523 removed outlier: 3.607A pdb=" N ILE a 510 " --> pdb=" O PRO a 506 " (cutoff:3.500A) Processing helix chain 'b' and resid 348 through 371 Processing helix chain 'b' and resid 375 through 390 Processing helix chain 'b' and resid 390 through 396 Processing helix chain 'b' and resid 413 through 416 Processing helix chain 'b' and resid 442 through 454 removed outlier: 3.585A pdb=" N LYS b 452 " --> pdb=" O SER b 448 " (cutoff:3.500A) Processing helix chain 'b' and resid 455 through 457 No H-bonds generated for 'chain 'b' and resid 455 through 457' Processing helix chain 'b' and resid 459 through 478 Processing helix chain 'b' and resid 506 through 523 removed outlier: 3.612A pdb=" N ILE b 510 " --> pdb=" O PRO b 506 " (cutoff:3.500A) Processing helix chain 'd' and resid 9 through 26 removed outlier: 3.970A pdb=" N ARG d 14 " --> pdb=" O GLU d 10 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG d 16 " --> pdb=" O ALA d 12 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N SER d 17 " --> pdb=" O MET d 13 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU d 18 " --> pdb=" O ARG d 14 " (cutoff:3.500A) Processing helix chain 'd' and resid 67 through 89 removed outlier: 4.004A pdb=" N ASN d 73 " --> pdb=" O ASN d 69 " (cutoff:3.500A) Processing helix chain 'd' and resid 95 through 114 Processing helix chain 'd' and resid 159 through 171 removed outlier: 4.675A pdb=" N ILE d 163 " --> pdb=" O THR d 159 " (cutoff:3.500A) Processing helix chain 'd' and resid 176 through 190 Processing helix chain 'd' and resid 227 through 234 Processing helix chain 'f' and resid 9 through 25 Processing helix chain 'f' and resid 67 through 89 removed outlier: 3.767A pdb=" N ASN f 73 " --> pdb=" O ASN f 69 " (cutoff:3.500A) Processing helix chain 'f' and resid 95 through 114 removed outlier: 3.823A pdb=" N THR f 112 " --> pdb=" O GLY f 108 " (cutoff:3.500A) Processing helix chain 'f' and resid 159 through 171 removed outlier: 4.057A pdb=" N ILE f 163 " --> pdb=" O THR f 159 " (cutoff:3.500A) Processing helix chain 'f' and resid 176 through 190 removed outlier: 3.542A pdb=" N ALA f 190 " --> pdb=" O ALA f 186 " (cutoff:3.500A) Processing helix chain 'f' and resid 227 through 234 Processing sheet with id=AA1, first strand: chain '0' and resid 153 through 156 removed outlier: 3.517A pdb=" N VAL 0 39 " --> pdb=" O LEU 0 213 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '0' and resid 53 through 55 removed outlier: 3.888A pdb=" N ALA 0 125 " --> pdb=" O GLY 0 61 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU 0 138 " --> pdb=" O GLU 0 150 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '2' and resid 153 through 156 removed outlier: 3.523A pdb=" N VAL 2 39 " --> pdb=" O LEU 2 213 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '2' and resid 53 through 55 removed outlier: 3.668A pdb=" N ALA 2 125 " --> pdb=" O GLY 2 61 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU 2 138 " --> pdb=" O GLU 2 150 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '4' and resid 153 through 156 Processing sheet with id=AA6, first strand: chain '4' and resid 53 through 55 removed outlier: 3.632A pdb=" N ALA 4 125 " --> pdb=" O GLY 4 61 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU 4 138 " --> pdb=" O GLU 4 150 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '6' and resid 153 through 156 removed outlier: 3.549A pdb=" N VAL 6 39 " --> pdb=" O LEU 6 213 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '6' and resid 53 through 55 removed outlier: 3.625A pdb=" N ALA 6 125 " --> pdb=" O GLY 6 61 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU 6 138 " --> pdb=" O GLU 6 150 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '8' and resid 153 through 156 Processing sheet with id=AB1, first strand: chain '8' and resid 53 through 55 removed outlier: 3.678A pdb=" N ALA 8 125 " --> pdb=" O GLY 8 61 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU 8 138 " --> pdb=" O GLU 8 150 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 436 through 440 Processing sheet with id=AB3, first strand: chain 'H' and resid 320 through 322 removed outlier: 6.530A pdb=" N SER H 320 " --> pdb=" O SER H 327 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET H 325 " --> pdb=" O GLN H 322 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 334 through 338 removed outlier: 6.878A pdb=" N THR H 341 " --> pdb=" O THR H 337 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N PHE H 423 " --> pdb=" O PRO H 402 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 153 through 156 Processing sheet with id=AB6, first strand: chain 'I' and resid 53 through 55 removed outlier: 3.592A pdb=" N ALA I 125 " --> pdb=" O GLY I 61 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU I 138 " --> pdb=" O GLU I 150 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 436 through 440 Processing sheet with id=AB8, first strand: chain 'J' and resid 320 through 322 removed outlier: 6.625A pdb=" N SER J 320 " --> pdb=" O SER J 327 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 334 through 338 removed outlier: 6.881A pdb=" N THR J 341 " --> pdb=" O THR J 337 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N PHE J 423 " --> pdb=" O PRO J 402 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 153 through 156 Processing sheet with id=AC2, first strand: chain 'K' and resid 53 through 55 removed outlier: 3.713A pdb=" N ALA K 125 " --> pdb=" O GLY K 61 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU K 138 " --> pdb=" O GLU K 150 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 436 through 440 Processing sheet with id=AC4, first strand: chain 'L' and resid 320 through 322 removed outlier: 6.544A pdb=" N SER L 320 " --> pdb=" O SER L 327 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 334 through 336 removed outlier: 4.142A pdb=" N PHE L 423 " --> pdb=" O PRO L 402 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 436 through 440 Processing sheet with id=AC7, first strand: chain 'M' and resid 320 through 322 removed outlier: 6.638A pdb=" N SER M 320 " --> pdb=" O SER M 327 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 334 through 336 removed outlier: 3.963A pdb=" N PHE M 423 " --> pdb=" O PRO M 402 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 436 through 440 Processing sheet with id=AD1, first strand: chain 'N' and resid 320 through 322 removed outlier: 6.552A pdb=" N SER N 320 " --> pdb=" O SER N 327 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 334 through 338 removed outlier: 6.860A pdb=" N THR N 341 " --> pdb=" O THR N 337 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N PHE N 423 " --> pdb=" O PRO N 402 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'O' and resid 153 through 156 removed outlier: 3.570A pdb=" N VAL O 39 " --> pdb=" O LEU O 213 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'O' and resid 53 through 55 removed outlier: 3.581A pdb=" N ALA O 125 " --> pdb=" O GLY O 61 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU O 138 " --> pdb=" O GLU O 150 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'P' and resid 436 through 440 Processing sheet with id=AD6, first strand: chain 'P' and resid 320 through 322 removed outlier: 6.571A pdb=" N SER P 320 " --> pdb=" O SER P 327 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'P' and resid 334 through 338 removed outlier: 6.857A pdb=" N THR P 341 " --> pdb=" O THR P 337 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N PHE P 423 " --> pdb=" O PRO P 402 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Q' and resid 153 through 156 removed outlier: 3.538A pdb=" N VAL Q 39 " --> pdb=" O LEU Q 213 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Q' and resid 53 through 55 removed outlier: 3.825A pdb=" N LEU Q 138 " --> pdb=" O GLU Q 150 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'R' and resid 436 through 440 Processing sheet with id=AE2, first strand: chain 'R' and resid 320 through 322 removed outlier: 6.554A pdb=" N SER R 320 " --> pdb=" O SER R 327 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET R 325 " --> pdb=" O GLN R 322 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'R' and resid 334 through 336 removed outlier: 4.184A pdb=" N PHE R 423 " --> pdb=" O PRO R 402 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'S' and resid 436 through 440 Processing sheet with id=AE5, first strand: chain 'S' and resid 320 through 322 removed outlier: 6.415A pdb=" N SER S 320 " --> pdb=" O SER S 327 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'S' and resid 334 through 336 removed outlier: 3.984A pdb=" N PHE S 423 " --> pdb=" O PRO S 402 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'T' and resid 153 through 156 Processing sheet with id=AE8, first strand: chain 'T' and resid 53 through 55 removed outlier: 3.522A pdb=" N ALA T 125 " --> pdb=" O GLY T 61 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU T 138 " --> pdb=" O GLU T 150 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'U' and resid 436 through 440 Processing sheet with id=AF1, first strand: chain 'U' and resid 320 through 322 removed outlier: 6.484A pdb=" N SER U 320 " --> pdb=" O SER U 327 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N MET U 325 " --> pdb=" O GLN U 322 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'U' and resid 334 through 338 removed outlier: 6.908A pdb=" N THR U 341 " --> pdb=" O THR U 337 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N PHE U 423 " --> pdb=" O PRO U 402 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ILE U 420 " --> pdb=" O GLU U 432 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'V' and resid 436 through 440 Processing sheet with id=AF4, first strand: chain 'V' and resid 320 through 322 removed outlier: 6.524A pdb=" N SER V 320 " --> pdb=" O SER V 327 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'V' and resid 334 through 338 removed outlier: 6.882A pdb=" N THR V 341 " --> pdb=" O THR V 337 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHE V 423 " --> pdb=" O PRO V 402 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'W' and resid 436 through 440 Processing sheet with id=AF7, first strand: chain 'W' and resid 320 through 322 removed outlier: 6.507A pdb=" N SER W 320 " --> pdb=" O SER W 327 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET W 325 " --> pdb=" O GLN W 322 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'W' and resid 334 through 338 removed outlier: 6.866A pdb=" N THR W 341 " --> pdb=" O THR W 337 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE W 423 " --> pdb=" O PRO W 402 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'X' and resid 153 through 156 Processing sheet with id=AG1, first strand: chain 'X' and resid 53 through 55 removed outlier: 3.570A pdb=" N ALA X 125 " --> pdb=" O GLY X 61 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'Y' and resid 436 through 440 Processing sheet with id=AG3, first strand: chain 'Y' and resid 320 through 322 removed outlier: 6.636A pdb=" N SER Y 320 " --> pdb=" O SER Y 327 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'Y' and resid 334 through 336 removed outlier: 4.191A pdb=" N PHE Y 423 " --> pdb=" O PRO Y 402 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'Z' and resid 153 through 156 removed outlier: 3.517A pdb=" N VAL Z 39 " --> pdb=" O LEU Z 213 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Z' and resid 53 through 55 removed outlier: 3.681A pdb=" N ALA Z 125 " --> pdb=" O GLY Z 61 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU Z 138 " --> pdb=" O GLU Z 150 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'a' and resid 436 through 440 Processing sheet with id=AG8, first strand: chain 'a' and resid 320 through 322 removed outlier: 6.559A pdb=" N SER a 320 " --> pdb=" O SER a 327 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET a 325 " --> pdb=" O GLN a 322 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'a' and resid 334 through 338 removed outlier: 6.877A pdb=" N THR a 341 " --> pdb=" O THR a 337 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N PHE a 423 " --> pdb=" O PRO a 402 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'b' and resid 436 through 440 Processing sheet with id=AH2, first strand: chain 'b' and resid 320 through 322 removed outlier: 6.578A pdb=" N SER b 320 " --> pdb=" O SER b 327 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'b' and resid 334 through 338 removed outlier: 6.862A pdb=" N THR b 341 " --> pdb=" O THR b 337 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N PHE b 423 " --> pdb=" O PRO b 402 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'd' and resid 153 through 156 removed outlier: 3.597A pdb=" N VAL d 39 " --> pdb=" O LEU d 213 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'd' and resid 53 through 55 removed outlier: 3.705A pdb=" N ALA d 125 " --> pdb=" O GLY d 61 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU d 138 " --> pdb=" O GLU d 150 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'f' and resid 153 through 156 Processing sheet with id=AH7, first strand: chain 'f' and resid 53 through 55 removed outlier: 3.792A pdb=" N ALA f 125 " --> pdb=" O GLY f 61 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU f 138 " --> pdb=" O GLU f 150 " (cutoff:3.500A) 3003 hydrogen bonds defined for protein. 8631 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: 20.30 Time building geometry restraints manager: 19.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 16087 1.34 - 1.46: 8704 1.46 - 1.58: 22301 1.58 - 1.69: 0 1.69 - 1.81: 210 Bond restraints: 47302 Sorted by residual: bond pdb=" C ASN X 45 " pdb=" O ASN X 45 " ideal model delta sigma weight residual 1.249 1.238 0.011 8.50e-03 1.38e+04 1.70e+00 bond pdb=" CA THR N 301 " pdb=" CB THR N 301 " ideal model delta sigma weight residual 1.540 1.519 0.021 2.70e-02 1.37e+03 5.90e-01 bond pdb=" CA THR a 301 " pdb=" CB THR a 301 " ideal model delta sigma weight residual 1.540 1.520 0.020 2.70e-02 1.37e+03 5.68e-01 bond pdb=" CA THR R 301 " pdb=" CB THR R 301 " ideal model delta sigma weight residual 1.540 1.520 0.020 2.70e-02 1.37e+03 5.51e-01 bond pdb=" CA THR M 301 " pdb=" CB THR M 301 " ideal model delta sigma weight residual 1.540 1.520 0.020 2.70e-02 1.37e+03 5.49e-01 ... (remaining 47297 not shown) Histogram of bond angle deviations from ideal: 100.46 - 107.16: 1028 107.16 - 113.86: 26207 113.86 - 120.56: 19519 120.56 - 127.26: 16993 127.26 - 133.96: 266 Bond angle restraints: 64013 Sorted by residual: angle pdb=" C GLU 6 70 " pdb=" N PHE 6 71 " pdb=" CA PHE 6 71 " ideal model delta sigma weight residual 120.72 117.65 3.07 1.67e+00 3.59e-01 3.37e+00 angle pdb=" C GLU f 44 " pdb=" N ASN f 45 " pdb=" CA ASN f 45 " ideal model delta sigma weight residual 122.52 120.41 2.11 1.16e+00 7.43e-01 3.30e+00 angle pdb=" CA GLY N 328 " pdb=" C GLY N 328 " pdb=" N ARG N 329 " ideal model delta sigma weight residual 114.98 117.01 -2.03 1.14e+00 7.69e-01 3.16e+00 angle pdb=" NE ARG f 26 " pdb=" CZ ARG f 26 " pdb=" NH1 ARG f 26 " ideal model delta sigma weight residual 121.50 119.83 1.67 1.00e+00 1.00e+00 2.79e+00 angle pdb=" CA ARG 8 26 " pdb=" C ARG 8 26 " pdb=" N ALA 8 27 " ideal model delta sigma weight residual 114.90 117.14 -2.24 1.37e+00 5.33e-01 2.67e+00 ... (remaining 64008 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 27492 17.80 - 35.59: 750 35.59 - 53.39: 171 53.39 - 71.19: 26 71.19 - 88.99: 23 Dihedral angle restraints: 28462 sinusoidal: 10841 harmonic: 17621 Sorted by residual: dihedral pdb=" CB GLU Y 432 " pdb=" CG GLU Y 432 " pdb=" CD GLU Y 432 " pdb=" OE1 GLU Y 432 " ideal model delta sinusoidal sigma weight residual 0.00 -88.99 88.99 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU T 15 " pdb=" CG GLU T 15 " pdb=" CD GLU T 15 " pdb=" OE1 GLU T 15 " ideal model delta sinusoidal sigma weight residual 0.00 -87.48 87.48 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" CB GLU P 512 " pdb=" CG GLU P 512 " pdb=" CD GLU P 512 " pdb=" OE1 GLU P 512 " ideal model delta sinusoidal sigma weight residual 0.00 85.35 -85.35 1 3.00e+01 1.11e-03 9.80e+00 ... (remaining 28459 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 4476 0.026 - 0.053: 1621 0.053 - 0.079: 574 0.079 - 0.106: 338 0.106 - 0.132: 261 Chirality restraints: 7270 Sorted by residual: chirality pdb=" CA ILE 0 53 " pdb=" N ILE 0 53 " pdb=" C ILE 0 53 " pdb=" CB ILE 0 53 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 chirality pdb=" CA ILE 4 53 " pdb=" N ILE 4 53 " pdb=" C ILE 4 53 " pdb=" CB ILE 4 53 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 chirality pdb=" CA ILE d 53 " pdb=" N ILE d 53 " pdb=" C ILE d 53 " pdb=" CB ILE d 53 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.32e-01 ... (remaining 7267 not shown) Planarity restraints: 8452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE 6 71 " 0.011 2.00e-02 2.50e+03 1.00e-02 1.75e+00 pdb=" CG PHE 6 71 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE 6 71 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE 6 71 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE 6 71 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE 6 71 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE 6 71 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE d 71 " 0.011 2.00e-02 2.50e+03 9.93e-03 1.73e+00 pdb=" CG PHE d 71 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE d 71 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE d 71 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE d 71 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE d 71 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE d 71 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE 0 71 " -0.011 2.00e-02 2.50e+03 9.68e-03 1.64e+00 pdb=" CG PHE 0 71 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE 0 71 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE 0 71 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE 0 71 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE 0 71 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE 0 71 " -0.001 2.00e-02 2.50e+03 ... (remaining 8449 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 692 2.70 - 3.25: 42804 3.25 - 3.80: 72499 3.80 - 4.35: 95209 4.35 - 4.90: 162249 Nonbonded interactions: 373453 Sorted by model distance: nonbonded pdb=" OD1 ASP J 338 " pdb=" OG1 THR J 341 " model vdw 2.147 2.440 nonbonded pdb=" OD1 ASP U 338 " pdb=" OG1 THR U 341 " model vdw 2.172 2.440 nonbonded pdb=" OD1 ASP H 338 " pdb=" OG1 THR H 341 " model vdw 2.180 2.440 nonbonded pdb=" OD1 ASP b 338 " pdb=" OG1 THR b 341 " model vdw 2.184 2.440 nonbonded pdb=" OD1 ASP P 338 " pdb=" OG1 THR P 341 " model vdw 2.191 2.440 ... (remaining 373448 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 '0' and (resid 8 through 190 or resid 204 through 234)) selection = (chain '2' and (resid 8 through 190 or resid 204 through 234)) selection = (chain '4' and (resid 8 through 190 or resid 204 through 234)) selection = (chain '6' and (resid 8 through 190 or resid 204 through 234)) selection = (chain '8' and (resid 8 through 190 or resid 204 through 234)) selection = chain 'I' selection = (chain 'K' and (resid 8 through 190 or resid 204 through 234)) selection = (chain 'O' and (resid 8 through 190 or resid 204 through 234)) selection = (chain 'Q' and (resid 8 through 190 or resid 204 through 234)) selection = chain 'T' selection = chain 'X' selection = (chain 'Z' and (resid 8 through 190 or resid 204 through 234)) selection = (chain 'd' and (resid 8 through 190 or resid 204 through 234)) selection = (chain 'f' and (resid 8 through 190 or resid 204 through 234)) } ncs_group { reference = chain '1' selection = chain 'A' selection = chain 'B' selection = chain 'D' } ncs_group { reference = (chain 'C' and resid 604 through 609) selection = (chain 'E' and resid 604 through 609) selection = chain 'F' } ncs_group { reference = chain 'H' selection = (chain 'J' and resid 301 through 522) selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = (chain 'P' and resid 301 through 522) selection = chain 'R' selection = chain 'S' selection = (chain 'U' and resid 301 through 522) selection = (chain 'V' and resid 301 through 522) selection = (chain 'W' and resid 301 through 522) selection = (chain 'Y' and resid 301 through 522) selection = (chain 'a' and resid 301 through 522) selection = (chain 'b' and resid 301 through 522) } 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: 3.000 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: 12.170 Check model and map are aligned: 0.730 Set scattering table: 0.430 Process input model: 119.730 Find NCS groups from input model: 3.710 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 151.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 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 : 0.002 0.024 47302 Z= 0.110 Angle : 0.420 5.235 64013 Z= 0.264 Chirality : 0.040 0.132 7270 Planarity : 0.002 0.026 8452 Dihedral : 9.390 88.986 17252 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.14 % Allowed : 2.88 % Favored : 95.98 % 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: 2.60 (0.11), residues: 6089 helix: 3.20 (0.10), residues: 2542 sheet: 1.19 (0.15), residues: 1483 loop : 0.25 (0.14), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP V 429 HIS 0.002 0.000 HIS K 152 PHE 0.023 0.001 PHE 6 71 TYR 0.009 0.001 TYR U 359 ARG 0.003 0.000 ARG 4 140 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12178 Ramachandran restraints generated. 6089 Oldfield, 0 Emsley, 6089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12178 Ramachandran restraints generated. 6089 Oldfield, 0 Emsley, 6089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1290 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 1237 time to evaluate : 5.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 44 GLU cc_start: 0.6394 (tt0) cc_final: 0.5789 (tm-30) REVERT: 0 72 ASP cc_start: 0.7871 (t70) cc_final: 0.7624 (t70) REVERT: 0 165 ASN cc_start: 0.7656 (m-40) cc_final: 0.7101 (t0) REVERT: 0 219 ARG cc_start: 0.8075 (ttp80) cc_final: 0.7832 (ttp-110) REVERT: 2 13 MET cc_start: 0.6014 (ttp) cc_final: 0.5700 (tmm) REVERT: 2 45 ASN cc_start: 0.8357 (t0) cc_final: 0.8144 (t0) REVERT: 2 146 SER cc_start: 0.8466 (m) cc_final: 0.8260 (t) REVERT: 4 67 LYS cc_start: 0.7803 (tttm) cc_final: 0.7523 (ttmt) REVERT: 4 183 ILE cc_start: 0.7905 (mt) cc_final: 0.7704 (mp) REVERT: 4 225 ILE cc_start: 0.8504 (mt) cc_final: 0.8212 (mm) REVERT: 6 22 LYS cc_start: 0.7750 (mtpt) cc_final: 0.7409 (mmmm) REVERT: 6 98 GLN cc_start: 0.8453 (mt0) cc_final: 0.8193 (mt0) REVERT: 6 144 ASP cc_start: 0.8281 (p0) cc_final: 0.8052 (p0) REVERT: 6 147 ILE cc_start: 0.8510 (OUTLIER) cc_final: 0.8179 (pt) REVERT: 6 233 LEU cc_start: 0.7772 (mp) cc_final: 0.7566 (mt) REVERT: 8 163 ILE cc_start: 0.7744 (mt) cc_final: 0.7424 (mt) REVERT: I 69 ASN cc_start: 0.7653 (p0) cc_final: 0.7389 (p0) REVERT: I 134 LYS cc_start: 0.7963 (ttpt) cc_final: 0.7585 (tttt) REVERT: I 182 ARG cc_start: 0.6416 (OUTLIER) cc_final: 0.5981 (mpt90) REVERT: I 228 SER cc_start: 0.6754 (p) cc_final: 0.6294 (m) REVERT: J 330 ASP cc_start: 0.8138 (p0) cc_final: 0.7787 (p0) REVERT: K 26 ARG cc_start: 0.6874 (ttm110) cc_final: 0.6339 (ppt90) REVERT: K 112 THR cc_start: 0.7323 (m) cc_final: 0.6934 (p) REVERT: K 209 GLU cc_start: 0.6094 (tt0) cc_final: 0.5676 (tt0) REVERT: K 214 ASP cc_start: 0.8090 (t0) cc_final: 0.7835 (t0) REVERT: K 216 ASN cc_start: 0.8023 (t0) cc_final: 0.7579 (m-40) REVERT: L 332 ARG cc_start: 0.7981 (mtt-85) cc_final: 0.7750 (mtt180) REVERT: O 52 LYS cc_start: 0.7882 (mtpt) cc_final: 0.6776 (mttm) REVERT: O 182 ARG cc_start: 0.5757 (OUTLIER) cc_final: 0.5486 (mpt-90) REVERT: P 330 ASP cc_start: 0.7969 (p0) cc_final: 0.7679 (p0) REVERT: Q 49 SER cc_start: 0.7512 (m) cc_final: 0.7242 (p) REVERT: Q 156 MET cc_start: 0.7011 (mtm) cc_final: 0.6711 (mtm) REVERT: Q 207 SER cc_start: 0.5878 (p) cc_final: 0.5590 (p) REVERT: R 507 GLU cc_start: 0.7814 (tt0) cc_final: 0.7401 (tp30) REVERT: T 52 LYS cc_start: 0.8280 (mtpt) cc_final: 0.7941 (mtmm) REVERT: T 98 GLN cc_start: 0.8329 (mt0) cc_final: 0.7948 (mt0) REVERT: T 109 THR cc_start: 0.6370 (m) cc_final: 0.6073 (m) REVERT: T 156 MET cc_start: 0.6698 (mtm) cc_final: 0.6299 (mtm) REVERT: U 330 ASP cc_start: 0.7870 (p0) cc_final: 0.7359 (p0) REVERT: U 401 LEU cc_start: 0.8661 (mt) cc_final: 0.8459 (mt) REVERT: V 335 TYR cc_start: 0.8784 (m-80) cc_final: 0.8560 (m-80) REVERT: W 314 MET cc_start: 0.9071 (ttm) cc_final: 0.8826 (ttp) REVERT: W 324 ASN cc_start: 0.7755 (m-40) cc_final: 0.7553 (m110) REVERT: X 26 ARG cc_start: 0.7191 (ttm110) cc_final: 0.6777 (ppt170) REVERT: X 216 ASN cc_start: 0.7843 (t0) cc_final: 0.7502 (t0) REVERT: X 233 LEU cc_start: 0.6262 (mp) cc_final: 0.5976 (mm) REVERT: Y 354 GLU cc_start: 0.7455 (tt0) cc_final: 0.7217 (tt0) REVERT: Z 150 GLU cc_start: 0.7120 (mm-30) cc_final: 0.6808 (mp0) REVERT: Z 214 ASP cc_start: 0.8224 (t0) cc_final: 0.8006 (t0) REVERT: Z 228 SER cc_start: 0.6552 (p) cc_final: 0.6332 (t) REVERT: b 324 ASN cc_start: 0.7601 (m-40) cc_final: 0.7386 (m-40) REVERT: b 398 LEU cc_start: 0.8177 (mm) cc_final: 0.7750 (mp) REVERT: b 430 ASN cc_start: 0.8057 (t0) cc_final: 0.7805 (t0) REVERT: d 67 LYS cc_start: 0.8333 (tttp) cc_final: 0.8076 (ttmm) REVERT: d 98 GLN cc_start: 0.8552 (mt0) cc_final: 0.8305 (mt0) REVERT: d 143 TYR cc_start: 0.7203 (p90) cc_final: 0.6999 (p90) REVERT: f 17 SER cc_start: 0.7849 (t) cc_final: 0.7263 (m) REVERT: f 29 SER cc_start: 0.8619 (m) cc_final: 0.8388 (t) REVERT: f 110 ILE cc_start: 0.8538 (mt) cc_final: 0.8201 (mm) outliers start: 53 outliers final: 8 residues processed: 1268 average time/residue: 1.7498 time to fit residues: 2679.7734 Evaluate side-chains 679 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 668 time to evaluate : 5.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 147 ILE Chi-restraints excluded: chain 4 residue 147 ILE Chi-restraints excluded: chain 6 residue 147 ILE Chi-restraints excluded: chain E residue 605 LEU Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain I residue 156 MET Chi-restraints excluded: chain I residue 182 ARG Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain O residue 182 ARG Chi-restraints excluded: chain T residue 147 ILE Chi-restraints excluded: chain X residue 15 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 510 optimal weight: 9.9990 chunk 457 optimal weight: 2.9990 chunk 254 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 308 optimal weight: 0.7980 chunk 244 optimal weight: 6.9990 chunk 473 optimal weight: 6.9990 chunk 183 optimal weight: 10.0000 chunk 287 optimal weight: 0.9980 chunk 352 optimal weight: 10.0000 chunk 548 optimal weight: 0.9980 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 69 ASN 0 73 ASN 0 174 ASN ** 1 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 165 ASN 4 45 ASN 6 101 ASN 6 165 ASN C 607 GLN ** I 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 396 GLN J 437 GLN ** K 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 174 ASN L 324 ASN M 390 ASN M 437 GLN N 322 GLN O 80 GLN ** O 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 174 ASN P 322 GLN Q 45 ASN ** Q 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 437 GLN T 69 ASN T 152 HIS U 322 GLN W 437 GLN ** X 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 390 ASN Z 80 GLN Z 98 GLN Z 101 ASN ** a 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 322 GLN b 437 GLN d 80 GLN ** d 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 80 GLN f 101 ASN f 165 ASN f 174 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 47302 Z= 0.211 Angle : 0.515 8.889 64013 Z= 0.273 Chirality : 0.043 0.169 7270 Planarity : 0.004 0.061 8452 Dihedral : 3.912 58.425 6922 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.70 % Allowed : 12.88 % Favored : 83.42 % 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: 2.58 (0.11), residues: 6089 helix: 3.18 (0.10), residues: 2583 sheet: 1.11 (0.14), residues: 1492 loop : 0.24 (0.14), residues: 2014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP V 429 HIS 0.004 0.001 HIS P 410 PHE 0.034 0.002 PHE 6 71 TYR 0.015 0.001 TYR L 359 ARG 0.008 0.001 ARG X 21 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12178 Ramachandran restraints generated. 6089 Oldfield, 0 Emsley, 6089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12178 Ramachandran restraints generated. 6089 Oldfield, 0 Emsley, 6089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 852 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 680 time to evaluate : 5.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 13 MET cc_start: 0.6951 (ttm) cc_final: 0.6200 (tmm) REVERT: 0 44 GLU cc_start: 0.6378 (tt0) cc_final: 0.5782 (tm-30) REVERT: 0 54 SER cc_start: 0.8549 (t) cc_final: 0.8343 (m) REVERT: 0 74 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8750 (mt) REVERT: 0 80 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7630 (tp40) REVERT: 0 149 ASP cc_start: 0.8035 (OUTLIER) cc_final: 0.7671 (m-30) REVERT: 0 219 ARG cc_start: 0.8160 (ttp80) cc_final: 0.7919 (ttt-90) REVERT: 2 234 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.7185 (pt) REVERT: 4 67 LYS cc_start: 0.7531 (tttm) cc_final: 0.7253 (tttp) REVERT: 4 98 GLN cc_start: 0.8740 (mt0) cc_final: 0.8521 (mt0) REVERT: 4 132 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.6926 (tt0) REVERT: 4 225 ILE cc_start: 0.8527 (mt) cc_final: 0.8252 (mm) REVERT: 6 22 LYS cc_start: 0.7941 (mtpt) cc_final: 0.7147 (mmpt) REVERT: 6 98 GLN cc_start: 0.8503 (mt0) cc_final: 0.8281 (mt0) REVERT: 6 144 ASP cc_start: 0.8337 (p0) cc_final: 0.8103 (p0) REVERT: 6 147 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8134 (pt) REVERT: 6 156 MET cc_start: 0.7891 (mtp) cc_final: 0.7658 (mtm) REVERT: 8 163 ILE cc_start: 0.7595 (mt) cc_final: 0.7347 (mt) REVERT: 8 174 ASN cc_start: 0.7830 (m110) cc_final: 0.7515 (m110) REVERT: B 605 LEU cc_start: 0.5146 (OUTLIER) cc_final: 0.4881 (mm) REVERT: F 607 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.7397 (tt0) REVERT: I 182 ARG cc_start: 0.6588 (OUTLIER) cc_final: 0.6177 (mpt90) REVERT: J 330 ASP cc_start: 0.8238 (p0) cc_final: 0.7948 (p0) REVERT: J 430 ASN cc_start: 0.8110 (t0) cc_final: 0.7907 (t0) REVERT: J 432 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7569 (mp0) REVERT: K 13 MET cc_start: 0.5915 (mmp) cc_final: 0.4845 (ppp) REVERT: K 26 ARG cc_start: 0.6647 (ttm110) cc_final: 0.6062 (ppt90) REVERT: K 112 THR cc_start: 0.7141 (m) cc_final: 0.6868 (p) REVERT: K 214 ASP cc_start: 0.7832 (t0) cc_final: 0.7600 (t0) REVERT: K 216 ASN cc_start: 0.8049 (t0) cc_final: 0.7578 (m-40) REVERT: M 364 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7507 (tt0) REVERT: M 399 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8788 (tt) REVERT: M 434 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.7030 (mt-10) REVERT: O 26 ARG cc_start: 0.7246 (ttm110) cc_final: 0.6478 (ppt170) REVERT: O 67 LYS cc_start: 0.7751 (OUTLIER) cc_final: 0.7417 (tttt) REVERT: O 93 ASP cc_start: 0.8915 (m-30) cc_final: 0.8498 (m-30) REVERT: O 156 MET cc_start: 0.7332 (mtm) cc_final: 0.6672 (mtm) REVERT: O 182 ARG cc_start: 0.5759 (OUTLIER) cc_final: 0.5534 (mtt-85) REVERT: P 432 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.6819 (mp0) REVERT: R 434 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6794 (tp30) REVERT: S 401 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8508 (mt) REVERT: T 52 LYS cc_start: 0.8257 (mtpt) cc_final: 0.7894 (mtmm) REVERT: T 98 GLN cc_start: 0.8411 (mt0) cc_final: 0.8064 (mt0) REVERT: T 109 THR cc_start: 0.6526 (m) cc_final: 0.6030 (m) REVERT: U 330 ASP cc_start: 0.7873 (p0) cc_final: 0.7534 (p0) REVERT: W 364 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.7185 (pt0) REVERT: X 26 ARG cc_start: 0.7275 (ttm110) cc_final: 0.6758 (ppt170) REVERT: Z 150 GLU cc_start: 0.7267 (mm-30) cc_final: 0.6741 (mp0) REVERT: b 324 ASN cc_start: 0.8029 (m-40) cc_final: 0.7723 (m-40) REVERT: b 401 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8533 (mp) REVERT: d 13 MET cc_start: 0.4215 (tmm) cc_final: 0.3379 (mmm) REVERT: d 21 ARG cc_start: 0.7412 (mtp-110) cc_final: 0.7119 (mtp85) REVERT: d 22 LYS cc_start: 0.7713 (mtpt) cc_final: 0.7463 (mtpt) REVERT: d 67 LYS cc_start: 0.7895 (tttp) cc_final: 0.7674 (tptp) REVERT: d 165 ASN cc_start: 0.6205 (m-40) cc_final: 0.5568 (m110) REVERT: d 167 LEU cc_start: 0.7786 (mt) cc_final: 0.7468 (mt) outliers start: 172 outliers final: 64 residues processed: 785 average time/residue: 1.5817 time to fit residues: 1529.7549 Evaluate side-chains 703 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 619 time to evaluate : 5.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 74 LEU Chi-restraints excluded: chain 0 residue 80 GLN Chi-restraints excluded: chain 0 residue 146 SER Chi-restraints excluded: chain 0 residue 149 ASP Chi-restraints excluded: chain 0 residue 233 LEU Chi-restraints excluded: chain 2 residue 147 ILE Chi-restraints excluded: chain 2 residue 179 ASP Chi-restraints excluded: chain 2 residue 226 THR Chi-restraints excluded: chain 2 residue 234 LEU Chi-restraints excluded: chain 4 residue 51 GLN Chi-restraints excluded: chain 4 residue 132 GLU Chi-restraints excluded: chain 4 residue 147 ILE Chi-restraints excluded: chain 4 residue 170 SER Chi-restraints excluded: chain 6 residue 147 ILE Chi-restraints excluded: chain 6 residue 149 ASP Chi-restraints excluded: chain 8 residue 33 LEU Chi-restraints excluded: chain 8 residue 51 GLN Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain F residue 607 GLN Chi-restraints excluded: chain H residue 388 ARG Chi-restraints excluded: chain H residue 399 LEU Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 146 SER Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 174 ASN Chi-restraints excluded: chain I residue 182 ARG Chi-restraints excluded: chain I residue 207 SER Chi-restraints excluded: chain J residue 432 GLU Chi-restraints excluded: chain K residue 67 LYS Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain L residue 325 MET Chi-restraints excluded: chain M residue 364 GLU Chi-restraints excluded: chain M residue 399 LEU Chi-restraints excluded: chain M residue 434 GLU Chi-restraints excluded: chain N residue 358 LEU Chi-restraints excluded: chain N residue 361 VAL Chi-restraints excluded: chain N residue 444 LEU Chi-restraints excluded: chain O residue 31 VAL Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain O residue 67 LYS Chi-restraints excluded: chain O residue 109 THR Chi-restraints excluded: chain O residue 146 SER Chi-restraints excluded: chain O residue 176 SER Chi-restraints excluded: chain O residue 182 ARG Chi-restraints excluded: chain P residue 395 MET Chi-restraints excluded: chain P residue 432 GLU Chi-restraints excluded: chain Q residue 228 SER Chi-restraints excluded: chain R residue 434 GLU Chi-restraints excluded: chain R residue 476 ASP Chi-restraints excluded: chain S residue 401 LEU Chi-restraints excluded: chain T residue 47 SER Chi-restraints excluded: chain T residue 49 SER Chi-restraints excluded: chain T residue 112 THR Chi-restraints excluded: chain T residue 147 ILE Chi-restraints excluded: chain T residue 178 THR Chi-restraints excluded: chain T residue 207 SER Chi-restraints excluded: chain U residue 348 THR Chi-restraints excluded: chain U residue 520 SER Chi-restraints excluded: chain W residue 364 GLU Chi-restraints excluded: chain W residue 522 SER Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 49 SER Chi-restraints excluded: chain X residue 106 THR Chi-restraints excluded: chain X residue 228 SER Chi-restraints excluded: chain Y residue 391 LEU Chi-restraints excluded: chain Y residue 409 ILE Chi-restraints excluded: chain Y residue 503 VAL Chi-restraints excluded: chain Z residue 83 ASP Chi-restraints excluded: chain Z residue 112 THR Chi-restraints excluded: chain Z residue 146 SER Chi-restraints excluded: chain Z residue 147 ILE Chi-restraints excluded: chain Z residue 178 THR Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain b residue 355 PHE Chi-restraints excluded: chain b residue 401 LEU Chi-restraints excluded: chain d residue 17 SER Chi-restraints excluded: chain d residue 109 THR Chi-restraints excluded: chain f residue 146 SER Chi-restraints excluded: chain f residue 149 ASP Chi-restraints excluded: chain f residue 207 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 304 optimal weight: 9.9990 chunk 170 optimal weight: 30.0000 chunk 456 optimal weight: 8.9990 chunk 373 optimal weight: 4.9990 chunk 151 optimal weight: 7.9990 chunk 549 optimal weight: 0.7980 chunk 593 optimal weight: 3.9990 chunk 489 optimal weight: 4.9990 chunk 544 optimal weight: 6.9990 chunk 187 optimal weight: 6.9990 chunk 440 optimal weight: 7.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 69 ASN 0 73 ASN 0 174 ASN 1 607 GLN 4 45 ASN 4 80 GLN ** I 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 129 HIS J 396 GLN ** K 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 129 HIS ** L 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 322 GLN O 80 GLN ** O 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 174 ASN ** Q 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 69 ASN U 322 GLN ** X 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 216 ASN Z 80 GLN Z 101 ASN Z 129 HIS Z 152 HIS a 437 GLN b 322 GLN d 80 GLN ** d 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 45 ASN f 80 GLN f 129 HIS f 174 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 47302 Z= 0.397 Angle : 0.623 10.781 64013 Z= 0.330 Chirality : 0.047 0.191 7270 Planarity : 0.005 0.065 8452 Dihedral : 4.396 57.118 6914 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 5.10 % Allowed : 12.96 % Favored : 81.94 % 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: 1.99 (0.11), residues: 6089 helix: 2.67 (0.10), residues: 2586 sheet: 0.88 (0.14), residues: 1486 loop : -0.11 (0.14), residues: 2017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 429 HIS 0.007 0.002 HIS T 129 PHE 0.039 0.003 PHE 0 71 TYR 0.022 0.002 TYR 4 118 ARG 0.011 0.001 ARG X 21 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12178 Ramachandran restraints generated. 6089 Oldfield, 0 Emsley, 6089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12178 Ramachandran restraints generated. 6089 Oldfield, 0 Emsley, 6089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 862 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 237 poor density : 625 time to evaluate : 4.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 13 MET cc_start: 0.7025 (ttm) cc_final: 0.6320 (tmm) REVERT: 0 44 GLU cc_start: 0.6458 (tt0) cc_final: 0.5767 (tm-30) REVERT: 0 54 SER cc_start: 0.8597 (t) cc_final: 0.8360 (m) REVERT: 0 74 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8720 (mt) REVERT: 0 80 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.7616 (tp40) REVERT: 0 149 ASP cc_start: 0.7979 (OUTLIER) cc_final: 0.7590 (m-30) REVERT: 1 609 LEU cc_start: 0.6542 (mt) cc_final: 0.6202 (mp) REVERT: 2 234 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.7333 (pt) REVERT: 4 28 LYS cc_start: 0.7406 (OUTLIER) cc_final: 0.6595 (mptp) REVERT: 4 45 ASN cc_start: 0.8321 (t0) cc_final: 0.7798 (t0) REVERT: 4 51 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7286 (mm-40) REVERT: 4 67 LYS cc_start: 0.8087 (tttm) cc_final: 0.7566 (tttp) REVERT: 4 74 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8475 (mp) REVERT: 4 132 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.7121 (tt0) REVERT: 4 214 ASP cc_start: 0.8299 (t0) cc_final: 0.7973 (t0) REVERT: 4 225 ILE cc_start: 0.8580 (mt) cc_final: 0.8292 (mm) REVERT: 6 22 LYS cc_start: 0.7820 (mtpt) cc_final: 0.7084 (mmtt) REVERT: 6 98 GLN cc_start: 0.8591 (mt0) cc_final: 0.8360 (mt0) REVERT: 6 144 ASP cc_start: 0.8425 (p0) cc_final: 0.8208 (p0) REVERT: 6 147 ILE cc_start: 0.8505 (OUTLIER) cc_final: 0.8015 (pt) REVERT: 6 156 MET cc_start: 0.7786 (mtp) cc_final: 0.7574 (mtm) REVERT: 8 171 TYR cc_start: 0.7045 (t80) cc_final: 0.6525 (t80) REVERT: 8 216 ASN cc_start: 0.8107 (m-40) cc_final: 0.7829 (t0) REVERT: B 605 LEU cc_start: 0.5083 (OUTLIER) cc_final: 0.4807 (mp) REVERT: F 607 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.7386 (tt0) REVERT: I 111 PHE cc_start: 0.7568 (t80) cc_final: 0.7137 (t80) REVERT: I 169 GLU cc_start: 0.6542 (OUTLIER) cc_final: 0.6314 (pp20) REVERT: I 182 ARG cc_start: 0.6543 (OUTLIER) cc_final: 0.6135 (mpt90) REVERT: J 330 ASP cc_start: 0.8208 (p0) cc_final: 0.7968 (p0) REVERT: J 395 MET cc_start: 0.7781 (mmm) cc_final: 0.7549 (mmm) REVERT: J 430 ASN cc_start: 0.8050 (t0) cc_final: 0.7759 (t0) REVERT: J 432 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7530 (mp0) REVERT: K 13 MET cc_start: 0.6372 (mmp) cc_final: 0.4804 (ttp) REVERT: K 14 ARG cc_start: 0.5731 (tpm170) cc_final: 0.5325 (tpm170) REVERT: K 26 ARG cc_start: 0.6696 (ttm110) cc_final: 0.6362 (ppt90) REVERT: K 85 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.8053 (ttt90) REVERT: K 112 THR cc_start: 0.7157 (m) cc_final: 0.6927 (p) REVERT: K 214 ASP cc_start: 0.8048 (t0) cc_final: 0.7841 (t0) REVERT: K 216 ASN cc_start: 0.8084 (t0) cc_final: 0.7552 (m-40) REVERT: M 399 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8904 (tt) REVERT: M 401 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8405 (mp) REVERT: M 434 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.7013 (mt-10) REVERT: N 395 MET cc_start: 0.7347 (mmm) cc_final: 0.7140 (mmm) REVERT: O 26 ARG cc_start: 0.7379 (ttm110) cc_final: 0.6631 (ppt170) REVERT: O 116 LYS cc_start: 0.6773 (tttm) cc_final: 0.6423 (tttm) REVERT: O 156 MET cc_start: 0.7314 (mtm) cc_final: 0.6494 (mtm) REVERT: O 178 THR cc_start: 0.5421 (OUTLIER) cc_final: 0.5162 (t) REVERT: P 432 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.6671 (mp0) REVERT: Q 74 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8518 (mt) REVERT: Q 156 MET cc_start: 0.6589 (mtm) cc_final: 0.6296 (mtm) REVERT: R 325 MET cc_start: 0.7611 (tmm) cc_final: 0.7143 (tmm) REVERT: R 434 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.6923 (tp30) REVERT: R 509 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7704 (ttm170) REVERT: T 47 SER cc_start: 0.7812 (OUTLIER) cc_final: 0.7543 (p) REVERT: T 52 LYS cc_start: 0.8180 (mtpt) cc_final: 0.7906 (mtmm) REVERT: T 98 GLN cc_start: 0.8481 (mt0) cc_final: 0.8016 (mt0) REVERT: T 113 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6494 (mp0) REVERT: V 345 ILE cc_start: 0.9195 (OUTLIER) cc_final: 0.8874 (mm) REVERT: W 364 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.7207 (pt0) REVERT: W 401 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8487 (mp) REVERT: X 216 ASN cc_start: 0.7817 (OUTLIER) cc_final: 0.7594 (t0) REVERT: Y 324 ASN cc_start: 0.8125 (m-40) cc_final: 0.7884 (t0) REVERT: Z 52 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.7674 (mttp) REVERT: Z 143 TYR cc_start: 0.6751 (p90) cc_final: 0.5960 (p90) REVERT: Z 150 GLU cc_start: 0.7470 (mm-30) cc_final: 0.7156 (mm-30) REVERT: b 339 ASP cc_start: 0.7710 (OUTLIER) cc_final: 0.7404 (m-30) REVERT: b 355 PHE cc_start: 0.8974 (OUTLIER) cc_final: 0.8384 (t80) REVERT: b 401 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8534 (mp) REVERT: d 165 ASN cc_start: 0.5953 (m-40) cc_final: 0.5676 (m-40) REVERT: d 167 LEU cc_start: 0.7848 (mt) cc_final: 0.7543 (mt) REVERT: f 14 ARG cc_start: 0.6180 (ttm110) cc_final: 0.5967 (ptp-110) REVERT: f 85 ARG cc_start: 0.9048 (OUTLIER) cc_final: 0.7252 (tpp80) outliers start: 237 outliers final: 105 residues processed: 782 average time/residue: 1.6156 time to fit residues: 1556.0735 Evaluate side-chains 716 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 577 time to evaluate : 5.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 70 GLU Chi-restraints excluded: chain 0 residue 74 LEU Chi-restraints excluded: chain 0 residue 80 GLN Chi-restraints excluded: chain 0 residue 146 SER Chi-restraints excluded: chain 0 residue 149 ASP Chi-restraints excluded: chain 0 residue 233 LEU Chi-restraints excluded: chain 2 residue 8 SER Chi-restraints excluded: chain 2 residue 29 SER Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 74 LEU Chi-restraints excluded: chain 2 residue 147 ILE Chi-restraints excluded: chain 2 residue 179 ASP Chi-restraints excluded: chain 2 residue 226 THR Chi-restraints excluded: chain 2 residue 228 SER Chi-restraints excluded: chain 2 residue 234 LEU Chi-restraints excluded: chain 4 residue 28 LYS Chi-restraints excluded: chain 4 residue 51 GLN Chi-restraints excluded: chain 4 residue 74 LEU Chi-restraints excluded: chain 4 residue 132 GLU Chi-restraints excluded: chain 4 residue 147 ILE Chi-restraints excluded: chain 4 residue 170 SER Chi-restraints excluded: chain 4 residue 176 SER Chi-restraints excluded: chain 4 residue 209 GLU Chi-restraints excluded: chain 4 residue 228 SER Chi-restraints excluded: chain 6 residue 99 LEU Chi-restraints excluded: chain 6 residue 147 ILE Chi-restraints excluded: chain 6 residue 149 ASP Chi-restraints excluded: chain 8 residue 33 LEU Chi-restraints excluded: chain 8 residue 51 GLN Chi-restraints excluded: chain 8 residue 233 LEU Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain F residue 607 GLN Chi-restraints excluded: chain H residue 388 ARG Chi-restraints excluded: chain H residue 396 GLN Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 146 SER Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 169 GLU Chi-restraints excluded: chain I residue 174 ASN Chi-restraints excluded: chain I residue 182 ARG Chi-restraints excluded: chain I residue 207 SER Chi-restraints excluded: chain J residue 432 GLU Chi-restraints excluded: chain K residue 67 LYS Chi-restraints excluded: chain K residue 85 ARG Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 179 ASP Chi-restraints excluded: chain L residue 325 MET Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain L residue 409 ILE Chi-restraints excluded: chain M residue 330 ASP Chi-restraints excluded: chain M residue 354 GLU Chi-restraints excluded: chain M residue 358 LEU Chi-restraints excluded: chain M residue 399 LEU Chi-restraints excluded: chain M residue 401 LEU Chi-restraints excluded: chain M residue 434 GLU Chi-restraints excluded: chain N residue 358 LEU Chi-restraints excluded: chain N residue 361 VAL Chi-restraints excluded: chain N residue 396 GLN Chi-restraints excluded: chain N residue 444 LEU Chi-restraints excluded: chain N residue 450 MET Chi-restraints excluded: chain N residue 461 ASP Chi-restraints excluded: chain O residue 31 VAL Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain O residue 113 GLU Chi-restraints excluded: chain O residue 176 SER Chi-restraints excluded: chain O residue 178 THR Chi-restraints excluded: chain P residue 409 ILE Chi-restraints excluded: chain P residue 432 GLU Chi-restraints excluded: chain Q residue 54 SER Chi-restraints excluded: chain Q residue 74 LEU Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 112 THR Chi-restraints excluded: chain Q residue 228 SER Chi-restraints excluded: chain R residue 396 GLN Chi-restraints excluded: chain R residue 401 LEU Chi-restraints excluded: chain R residue 434 GLU Chi-restraints excluded: chain R residue 476 ASP Chi-restraints excluded: chain R residue 509 ARG Chi-restraints excluded: chain S residue 330 ASP Chi-restraints excluded: chain T residue 26 ARG Chi-restraints excluded: chain T residue 47 SER Chi-restraints excluded: chain T residue 49 SER Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain T residue 113 GLU Chi-restraints excluded: chain T residue 147 ILE Chi-restraints excluded: chain T residue 178 THR Chi-restraints excluded: chain T residue 207 SER Chi-restraints excluded: chain U residue 313 VAL Chi-restraints excluded: chain U residue 348 THR Chi-restraints excluded: chain U residue 520 SER Chi-restraints excluded: chain V residue 345 ILE Chi-restraints excluded: chain V residue 401 LEU Chi-restraints excluded: chain V residue 412 SER Chi-restraints excluded: chain V residue 504 ASP Chi-restraints excluded: chain W residue 330 ASP Chi-restraints excluded: chain W residue 364 GLU Chi-restraints excluded: chain W residue 401 LEU Chi-restraints excluded: chain W residue 416 SER Chi-restraints excluded: chain W residue 522 SER Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 49 SER Chi-restraints excluded: chain X residue 106 THR Chi-restraints excluded: chain X residue 112 THR Chi-restraints excluded: chain X residue 146 SER Chi-restraints excluded: chain X residue 214 ASP Chi-restraints excluded: chain X residue 216 ASN Chi-restraints excluded: chain X residue 228 SER Chi-restraints excluded: chain Y residue 320 SER Chi-restraints excluded: chain Y residue 409 ILE Chi-restraints excluded: chain Y residue 503 VAL Chi-restraints excluded: chain Z residue 42 VAL Chi-restraints excluded: chain Z residue 52 LYS Chi-restraints excluded: chain Z residue 83 ASP Chi-restraints excluded: chain Z residue 106 THR Chi-restraints excluded: chain Z residue 112 THR Chi-restraints excluded: chain Z residue 146 SER Chi-restraints excluded: chain Z residue 147 ILE Chi-restraints excluded: chain Z residue 178 THR Chi-restraints excluded: chain a residue 317 ASP Chi-restraints excluded: chain a residue 341 THR Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain b residue 339 ASP Chi-restraints excluded: chain b residue 341 THR Chi-restraints excluded: chain b residue 355 PHE Chi-restraints excluded: chain b residue 401 LEU Chi-restraints excluded: chain d residue 17 SER Chi-restraints excluded: chain d residue 49 SER Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain d residue 109 THR Chi-restraints excluded: chain d residue 160 THR Chi-restraints excluded: chain f residue 85 ARG Chi-restraints excluded: chain f residue 146 SER Chi-restraints excluded: chain f residue 149 ASP Chi-restraints excluded: chain f residue 228 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 542 optimal weight: 5.9990 chunk 413 optimal weight: 6.9990 chunk 285 optimal weight: 10.0000 chunk 60 optimal weight: 8.9990 chunk 262 optimal weight: 10.0000 chunk 368 optimal weight: 9.9990 chunk 551 optimal weight: 7.9990 chunk 583 optimal weight: 0.9980 chunk 288 optimal weight: 6.9990 chunk 522 optimal weight: 5.9990 chunk 157 optimal weight: 10.0000 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 69 ASN 0 73 ASN 0 174 ASN 1 607 GLN 2 45 ASN 4 98 GLN E 607 GLN ** I 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 396 GLN ** K 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 80 GLN O 114 GLN Q 114 GLN Q 165 ASN ** T 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 322 GLN U 396 GLN V 322 GLN X 69 ASN ** X 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 396 GLN Z 80 GLN Z 98 GLN Z 101 ASN a 322 GLN b 322 GLN d 98 GLN ** d 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 216 ASN f 80 GLN f 174 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 47302 Z= 0.478 Angle : 0.661 11.067 64013 Z= 0.350 Chirality : 0.049 0.203 7270 Planarity : 0.006 0.069 8452 Dihedral : 4.567 49.030 6910 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 5.12 % Allowed : 14.19 % Favored : 80.69 % 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: 1.58 (0.11), residues: 6089 helix: 2.31 (0.10), residues: 2597 sheet: 0.71 (0.14), residues: 1482 loop : -0.35 (0.14), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP P 429 HIS 0.007 0.002 HIS T 129 PHE 0.039 0.004 PHE 2 71 TYR 0.024 0.002 TYR I 143 ARG 0.011 0.001 ARG X 21 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12178 Ramachandran restraints generated. 6089 Oldfield, 0 Emsley, 6089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12178 Ramachandran restraints generated. 6089 Oldfield, 0 Emsley, 6089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 831 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 593 time to evaluate : 5.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 13 MET cc_start: 0.7037 (ttm) cc_final: 0.6355 (tmm) REVERT: 0 44 GLU cc_start: 0.6498 (tt0) cc_final: 0.5769 (tm-30) REVERT: 0 54 SER cc_start: 0.8608 (t) cc_final: 0.8359 (m) REVERT: 0 74 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8745 (mt) REVERT: 0 80 GLN cc_start: 0.7952 (OUTLIER) cc_final: 0.7658 (tp40) REVERT: 0 149 ASP cc_start: 0.7980 (OUTLIER) cc_final: 0.7624 (m-30) REVERT: 2 234 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7455 (pt) REVERT: 4 28 LYS cc_start: 0.7544 (OUTLIER) cc_final: 0.6682 (mptp) REVERT: 4 45 ASN cc_start: 0.8145 (t0) cc_final: 0.7623 (t0) REVERT: 4 51 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.7030 (mm-40) REVERT: 4 74 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8472 (mp) REVERT: 4 99 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8641 (mm) REVERT: 4 132 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.7055 (tt0) REVERT: 4 214 ASP cc_start: 0.8371 (t0) cc_final: 0.8041 (t0) REVERT: 4 225 ILE cc_start: 0.8566 (mt) cc_final: 0.8285 (mm) REVERT: 6 22 LYS cc_start: 0.7881 (mtpt) cc_final: 0.7060 (mmtt) REVERT: 6 98 GLN cc_start: 0.8670 (mt0) cc_final: 0.8469 (mt0) REVERT: 6 147 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.8019 (pt) REVERT: 8 98 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7968 (mt0) REVERT: 8 149 ASP cc_start: 0.8152 (OUTLIER) cc_final: 0.7520 (m-30) REVERT: 8 174 ASN cc_start: 0.7982 (m110) cc_final: 0.7676 (m110) REVERT: 8 205 VAL cc_start: 0.7630 (m) cc_final: 0.7333 (p) REVERT: 8 216 ASN cc_start: 0.8176 (m-40) cc_final: 0.7933 (t0) REVERT: B 605 LEU cc_start: 0.4924 (OUTLIER) cc_final: 0.4662 (mp) REVERT: F 607 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.7420 (tt0) REVERT: H 395 MET cc_start: 0.7320 (OUTLIER) cc_final: 0.6810 (mpm) REVERT: I 53 ILE cc_start: 0.8475 (OUTLIER) cc_final: 0.8253 (mt) REVERT: I 80 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7608 (tm-30) REVERT: I 169 GLU cc_start: 0.6537 (OUTLIER) cc_final: 0.6313 (pp20) REVERT: I 182 ARG cc_start: 0.6422 (OUTLIER) cc_final: 0.6019 (mpt90) REVERT: J 330 ASP cc_start: 0.8263 (p0) cc_final: 0.8051 (p0) REVERT: J 364 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.7077 (pt0) REVERT: J 395 MET cc_start: 0.7835 (mmm) cc_final: 0.7633 (mmm) REVERT: J 430 ASN cc_start: 0.8009 (t0) cc_final: 0.7731 (t0) REVERT: J 432 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7534 (mp0) REVERT: K 13 MET cc_start: 0.6376 (mmp) cc_final: 0.5118 (tmm) REVERT: K 14 ARG cc_start: 0.5714 (tpm170) cc_final: 0.5403 (tpm170) REVERT: K 26 ARG cc_start: 0.6706 (ttm110) cc_final: 0.6242 (ppt90) REVERT: K 85 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.8047 (ttt90) REVERT: K 216 ASN cc_start: 0.8051 (t0) cc_final: 0.7545 (m-40) REVERT: M 363 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8787 (mp) REVERT: M 364 GLU cc_start: 0.7620 (tt0) cc_final: 0.7297 (tt0) REVERT: M 399 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8932 (tt) REVERT: M 401 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8369 (mp) REVERT: M 434 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.7015 (mt-10) REVERT: N 395 MET cc_start: 0.7225 (mmm) cc_final: 0.6958 (mmm) REVERT: N 432 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7354 (mp0) REVERT: O 26 ARG cc_start: 0.7404 (ttm110) cc_final: 0.6557 (ppt170) REVERT: O 67 LYS cc_start: 0.8046 (OUTLIER) cc_final: 0.7276 (tttt) REVERT: O 70 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.6247 (mp0) REVERT: O 93 ASP cc_start: 0.8921 (m-30) cc_final: 0.8494 (m-30) REVERT: O 97 ARG cc_start: 0.7383 (OUTLIER) cc_final: 0.6974 (ttm-80) REVERT: O 99 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8405 (mt) REVERT: O 116 LYS cc_start: 0.6670 (tttm) cc_final: 0.6335 (tttm) REVERT: O 156 MET cc_start: 0.7142 (mtm) cc_final: 0.6179 (mtm) REVERT: P 432 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.6764 (mp0) REVERT: Q 26 ARG cc_start: 0.7708 (ttm-80) cc_final: 0.6463 (ttp-110) REVERT: R 434 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6885 (tp30) REVERT: R 509 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7626 (ttm170) REVERT: S 444 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8475 (mp) REVERT: T 52 LYS cc_start: 0.8056 (mtpt) cc_final: 0.7724 (mtmm) REVERT: T 173 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7746 (mm-30) REVERT: V 345 ILE cc_start: 0.9239 (OUTLIER) cc_final: 0.8923 (mm) REVERT: W 364 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.7257 (pt0) REVERT: W 401 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8523 (mp) REVERT: Y 324 ASN cc_start: 0.8180 (m-40) cc_final: 0.7904 (t0) REVERT: Z 52 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7696 (mttp) REVERT: Z 150 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7277 (tm-30) REVERT: b 325 MET cc_start: 0.7572 (OUTLIER) cc_final: 0.7339 (mtt) REVERT: b 339 ASP cc_start: 0.7705 (OUTLIER) cc_final: 0.7404 (m-30) REVERT: b 355 PHE cc_start: 0.8986 (OUTLIER) cc_final: 0.8386 (t80) REVERT: b 401 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8515 (mp) REVERT: d 165 ASN cc_start: 0.6136 (m-40) cc_final: 0.5790 (m-40) REVERT: d 167 LEU cc_start: 0.7892 (mt) cc_final: 0.7606 (mt) REVERT: d 185 VAL cc_start: 0.8074 (t) cc_final: 0.7782 (m) REVERT: f 14 ARG cc_start: 0.6194 (ttm110) cc_final: 0.5946 (ptp-110) REVERT: f 22 LYS cc_start: 0.7811 (ttpp) cc_final: 0.7260 (tmtt) REVERT: f 85 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.7218 (tpp80) outliers start: 238 outliers final: 118 residues processed: 754 average time/residue: 1.5450 time to fit residues: 1448.1841 Evaluate side-chains 730 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 567 time to evaluate : 5.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 51 GLN Chi-restraints excluded: chain 0 residue 70 GLU Chi-restraints excluded: chain 0 residue 72 ASP Chi-restraints excluded: chain 0 residue 74 LEU Chi-restraints excluded: chain 0 residue 80 GLN Chi-restraints excluded: chain 0 residue 146 SER Chi-restraints excluded: chain 0 residue 149 ASP Chi-restraints excluded: chain 0 residue 233 LEU Chi-restraints excluded: chain 2 residue 8 SER Chi-restraints excluded: chain 2 residue 22 LYS Chi-restraints excluded: chain 2 residue 29 SER Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 67 LYS Chi-restraints excluded: chain 2 residue 74 LEU Chi-restraints excluded: chain 2 residue 147 ILE Chi-restraints excluded: chain 2 residue 179 ASP Chi-restraints excluded: chain 2 residue 226 THR Chi-restraints excluded: chain 2 residue 228 SER Chi-restraints excluded: chain 2 residue 234 LEU Chi-restraints excluded: chain 4 residue 28 LYS Chi-restraints excluded: chain 4 residue 51 GLN Chi-restraints excluded: chain 4 residue 74 LEU Chi-restraints excluded: chain 4 residue 99 LEU Chi-restraints excluded: chain 4 residue 102 VAL Chi-restraints excluded: chain 4 residue 132 GLU Chi-restraints excluded: chain 4 residue 134 LYS Chi-restraints excluded: chain 4 residue 147 ILE Chi-restraints excluded: chain 4 residue 170 SER Chi-restraints excluded: chain 4 residue 176 SER Chi-restraints excluded: chain 4 residue 183 ILE Chi-restraints excluded: chain 4 residue 209 GLU Chi-restraints excluded: chain 6 residue 99 LEU Chi-restraints excluded: chain 6 residue 147 ILE Chi-restraints excluded: chain 6 residue 149 ASP Chi-restraints excluded: chain 6 residue 179 ASP Chi-restraints excluded: chain 8 residue 33 LEU Chi-restraints excluded: chain 8 residue 51 GLN Chi-restraints excluded: chain 8 residue 98 GLN Chi-restraints excluded: chain 8 residue 99 LEU Chi-restraints excluded: chain 8 residue 149 ASP Chi-restraints excluded: chain 8 residue 233 LEU Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain F residue 607 GLN Chi-restraints excluded: chain H residue 388 ARG Chi-restraints excluded: chain H residue 395 MET Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 80 GLN Chi-restraints excluded: chain I residue 146 SER Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 169 GLU Chi-restraints excluded: chain I residue 174 ASN Chi-restraints excluded: chain I residue 182 ARG Chi-restraints excluded: chain J residue 364 GLU Chi-restraints excluded: chain J residue 432 GLU Chi-restraints excluded: chain K residue 67 LYS Chi-restraints excluded: chain K residue 73 ASN Chi-restraints excluded: chain K residue 85 ARG Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 143 TYR Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 179 ASP Chi-restraints excluded: chain L residue 325 MET Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain L residue 409 ILE Chi-restraints excluded: chain L residue 430 ASN Chi-restraints excluded: chain M residue 330 ASP Chi-restraints excluded: chain M residue 358 LEU Chi-restraints excluded: chain M residue 363 LEU Chi-restraints excluded: chain M residue 399 LEU Chi-restraints excluded: chain M residue 401 LEU Chi-restraints excluded: chain M residue 434 GLU Chi-restraints excluded: chain N residue 341 THR Chi-restraints excluded: chain N residue 358 LEU Chi-restraints excluded: chain N residue 361 VAL Chi-restraints excluded: chain N residue 396 GLN Chi-restraints excluded: chain N residue 409 ILE Chi-restraints excluded: chain N residue 432 GLU Chi-restraints excluded: chain N residue 444 LEU Chi-restraints excluded: chain N residue 450 MET Chi-restraints excluded: chain N residue 461 ASP Chi-restraints excluded: chain O residue 31 VAL Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain O residue 67 LYS Chi-restraints excluded: chain O residue 70 GLU Chi-restraints excluded: chain O residue 97 ARG Chi-restraints excluded: chain O residue 99 LEU Chi-restraints excluded: chain O residue 113 GLU Chi-restraints excluded: chain O residue 146 SER Chi-restraints excluded: chain O residue 176 SER Chi-restraints excluded: chain P residue 395 MET Chi-restraints excluded: chain P residue 409 ILE Chi-restraints excluded: chain P residue 432 GLU Chi-restraints excluded: chain Q residue 112 THR Chi-restraints excluded: chain Q residue 228 SER Chi-restraints excluded: chain R residue 396 GLN Chi-restraints excluded: chain R residue 401 LEU Chi-restraints excluded: chain R residue 434 GLU Chi-restraints excluded: chain R residue 476 ASP Chi-restraints excluded: chain R residue 509 ARG Chi-restraints excluded: chain S residue 330 ASP Chi-restraints excluded: chain S residue 444 LEU Chi-restraints excluded: chain T residue 26 ARG Chi-restraints excluded: chain T residue 49 SER Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain T residue 147 ILE Chi-restraints excluded: chain T residue 173 GLU Chi-restraints excluded: chain T residue 178 THR Chi-restraints excluded: chain T residue 207 SER Chi-restraints excluded: chain U residue 313 VAL Chi-restraints excluded: chain U residue 348 THR Chi-restraints excluded: chain U residue 401 LEU Chi-restraints excluded: chain U residue 503 VAL Chi-restraints excluded: chain U residue 520 SER Chi-restraints excluded: chain V residue 338 ASP Chi-restraints excluded: chain V residue 345 ILE Chi-restraints excluded: chain V residue 412 SER Chi-restraints excluded: chain V residue 504 ASP Chi-restraints excluded: chain W residue 330 ASP Chi-restraints excluded: chain W residue 337 THR Chi-restraints excluded: chain W residue 363 LEU Chi-restraints excluded: chain W residue 364 GLU Chi-restraints excluded: chain W residue 401 LEU Chi-restraints excluded: chain W residue 412 SER Chi-restraints excluded: chain W residue 416 SER Chi-restraints excluded: chain W residue 522 SER Chi-restraints excluded: chain X residue 8 SER Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 49 SER Chi-restraints excluded: chain X residue 106 THR Chi-restraints excluded: chain X residue 112 THR Chi-restraints excluded: chain X residue 146 SER Chi-restraints excluded: chain X residue 214 ASP Chi-restraints excluded: chain X residue 228 SER Chi-restraints excluded: chain Y residue 409 ILE Chi-restraints excluded: chain Y residue 503 VAL Chi-restraints excluded: chain Z residue 52 LYS Chi-restraints excluded: chain Z residue 74 LEU Chi-restraints excluded: chain Z residue 83 ASP Chi-restraints excluded: chain Z residue 99 LEU Chi-restraints excluded: chain Z residue 106 THR Chi-restraints excluded: chain Z residue 146 SER Chi-restraints excluded: chain Z residue 147 ILE Chi-restraints excluded: chain Z residue 178 THR Chi-restraints excluded: chain a residue 317 ASP Chi-restraints excluded: chain a residue 341 THR Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain b residue 325 MET Chi-restraints excluded: chain b residue 339 ASP Chi-restraints excluded: chain b residue 341 THR Chi-restraints excluded: chain b residue 355 PHE Chi-restraints excluded: chain b residue 401 LEU Chi-restraints excluded: chain d residue 17 SER Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain d residue 109 THR Chi-restraints excluded: chain d residue 160 THR Chi-restraints excluded: chain f residue 85 ARG Chi-restraints excluded: chain f residue 146 SER Chi-restraints excluded: chain f residue 149 ASP Chi-restraints excluded: chain f residue 228 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 486 optimal weight: 6.9990 chunk 331 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 434 optimal weight: 0.9980 chunk 240 optimal weight: 1.9990 chunk 498 optimal weight: 0.9990 chunk 403 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 298 optimal weight: 2.9990 chunk 524 optimal weight: 0.7980 chunk 147 optimal weight: 9.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 69 ASN 0 174 ASN 1 607 GLN 4 80 GLN E 607 GLN ** I 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 396 GLN ** K 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 80 GLN Q 165 ASN ** T 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 322 GLN U 396 GLN V 322 GLN X 69 ASN ** X 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 216 ASN Z 80 GLN Z 101 ASN a 322 GLN b 322 GLN ** d 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 216 ASN f 80 GLN f 174 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 47302 Z= 0.154 Angle : 0.492 10.067 64013 Z= 0.261 Chirality : 0.042 0.164 7270 Planarity : 0.004 0.052 8452 Dihedral : 4.014 48.995 6910 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.40 % Allowed : 16.47 % Favored : 80.13 % 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: 2.18 (0.11), residues: 6089 helix: 3.05 (0.10), residues: 2582 sheet: 0.84 (0.14), residues: 1436 loop : -0.19 (0.14), residues: 2071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP H 429 HIS 0.006 0.001 HIS Z 152 PHE 0.033 0.002 PHE 6 71 TYR 0.022 0.001 TYR I 143 ARG 0.010 0.000 ARG X 21 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12178 Ramachandran restraints generated. 6089 Oldfield, 0 Emsley, 6089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12178 Ramachandran restraints generated. 6089 Oldfield, 0 Emsley, 6089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 760 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 602 time to evaluate : 5.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 13 MET cc_start: 0.6896 (ttm) cc_final: 0.6212 (tmm) REVERT: 0 44 GLU cc_start: 0.6513 (tt0) cc_final: 0.5799 (tm-30) REVERT: 0 54 SER cc_start: 0.8594 (t) cc_final: 0.8354 (m) REVERT: 0 74 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8715 (mt) REVERT: 0 80 GLN cc_start: 0.7901 (OUTLIER) cc_final: 0.7603 (tp40) REVERT: 4 45 ASN cc_start: 0.8179 (t0) cc_final: 0.7763 (t0) REVERT: 4 74 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8361 (mp) REVERT: 4 163 ILE cc_start: 0.7619 (mt) cc_final: 0.7336 (mp) REVERT: 4 214 ASP cc_start: 0.8263 (t0) cc_final: 0.8041 (t0) REVERT: 4 225 ILE cc_start: 0.8428 (mt) cc_final: 0.8170 (mm) REVERT: 6 22 LYS cc_start: 0.7970 (mtpt) cc_final: 0.7139 (mmtt) REVERT: 6 67 LYS cc_start: 0.7882 (OUTLIER) cc_final: 0.7490 (tttp) REVERT: 6 98 GLN cc_start: 0.8551 (mt0) cc_final: 0.8345 (mt0) REVERT: 6 147 ILE cc_start: 0.8374 (OUTLIER) cc_final: 0.7985 (pt) REVERT: 8 33 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8629 (pp) REVERT: 8 98 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.7868 (mt0) REVERT: 8 205 VAL cc_start: 0.7698 (m) cc_final: 0.7346 (p) REVERT: 8 216 ASN cc_start: 0.8162 (m-40) cc_final: 0.7918 (t0) REVERT: F 605 LEU cc_start: 0.5352 (OUTLIER) cc_final: 0.4882 (mm) REVERT: F 607 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.7388 (tt0) REVERT: I 45 ASN cc_start: 0.7786 (t0) cc_final: 0.7324 (t0) REVERT: I 182 ARG cc_start: 0.6263 (OUTLIER) cc_final: 0.6031 (mpt90) REVERT: J 364 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6978 (pt0) REVERT: J 430 ASN cc_start: 0.7934 (t0) cc_final: 0.7630 (t0) REVERT: J 432 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7550 (mp0) REVERT: K 13 MET cc_start: 0.6388 (mmp) cc_final: 0.5039 (tmm) REVERT: K 18 GLU cc_start: 0.6612 (tp30) cc_final: 0.6261 (tp30) REVERT: K 26 ARG cc_start: 0.6721 (ttm110) cc_final: 0.6311 (ppt90) REVERT: K 216 ASN cc_start: 0.7988 (t0) cc_final: 0.7561 (m-40) REVERT: L 432 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7429 (mp0) REVERT: M 364 GLU cc_start: 0.7556 (tt0) cc_final: 0.7222 (tt0) REVERT: M 399 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8823 (tt) REVERT: M 401 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8348 (mp) REVERT: N 395 MET cc_start: 0.7225 (mmm) cc_final: 0.6950 (mmm) REVERT: O 26 ARG cc_start: 0.7466 (ttm110) cc_final: 0.6577 (ppt170) REVERT: O 67 LYS cc_start: 0.7782 (OUTLIER) cc_final: 0.7391 (tttt) REVERT: O 93 ASP cc_start: 0.8892 (m-30) cc_final: 0.8506 (m-30) REVERT: O 105 GLN cc_start: 0.7022 (tp40) cc_final: 0.6588 (tp-100) REVERT: O 113 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6643 (tm-30) REVERT: O 116 LYS cc_start: 0.6743 (tttm) cc_final: 0.6476 (tttm) REVERT: P 424 ASP cc_start: 0.8036 (p0) cc_final: 0.7666 (p0) REVERT: P 432 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.6838 (mp0) REVERT: Q 13 MET cc_start: 0.5232 (tmm) cc_final: 0.5032 (tmm) REVERT: Q 26 ARG cc_start: 0.7610 (ttm-80) cc_final: 0.6451 (ttp-110) REVERT: R 434 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6836 (tp30) REVERT: R 509 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.7445 (ttm170) REVERT: S 401 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8446 (mt) REVERT: T 52 LYS cc_start: 0.8017 (mtpt) cc_final: 0.7609 (mtmm) REVERT: T 98 GLN cc_start: 0.8353 (mt0) cc_final: 0.8124 (mt0) REVERT: V 345 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8846 (mm) REVERT: W 401 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8474 (mp) REVERT: Y 324 ASN cc_start: 0.8013 (m-40) cc_final: 0.7784 (t0) REVERT: Z 52 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7740 (mtpp) REVERT: Z 111 PHE cc_start: 0.6412 (t80) cc_final: 0.6100 (t80) REVERT: b 339 ASP cc_start: 0.7677 (OUTLIER) cc_final: 0.7374 (m-30) REVERT: b 401 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8515 (mp) REVERT: d 167 LEU cc_start: 0.7872 (mt) cc_final: 0.7612 (mt) REVERT: f 14 ARG cc_start: 0.6168 (ttm110) cc_final: 0.5919 (ptp-110) REVERT: f 22 LYS cc_start: 0.7779 (ttpp) cc_final: 0.7285 (tmtt) outliers start: 158 outliers final: 63 residues processed: 700 average time/residue: 1.5447 time to fit residues: 1340.9216 Evaluate side-chains 666 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 577 time to evaluate : 5.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 51 GLN Chi-restraints excluded: chain 0 residue 72 ASP Chi-restraints excluded: chain 0 residue 74 LEU Chi-restraints excluded: chain 0 residue 80 GLN Chi-restraints excluded: chain 0 residue 146 SER Chi-restraints excluded: chain 0 residue 233 LEU Chi-restraints excluded: chain 2 residue 29 SER Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 147 ILE Chi-restraints excluded: chain 2 residue 179 ASP Chi-restraints excluded: chain 2 residue 226 THR Chi-restraints excluded: chain 4 residue 74 LEU Chi-restraints excluded: chain 4 residue 102 VAL Chi-restraints excluded: chain 4 residue 147 ILE Chi-restraints excluded: chain 4 residue 149 ASP Chi-restraints excluded: chain 4 residue 170 SER Chi-restraints excluded: chain 6 residue 67 LYS Chi-restraints excluded: chain 6 residue 99 LEU Chi-restraints excluded: chain 6 residue 147 ILE Chi-restraints excluded: chain 6 residue 149 ASP Chi-restraints excluded: chain 8 residue 33 LEU Chi-restraints excluded: chain 8 residue 98 GLN Chi-restraints excluded: chain 8 residue 233 LEU Chi-restraints excluded: chain F residue 605 LEU Chi-restraints excluded: chain F residue 607 GLN Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain I residue 174 ASN Chi-restraints excluded: chain I residue 182 ARG Chi-restraints excluded: chain J residue 364 GLU Chi-restraints excluded: chain J residue 432 GLU Chi-restraints excluded: chain K residue 67 LYS Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 143 TYR Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain L residue 364 GLU Chi-restraints excluded: chain L residue 432 GLU Chi-restraints excluded: chain M residue 330 ASP Chi-restraints excluded: chain M residue 399 LEU Chi-restraints excluded: chain M residue 401 LEU Chi-restraints excluded: chain O residue 31 VAL Chi-restraints excluded: chain O residue 67 LYS Chi-restraints excluded: chain O residue 113 GLU Chi-restraints excluded: chain O residue 146 SER Chi-restraints excluded: chain O residue 176 SER Chi-restraints excluded: chain P residue 395 MET Chi-restraints excluded: chain P residue 409 ILE Chi-restraints excluded: chain P residue 432 GLU Chi-restraints excluded: chain R residue 396 GLN Chi-restraints excluded: chain R residue 401 LEU Chi-restraints excluded: chain R residue 434 GLU Chi-restraints excluded: chain R residue 509 ARG Chi-restraints excluded: chain S residue 401 LEU Chi-restraints excluded: chain T residue 49 SER Chi-restraints excluded: chain T residue 147 ILE Chi-restraints excluded: chain T residue 178 THR Chi-restraints excluded: chain T residue 207 SER Chi-restraints excluded: chain U residue 313 VAL Chi-restraints excluded: chain U residue 348 THR Chi-restraints excluded: chain U residue 520 SER Chi-restraints excluded: chain V residue 345 ILE Chi-restraints excluded: chain V residue 401 LEU Chi-restraints excluded: chain W residue 330 ASP Chi-restraints excluded: chain W residue 401 LEU Chi-restraints excluded: chain W residue 412 SER Chi-restraints excluded: chain W residue 416 SER Chi-restraints excluded: chain W residue 522 SER Chi-restraints excluded: chain X residue 8 SER Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 49 SER Chi-restraints excluded: chain X residue 146 SER Chi-restraints excluded: chain X residue 228 SER Chi-restraints excluded: chain Y residue 391 LEU Chi-restraints excluded: chain Y residue 409 ILE Chi-restraints excluded: chain Y residue 503 VAL Chi-restraints excluded: chain Z residue 52 LYS Chi-restraints excluded: chain Z residue 83 ASP Chi-restraints excluded: chain Z residue 146 SER Chi-restraints excluded: chain Z residue 147 ILE Chi-restraints excluded: chain Z residue 178 THR Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain b residue 339 ASP Chi-restraints excluded: chain b residue 355 PHE Chi-restraints excluded: chain b residue 401 LEU Chi-restraints excluded: chain d residue 17 SER Chi-restraints excluded: chain f residue 146 SER Chi-restraints excluded: chain f residue 149 ASP Chi-restraints excluded: chain f residue 228 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 196 optimal weight: 0.9980 chunk 525 optimal weight: 4.9990 chunk 115 optimal weight: 0.9990 chunk 342 optimal weight: 0.9980 chunk 144 optimal weight: 0.9990 chunk 584 optimal weight: 1.9990 chunk 485 optimal weight: 5.9990 chunk 270 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 chunk 193 optimal weight: 7.9990 chunk 306 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 174 ASN 1 607 GLN 8 45 ASN E 607 GLN I 114 GLN J 396 GLN ** K 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 80 GLN Q 45 ASN Q 73 ASN U 322 GLN U 396 GLN V 322 GLN ** X 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 216 ASN Z 80 GLN Z 101 ASN a 322 GLN ** d 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 216 ASN f 80 GLN f 165 ASN f 174 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 47302 Z= 0.139 Angle : 0.475 9.711 64013 Z= 0.250 Chirality : 0.042 0.161 7270 Planarity : 0.003 0.043 8452 Dihedral : 3.797 48.010 6910 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.40 % Allowed : 16.68 % Favored : 79.92 % 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: 2.43 (0.11), residues: 6089 helix: 3.36 (0.10), residues: 2562 sheet: 0.88 (0.14), residues: 1442 loop : -0.12 (0.14), residues: 2085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP V 429 HIS 0.003 0.001 HIS S 365 PHE 0.031 0.002 PHE 6 71 TYR 0.024 0.001 TYR I 143 ARG 0.013 0.000 ARG K 21 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12178 Ramachandran restraints generated. 6089 Oldfield, 0 Emsley, 6089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12178 Ramachandran restraints generated. 6089 Oldfield, 0 Emsley, 6089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 757 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 599 time to evaluate : 5.620 Fit side-chains revert: symmetry clash REVERT: 0 13 MET cc_start: 0.6853 (ttm) cc_final: 0.6189 (tmm) REVERT: 0 21 ARG cc_start: 0.7001 (mtm-85) cc_final: 0.6715 (mtm-85) REVERT: 0 44 GLU cc_start: 0.6474 (tt0) cc_final: 0.5779 (tm-30) REVERT: 0 54 SER cc_start: 0.8573 (t) cc_final: 0.8302 (m) REVERT: 0 74 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8711 (mt) REVERT: 0 80 GLN cc_start: 0.7894 (OUTLIER) cc_final: 0.7599 (tp40) REVERT: 2 183 ILE cc_start: 0.8231 (mp) cc_final: 0.8019 (mt) REVERT: 4 74 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8355 (mp) REVERT: 4 132 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.7152 (tt0) REVERT: 4 163 ILE cc_start: 0.7707 (mt) cc_final: 0.7428 (mp) REVERT: 4 214 ASP cc_start: 0.8108 (t0) cc_final: 0.7894 (t0) REVERT: 4 225 ILE cc_start: 0.8433 (mt) cc_final: 0.8160 (mm) REVERT: 6 22 LYS cc_start: 0.7924 (mtpt) cc_final: 0.7078 (mmtt) REVERT: 6 98 GLN cc_start: 0.8577 (mt0) cc_final: 0.8359 (mt0) REVERT: 6 147 ILE cc_start: 0.8369 (OUTLIER) cc_final: 0.7988 (pt) REVERT: 8 33 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8571 (pp) REVERT: 8 205 VAL cc_start: 0.7698 (m) cc_final: 0.7354 (p) REVERT: 8 216 ASN cc_start: 0.8167 (m-40) cc_final: 0.7925 (t0) REVERT: F 605 LEU cc_start: 0.5380 (OUTLIER) cc_final: 0.4939 (mm) REVERT: F 607 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.7301 (tt0) REVERT: I 45 ASN cc_start: 0.7731 (t0) cc_final: 0.7231 (t0) REVERT: I 111 PHE cc_start: 0.7652 (t80) cc_final: 0.7305 (t80) REVERT: J 364 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.7015 (pt0) REVERT: J 430 ASN cc_start: 0.7931 (t0) cc_final: 0.7565 (t0) REVERT: J 432 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7585 (mp0) REVERT: K 13 MET cc_start: 0.6237 (mmp) cc_final: 0.4985 (tmm) REVERT: K 14 ARG cc_start: 0.6010 (tpm170) cc_final: 0.5370 (tpm170) REVERT: K 18 GLU cc_start: 0.6439 (tp30) cc_final: 0.6205 (tp30) REVERT: K 26 ARG cc_start: 0.6749 (ttm110) cc_final: 0.6166 (ppt90) REVERT: K 216 ASN cc_start: 0.7967 (t0) cc_final: 0.7546 (m-40) REVERT: L 432 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7437 (mp0) REVERT: M 363 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8656 (mp) REVERT: M 364 GLU cc_start: 0.7517 (tt0) cc_final: 0.7204 (tt0) REVERT: M 399 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8789 (tt) REVERT: M 401 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8348 (mp) REVERT: N 395 MET cc_start: 0.7217 (mmm) cc_final: 0.6890 (mmm) REVERT: N 432 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7343 (mp0) REVERT: O 26 ARG cc_start: 0.7410 (ttm110) cc_final: 0.6504 (ppt170) REVERT: O 67 LYS cc_start: 0.7662 (OUTLIER) cc_final: 0.7272 (tttt) REVERT: O 105 GLN cc_start: 0.6960 (tp40) cc_final: 0.6538 (tp-100) REVERT: O 113 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6646 (tm-30) REVERT: O 116 LYS cc_start: 0.6703 (tttm) cc_final: 0.6288 (tttm) REVERT: O 156 MET cc_start: 0.6706 (mtm) cc_final: 0.5843 (mtm) REVERT: P 424 ASP cc_start: 0.7984 (p0) cc_final: 0.7651 (p0) REVERT: P 432 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.6906 (mp0) REVERT: S 401 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8475 (mt) REVERT: S 444 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8439 (mp) REVERT: T 52 LYS cc_start: 0.8012 (mtpt) cc_final: 0.7615 (mtmm) REVERT: W 364 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.7090 (pt0) REVERT: W 401 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8473 (mp) REVERT: X 21 ARG cc_start: 0.6528 (ttp-110) cc_final: 0.5971 (ttp80) REVERT: Y 324 ASN cc_start: 0.7930 (m-40) cc_final: 0.7709 (t0) REVERT: Z 52 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7760 (mtpp) REVERT: Z 111 PHE cc_start: 0.6542 (t80) cc_final: 0.6293 (t80) REVERT: b 339 ASP cc_start: 0.7678 (OUTLIER) cc_final: 0.7375 (m-30) REVERT: b 401 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8508 (mp) REVERT: d 167 LEU cc_start: 0.7850 (mt) cc_final: 0.7593 (mt) REVERT: f 14 ARG cc_start: 0.6167 (ttm110) cc_final: 0.5937 (ptp-110) REVERT: f 22 LYS cc_start: 0.7737 (ttpp) cc_final: 0.7304 (tmtt) REVERT: f 72 ASP cc_start: 0.7997 (t70) cc_final: 0.7607 (t0) REVERT: f 214 ASP cc_start: 0.8163 (t0) cc_final: 0.7949 (t0) outliers start: 158 outliers final: 68 residues processed: 698 average time/residue: 1.5428 time to fit residues: 1339.7356 Evaluate side-chains 675 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 582 time to evaluate : 5.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 70 GLU Chi-restraints excluded: chain 0 residue 72 ASP Chi-restraints excluded: chain 0 residue 74 LEU Chi-restraints excluded: chain 0 residue 80 GLN Chi-restraints excluded: chain 0 residue 146 SER Chi-restraints excluded: chain 2 residue 29 SER Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 147 ILE Chi-restraints excluded: chain 2 residue 179 ASP Chi-restraints excluded: chain 2 residue 226 THR Chi-restraints excluded: chain 2 residue 228 SER Chi-restraints excluded: chain 4 residue 74 LEU Chi-restraints excluded: chain 4 residue 102 VAL Chi-restraints excluded: chain 4 residue 132 GLU Chi-restraints excluded: chain 4 residue 149 ASP Chi-restraints excluded: chain 4 residue 170 SER Chi-restraints excluded: chain 6 residue 99 LEU Chi-restraints excluded: chain 6 residue 147 ILE Chi-restraints excluded: chain 6 residue 149 ASP Chi-restraints excluded: chain 8 residue 33 LEU Chi-restraints excluded: chain 8 residue 233 LEU Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain F residue 605 LEU Chi-restraints excluded: chain F residue 607 GLN Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain I residue 174 ASN Chi-restraints excluded: chain J residue 364 GLU Chi-restraints excluded: chain J residue 432 GLU Chi-restraints excluded: chain K residue 67 LYS Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 143 TYR Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain L residue 325 MET Chi-restraints excluded: chain L residue 364 GLU Chi-restraints excluded: chain L residue 430 ASN Chi-restraints excluded: chain L residue 432 GLU Chi-restraints excluded: chain M residue 330 ASP Chi-restraints excluded: chain M residue 363 LEU Chi-restraints excluded: chain M residue 399 LEU Chi-restraints excluded: chain M residue 401 LEU Chi-restraints excluded: chain M residue 461 ASP Chi-restraints excluded: chain N residue 345 ILE Chi-restraints excluded: chain N residue 432 GLU Chi-restraints excluded: chain N residue 444 LEU Chi-restraints excluded: chain N residue 504 ASP Chi-restraints excluded: chain O residue 31 VAL Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain O residue 67 LYS Chi-restraints excluded: chain O residue 113 GLU Chi-restraints excluded: chain O residue 176 SER Chi-restraints excluded: chain P residue 395 MET Chi-restraints excluded: chain P residue 409 ILE Chi-restraints excluded: chain P residue 432 GLU Chi-restraints excluded: chain Q residue 54 SER Chi-restraints excluded: chain R residue 401 LEU Chi-restraints excluded: chain R residue 476 ASP Chi-restraints excluded: chain S residue 330 ASP Chi-restraints excluded: chain S residue 401 LEU Chi-restraints excluded: chain S residue 444 LEU Chi-restraints excluded: chain T residue 26 ARG Chi-restraints excluded: chain T residue 49 SER Chi-restraints excluded: chain T residue 147 ILE Chi-restraints excluded: chain T residue 178 THR Chi-restraints excluded: chain T residue 207 SER Chi-restraints excluded: chain U residue 313 VAL Chi-restraints excluded: chain U residue 348 THR Chi-restraints excluded: chain U residue 401 LEU Chi-restraints excluded: chain W residue 330 ASP Chi-restraints excluded: chain W residue 364 GLU Chi-restraints excluded: chain W residue 401 LEU Chi-restraints excluded: chain W residue 416 SER Chi-restraints excluded: chain X residue 8 SER Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 49 SER Chi-restraints excluded: chain X residue 146 SER Chi-restraints excluded: chain X residue 216 ASN Chi-restraints excluded: chain X residue 228 SER Chi-restraints excluded: chain Y residue 391 LEU Chi-restraints excluded: chain Y residue 409 ILE Chi-restraints excluded: chain Y residue 503 VAL Chi-restraints excluded: chain Z residue 52 LYS Chi-restraints excluded: chain Z residue 83 ASP Chi-restraints excluded: chain Z residue 99 LEU Chi-restraints excluded: chain Z residue 146 SER Chi-restraints excluded: chain Z residue 147 ILE Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain b residue 339 ASP Chi-restraints excluded: chain b residue 355 PHE Chi-restraints excluded: chain b residue 401 LEU Chi-restraints excluded: chain d residue 160 THR Chi-restraints excluded: chain f residue 146 SER Chi-restraints excluded: chain f residue 149 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 563 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 332 optimal weight: 0.8980 chunk 426 optimal weight: 7.9990 chunk 330 optimal weight: 10.0000 chunk 491 optimal weight: 5.9990 chunk 326 optimal weight: 8.9990 chunk 582 optimal weight: 10.0000 chunk 364 optimal weight: 0.9990 chunk 354 optimal weight: 0.9990 chunk 268 optimal weight: 10.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 69 ASN 0 73 ASN 0 174 ASN 1 607 GLN 4 45 ASN E 607 GLN J 396 GLN ** K 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 410 HIS O 80 GLN Q 165 ASN U 322 GLN U 396 GLN V 322 GLN W 430 ASN ** X 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 216 ASN Z 80 GLN Z 101 ASN a 322 GLN ** d 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 216 ASN f 69 ASN f 80 GLN f 165 ASN f 174 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 47302 Z= 0.285 Angle : 0.548 11.310 64013 Z= 0.288 Chirality : 0.044 0.178 7270 Planarity : 0.004 0.043 8452 Dihedral : 3.999 30.381 6904 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.66 % Allowed : 16.94 % Favored : 79.40 % 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: 2.19 (0.11), residues: 6089 helix: 3.05 (0.10), residues: 2597 sheet: 0.84 (0.14), residues: 1418 loop : -0.20 (0.14), residues: 2074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 429 HIS 0.004 0.001 HIS T 129 PHE 0.033 0.003 PHE 6 71 TYR 0.024 0.002 TYR I 143 ARG 0.011 0.001 ARG O 21 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12178 Ramachandran restraints generated. 6089 Oldfield, 0 Emsley, 6089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12178 Ramachandran restraints generated. 6089 Oldfield, 0 Emsley, 6089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 756 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 586 time to evaluate : 5.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 13 MET cc_start: 0.6888 (ttm) cc_final: 0.6222 (tmm) REVERT: 0 44 GLU cc_start: 0.6508 (tt0) cc_final: 0.5788 (tm-30) REVERT: 0 54 SER cc_start: 0.8584 (t) cc_final: 0.8332 (m) REVERT: 0 74 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8717 (mt) REVERT: 0 80 GLN cc_start: 0.7929 (OUTLIER) cc_final: 0.7638 (tp40) REVERT: 4 45 ASN cc_start: 0.8244 (t0) cc_final: 0.7802 (t0) REVERT: 4 74 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8392 (mp) REVERT: 4 132 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7147 (tt0) REVERT: 4 163 ILE cc_start: 0.7640 (mt) cc_final: 0.7351 (mp) REVERT: 4 214 ASP cc_start: 0.8304 (t0) cc_final: 0.8056 (t0) REVERT: 4 225 ILE cc_start: 0.8479 (mt) cc_final: 0.8215 (mm) REVERT: 6 22 LYS cc_start: 0.7949 (mtpt) cc_final: 0.7104 (mmtt) REVERT: 6 147 ILE cc_start: 0.8379 (OUTLIER) cc_final: 0.7990 (pt) REVERT: 8 33 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8611 (pp) REVERT: 8 98 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7895 (mt0) REVERT: 8 149 ASP cc_start: 0.8148 (OUTLIER) cc_final: 0.7506 (m-30) REVERT: 8 174 ASN cc_start: 0.7917 (m110) cc_final: 0.7603 (m110) REVERT: 8 205 VAL cc_start: 0.7726 (m) cc_final: 0.7367 (p) REVERT: 8 216 ASN cc_start: 0.8160 (m-40) cc_final: 0.7920 (t0) REVERT: F 605 LEU cc_start: 0.5424 (OUTLIER) cc_final: 0.5012 (mm) REVERT: F 607 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.7399 (tt0) REVERT: I 45 ASN cc_start: 0.7672 (t0) cc_final: 0.7148 (t0) REVERT: J 395 MET cc_start: 0.7719 (mmm) cc_final: 0.7506 (mmm) REVERT: J 430 ASN cc_start: 0.7990 (t0) cc_final: 0.7677 (t0) REVERT: J 432 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7571 (mp0) REVERT: K 13 MET cc_start: 0.6329 (mmp) cc_final: 0.5069 (tmm) REVERT: K 14 ARG cc_start: 0.5934 (tpm170) cc_final: 0.5311 (tpm170) REVERT: K 18 GLU cc_start: 0.6665 (tp30) cc_final: 0.6030 (tp30) REVERT: K 26 ARG cc_start: 0.6536 (ttm110) cc_final: 0.6182 (ppt90) REVERT: K 216 ASN cc_start: 0.7984 (t0) cc_final: 0.7547 (m-40) REVERT: L 432 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7312 (mp0) REVERT: M 363 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8751 (mp) REVERT: M 364 GLU cc_start: 0.7605 (tt0) cc_final: 0.7270 (tt0) REVERT: M 399 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8856 (tt) REVERT: M 401 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8358 (mp) REVERT: N 395 MET cc_start: 0.7224 (mmm) cc_final: 0.6922 (mmm) REVERT: N 432 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7339 (mp0) REVERT: O 26 ARG cc_start: 0.7453 (ttm110) cc_final: 0.6380 (ppt170) REVERT: O 67 LYS cc_start: 0.7935 (OUTLIER) cc_final: 0.7542 (tttt) REVERT: O 99 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8371 (mt) REVERT: O 105 GLN cc_start: 0.7025 (tp40) cc_final: 0.6578 (tp-100) REVERT: P 430 ASN cc_start: 0.7678 (t0) cc_final: 0.7302 (t0) REVERT: P 432 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.6894 (mp0) REVERT: R 434 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6853 (tp30) REVERT: R 509 ARG cc_start: 0.7814 (OUTLIER) cc_final: 0.7463 (ttm170) REVERT: S 401 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8469 (mt) REVERT: S 444 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8481 (mp) REVERT: T 52 LYS cc_start: 0.7955 (mtpt) cc_final: 0.7519 (mtmm) REVERT: V 345 ILE cc_start: 0.9188 (OUTLIER) cc_final: 0.8890 (mm) REVERT: W 401 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8514 (mp) REVERT: Y 324 ASN cc_start: 0.8045 (m-40) cc_final: 0.7792 (t0) REVERT: Z 52 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7771 (mtpp) REVERT: b 339 ASP cc_start: 0.7689 (OUTLIER) cc_final: 0.7393 (m-30) REVERT: b 401 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8535 (mp) REVERT: d 51 GLN cc_start: 0.7060 (OUTLIER) cc_final: 0.6509 (mt0) REVERT: d 167 LEU cc_start: 0.7878 (mt) cc_final: 0.7625 (mt) REVERT: f 22 LYS cc_start: 0.7739 (ttpp) cc_final: 0.7262 (tmtt) REVERT: f 214 ASP cc_start: 0.8225 (t0) cc_final: 0.7988 (t0) outliers start: 170 outliers final: 86 residues processed: 696 average time/residue: 1.5640 time to fit residues: 1351.4395 Evaluate side-chains 692 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 577 time to evaluate : 5.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 70 GLU Chi-restraints excluded: chain 0 residue 72 ASP Chi-restraints excluded: chain 0 residue 74 LEU Chi-restraints excluded: chain 0 residue 80 GLN Chi-restraints excluded: chain 0 residue 146 SER Chi-restraints excluded: chain 2 residue 29 SER Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 147 ILE Chi-restraints excluded: chain 2 residue 179 ASP Chi-restraints excluded: chain 2 residue 226 THR Chi-restraints excluded: chain 2 residue 228 SER Chi-restraints excluded: chain 4 residue 74 LEU Chi-restraints excluded: chain 4 residue 102 VAL Chi-restraints excluded: chain 4 residue 132 GLU Chi-restraints excluded: chain 4 residue 147 ILE Chi-restraints excluded: chain 4 residue 170 SER Chi-restraints excluded: chain 6 residue 99 LEU Chi-restraints excluded: chain 6 residue 112 THR Chi-restraints excluded: chain 6 residue 147 ILE Chi-restraints excluded: chain 6 residue 149 ASP Chi-restraints excluded: chain 8 residue 33 LEU Chi-restraints excluded: chain 8 residue 51 GLN Chi-restraints excluded: chain 8 residue 98 GLN Chi-restraints excluded: chain 8 residue 149 ASP Chi-restraints excluded: chain 8 residue 233 LEU Chi-restraints excluded: chain F residue 605 LEU Chi-restraints excluded: chain F residue 607 GLN Chi-restraints excluded: chain H residue 396 GLN Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain I residue 174 ASN Chi-restraints excluded: chain J residue 432 GLU Chi-restraints excluded: chain K residue 67 LYS Chi-restraints excluded: chain K residue 73 ASN Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 143 TYR Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain L residue 325 MET Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain L residue 432 GLU Chi-restraints excluded: chain M residue 330 ASP Chi-restraints excluded: chain M residue 363 LEU Chi-restraints excluded: chain M residue 399 LEU Chi-restraints excluded: chain M residue 401 LEU Chi-restraints excluded: chain N residue 345 ILE Chi-restraints excluded: chain N residue 361 VAL Chi-restraints excluded: chain N residue 432 GLU Chi-restraints excluded: chain N residue 444 LEU Chi-restraints excluded: chain N residue 504 ASP Chi-restraints excluded: chain O residue 31 VAL Chi-restraints excluded: chain O residue 40 LEU Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain O residue 67 LYS Chi-restraints excluded: chain O residue 99 LEU Chi-restraints excluded: chain O residue 113 GLU Chi-restraints excluded: chain O residue 144 ASP Chi-restraints excluded: chain O residue 176 SER Chi-restraints excluded: chain P residue 395 MET Chi-restraints excluded: chain P residue 409 ILE Chi-restraints excluded: chain P residue 432 GLU Chi-restraints excluded: chain Q residue 15 GLU Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain R residue 396 GLN Chi-restraints excluded: chain R residue 401 LEU Chi-restraints excluded: chain R residue 434 GLU Chi-restraints excluded: chain R residue 476 ASP Chi-restraints excluded: chain R residue 509 ARG Chi-restraints excluded: chain S residue 325 MET Chi-restraints excluded: chain S residue 330 ASP Chi-restraints excluded: chain S residue 401 LEU Chi-restraints excluded: chain S residue 444 LEU Chi-restraints excluded: chain T residue 26 ARG Chi-restraints excluded: chain T residue 49 SER Chi-restraints excluded: chain T residue 133 THR Chi-restraints excluded: chain T residue 147 ILE Chi-restraints excluded: chain T residue 178 THR Chi-restraints excluded: chain T residue 207 SER Chi-restraints excluded: chain U residue 313 VAL Chi-restraints excluded: chain U residue 348 THR Chi-restraints excluded: chain U residue 401 LEU Chi-restraints excluded: chain U residue 520 SER Chi-restraints excluded: chain V residue 338 ASP Chi-restraints excluded: chain V residue 345 ILE Chi-restraints excluded: chain V residue 399 LEU Chi-restraints excluded: chain V residue 504 ASP Chi-restraints excluded: chain W residue 330 ASP Chi-restraints excluded: chain W residue 401 LEU Chi-restraints excluded: chain W residue 412 SER Chi-restraints excluded: chain W residue 416 SER Chi-restraints excluded: chain W residue 522 SER Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 49 SER Chi-restraints excluded: chain X residue 146 SER Chi-restraints excluded: chain X residue 228 SER Chi-restraints excluded: chain Y residue 391 LEU Chi-restraints excluded: chain Y residue 409 ILE Chi-restraints excluded: chain Y residue 503 VAL Chi-restraints excluded: chain Z residue 52 LYS Chi-restraints excluded: chain Z residue 74 LEU Chi-restraints excluded: chain Z residue 83 ASP Chi-restraints excluded: chain Z residue 99 LEU Chi-restraints excluded: chain Z residue 146 SER Chi-restraints excluded: chain Z residue 147 ILE Chi-restraints excluded: chain Z residue 178 THR Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain b residue 339 ASP Chi-restraints excluded: chain b residue 355 PHE Chi-restraints excluded: chain b residue 401 LEU Chi-restraints excluded: chain d residue 51 GLN Chi-restraints excluded: chain d residue 160 THR Chi-restraints excluded: chain f residue 133 THR Chi-restraints excluded: chain f residue 146 SER Chi-restraints excluded: chain f residue 149 ASP Chi-restraints excluded: chain f residue 228 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 360 optimal weight: 2.9990 chunk 232 optimal weight: 0.7980 chunk 347 optimal weight: 6.9990 chunk 175 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 370 optimal weight: 8.9990 chunk 396 optimal weight: 8.9990 chunk 287 optimal weight: 0.9980 chunk 54 optimal weight: 0.4980 chunk 457 optimal weight: 5.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 69 ASN 0 73 ASN 0 174 ASN 1 607 GLN 2 105 GLN 4 80 GLN J 396 GLN K 114 GLN L 410 HIS O 80 GLN Q 45 ASN Q 165 ASN U 322 GLN U 396 GLN V 322 GLN ** X 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 80 GLN Z 98 GLN Z 101 ASN a 322 GLN ** d 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 216 ASN f 69 ASN f 80 GLN f 165 ASN f 174 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 47302 Z= 0.185 Angle : 0.497 9.069 64013 Z= 0.263 Chirality : 0.043 0.166 7270 Planarity : 0.004 0.047 8452 Dihedral : 3.844 32.049 6904 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.18 % Allowed : 17.48 % Favored : 79.34 % 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: 2.33 (0.11), residues: 6089 helix: 3.25 (0.10), residues: 2574 sheet: 0.91 (0.14), residues: 1486 loop : -0.26 (0.14), residues: 2029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP V 429 HIS 0.003 0.001 HIS K 152 PHE 0.039 0.002 PHE K 111 TYR 0.022 0.001 TYR I 143 ARG 0.013 0.000 ARG X 21 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12178 Ramachandran restraints generated. 6089 Oldfield, 0 Emsley, 6089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12178 Ramachandran restraints generated. 6089 Oldfield, 0 Emsley, 6089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 590 time to evaluate : 4.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 13 MET cc_start: 0.6857 (ttm) cc_final: 0.6213 (tmm) REVERT: 0 21 ARG cc_start: 0.6982 (mtm-85) cc_final: 0.6696 (mtm-85) REVERT: 0 44 GLU cc_start: 0.6490 (tt0) cc_final: 0.5775 (tm-30) REVERT: 0 54 SER cc_start: 0.8596 (t) cc_final: 0.8347 (m) REVERT: 0 74 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8737 (mt) REVERT: 0 80 GLN cc_start: 0.7908 (OUTLIER) cc_final: 0.7610 (tp40) REVERT: 0 156 MET cc_start: 0.7718 (OUTLIER) cc_final: 0.7491 (mtt) REVERT: 1 609 LEU cc_start: 0.6655 (OUTLIER) cc_final: 0.6211 (mp) REVERT: 2 183 ILE cc_start: 0.8202 (mp) cc_final: 0.8001 (mt) REVERT: 4 74 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8364 (mp) REVERT: 4 132 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7175 (tt0) REVERT: 4 163 ILE cc_start: 0.7649 (mt) cc_final: 0.7360 (mp) REVERT: 4 214 ASP cc_start: 0.8222 (t0) cc_final: 0.7991 (t0) REVERT: 4 225 ILE cc_start: 0.8444 (mt) cc_final: 0.8183 (mm) REVERT: 6 22 LYS cc_start: 0.7893 (mtpt) cc_final: 0.7048 (mmtt) REVERT: 6 147 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.7980 (pt) REVERT: 8 22 LYS cc_start: 0.7594 (mtmm) cc_final: 0.7350 (pttm) REVERT: 8 33 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8556 (pp) REVERT: 8 168 LYS cc_start: 0.7441 (ttmp) cc_final: 0.7019 (ttmm) REVERT: 8 205 VAL cc_start: 0.7816 (m) cc_final: 0.7462 (p) REVERT: 8 216 ASN cc_start: 0.8176 (m-40) cc_final: 0.7932 (t0) REVERT: F 605 LEU cc_start: 0.5389 (OUTLIER) cc_final: 0.5012 (mm) REVERT: F 607 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.7364 (tt0) REVERT: I 45 ASN cc_start: 0.7495 (t0) cc_final: 0.7004 (t0) REVERT: I 111 PHE cc_start: 0.7699 (t80) cc_final: 0.7155 (t80) REVERT: I 168 LYS cc_start: 0.7015 (mtpt) cc_final: 0.6583 (mttt) REVERT: J 395 MET cc_start: 0.7696 (mmm) cc_final: 0.7493 (mmm) REVERT: J 430 ASN cc_start: 0.7965 (t0) cc_final: 0.7680 (t0) REVERT: J 432 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7534 (mp0) REVERT: K 13 MET cc_start: 0.6333 (mmp) cc_final: 0.5002 (tmm) REVERT: K 14 ARG cc_start: 0.5703 (tpm170) cc_final: 0.5126 (tpm170) REVERT: K 18 GLU cc_start: 0.6777 (tp30) cc_final: 0.6052 (tp30) REVERT: K 26 ARG cc_start: 0.6610 (ttm110) cc_final: 0.6197 (ppt90) REVERT: K 216 ASN cc_start: 0.7938 (t0) cc_final: 0.7536 (m-40) REVERT: L 432 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7367 (mp0) REVERT: M 363 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8699 (mp) REVERT: M 364 GLU cc_start: 0.7556 (tt0) cc_final: 0.7232 (tt0) REVERT: M 399 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8819 (tt) REVERT: M 401 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8366 (mp) REVERT: N 395 MET cc_start: 0.7193 (mmm) cc_final: 0.6925 (mmm) REVERT: N 432 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7352 (mp0) REVERT: O 26 ARG cc_start: 0.7407 (ttm110) cc_final: 0.6305 (ppt170) REVERT: O 67 LYS cc_start: 0.7783 (OUTLIER) cc_final: 0.7498 (tttt) REVERT: O 99 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8410 (mt) REVERT: O 105 GLN cc_start: 0.7014 (tp40) cc_final: 0.6590 (tp-100) REVERT: O 113 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6651 (tm-30) REVERT: O 116 LYS cc_start: 0.6669 (tttm) cc_final: 0.6304 (tttm) REVERT: P 424 ASP cc_start: 0.8065 (p0) cc_final: 0.7649 (p0) REVERT: P 430 ASN cc_start: 0.7650 (t0) cc_final: 0.7282 (t0) REVERT: P 432 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.6900 (mp0) REVERT: R 434 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.6821 (tp30) REVERT: R 509 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.7422 (ttm170) REVERT: S 401 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8474 (mt) REVERT: S 444 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8465 (mp) REVERT: T 52 LYS cc_start: 0.7929 (mtpt) cc_final: 0.7523 (mtmm) REVERT: T 209 GLU cc_start: 0.6869 (tt0) cc_final: 0.6383 (tt0) REVERT: V 345 ILE cc_start: 0.9154 (OUTLIER) cc_final: 0.8842 (mm) REVERT: W 401 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8469 (mp) REVERT: X 21 ARG cc_start: 0.6500 (ttp-110) cc_final: 0.5947 (ttp80) REVERT: Y 324 ASN cc_start: 0.8001 (m-40) cc_final: 0.7739 (t0) REVERT: Z 52 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7779 (mtpp) REVERT: b 339 ASP cc_start: 0.7691 (OUTLIER) cc_final: 0.7385 (m-30) REVERT: b 401 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8518 (mp) REVERT: d 51 GLN cc_start: 0.7047 (OUTLIER) cc_final: 0.6462 (mt0) REVERT: d 167 LEU cc_start: 0.7864 (mt) cc_final: 0.7602 (mt) REVERT: f 22 LYS cc_start: 0.7779 (ttpp) cc_final: 0.7329 (tmtt) REVERT: f 214 ASP cc_start: 0.8126 (t0) cc_final: 0.7915 (t0) outliers start: 148 outliers final: 87 residues processed: 685 average time/residue: 1.5551 time to fit residues: 1336.0263 Evaluate side-chains 697 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 580 time to evaluate : 5.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 70 GLU Chi-restraints excluded: chain 0 residue 72 ASP Chi-restraints excluded: chain 0 residue 74 LEU Chi-restraints excluded: chain 0 residue 80 GLN Chi-restraints excluded: chain 0 residue 146 SER Chi-restraints excluded: chain 0 residue 156 MET Chi-restraints excluded: chain 1 residue 609 LEU Chi-restraints excluded: chain 2 residue 29 SER Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 147 ILE Chi-restraints excluded: chain 2 residue 179 ASP Chi-restraints excluded: chain 2 residue 226 THR Chi-restraints excluded: chain 4 residue 74 LEU Chi-restraints excluded: chain 4 residue 102 VAL Chi-restraints excluded: chain 4 residue 132 GLU Chi-restraints excluded: chain 4 residue 147 ILE Chi-restraints excluded: chain 4 residue 170 SER Chi-restraints excluded: chain 4 residue 176 SER Chi-restraints excluded: chain 6 residue 99 LEU Chi-restraints excluded: chain 6 residue 112 THR Chi-restraints excluded: chain 6 residue 147 ILE Chi-restraints excluded: chain 6 residue 149 ASP Chi-restraints excluded: chain 8 residue 33 LEU Chi-restraints excluded: chain 8 residue 51 GLN Chi-restraints excluded: chain 8 residue 80 GLN Chi-restraints excluded: chain 8 residue 99 LEU Chi-restraints excluded: chain 8 residue 233 LEU Chi-restraints excluded: chain F residue 605 LEU Chi-restraints excluded: chain F residue 607 GLN Chi-restraints excluded: chain H residue 395 MET Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain I residue 174 ASN Chi-restraints excluded: chain J residue 432 GLU Chi-restraints excluded: chain K residue 67 LYS Chi-restraints excluded: chain K residue 73 ASN Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 143 TYR Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain L residue 325 MET Chi-restraints excluded: chain L residue 364 GLU Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain L residue 430 ASN Chi-restraints excluded: chain L residue 432 GLU Chi-restraints excluded: chain M residue 330 ASP Chi-restraints excluded: chain M residue 363 LEU Chi-restraints excluded: chain M residue 399 LEU Chi-restraints excluded: chain M residue 401 LEU Chi-restraints excluded: chain M residue 461 ASP Chi-restraints excluded: chain N residue 345 ILE Chi-restraints excluded: chain N residue 432 GLU Chi-restraints excluded: chain N residue 444 LEU Chi-restraints excluded: chain O residue 31 VAL Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain O residue 67 LYS Chi-restraints excluded: chain O residue 99 LEU Chi-restraints excluded: chain O residue 113 GLU Chi-restraints excluded: chain O residue 144 ASP Chi-restraints excluded: chain O residue 146 SER Chi-restraints excluded: chain O residue 176 SER Chi-restraints excluded: chain P residue 395 MET Chi-restraints excluded: chain P residue 409 ILE Chi-restraints excluded: chain P residue 432 GLU Chi-restraints excluded: chain Q residue 179 ASP Chi-restraints excluded: chain R residue 401 LEU Chi-restraints excluded: chain R residue 434 GLU Chi-restraints excluded: chain R residue 476 ASP Chi-restraints excluded: chain R residue 509 ARG Chi-restraints excluded: chain S residue 325 MET Chi-restraints excluded: chain S residue 330 ASP Chi-restraints excluded: chain S residue 401 LEU Chi-restraints excluded: chain S residue 444 LEU Chi-restraints excluded: chain T residue 26 ARG Chi-restraints excluded: chain T residue 49 SER Chi-restraints excluded: chain T residue 147 ILE Chi-restraints excluded: chain T residue 178 THR Chi-restraints excluded: chain T residue 207 SER Chi-restraints excluded: chain U residue 313 VAL Chi-restraints excluded: chain U residue 348 THR Chi-restraints excluded: chain U residue 401 LEU Chi-restraints excluded: chain U residue 520 SER Chi-restraints excluded: chain V residue 345 ILE Chi-restraints excluded: chain V residue 399 LEU Chi-restraints excluded: chain V residue 504 ASP Chi-restraints excluded: chain W residue 330 ASP Chi-restraints excluded: chain W residue 401 LEU Chi-restraints excluded: chain W residue 412 SER Chi-restraints excluded: chain W residue 416 SER Chi-restraints excluded: chain W residue 522 SER Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 49 SER Chi-restraints excluded: chain X residue 146 SER Chi-restraints excluded: chain X residue 228 SER Chi-restraints excluded: chain Y residue 391 LEU Chi-restraints excluded: chain Y residue 409 ILE Chi-restraints excluded: chain Y residue 503 VAL Chi-restraints excluded: chain Z residue 52 LYS Chi-restraints excluded: chain Z residue 74 LEU Chi-restraints excluded: chain Z residue 83 ASP Chi-restraints excluded: chain Z residue 99 LEU Chi-restraints excluded: chain Z residue 146 SER Chi-restraints excluded: chain Z residue 147 ILE Chi-restraints excluded: chain Z residue 178 THR Chi-restraints excluded: chain a residue 307 LYS Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain b residue 339 ASP Chi-restraints excluded: chain b residue 355 PHE Chi-restraints excluded: chain b residue 401 LEU Chi-restraints excluded: chain d residue 51 GLN Chi-restraints excluded: chain d residue 149 ASP Chi-restraints excluded: chain d residue 160 THR Chi-restraints excluded: chain f residue 146 SER Chi-restraints excluded: chain f residue 149 ASP Chi-restraints excluded: chain f residue 228 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 529 optimal weight: 0.8980 chunk 557 optimal weight: 4.9990 chunk 508 optimal weight: 10.0000 chunk 542 optimal weight: 6.9990 chunk 326 optimal weight: 4.9990 chunk 236 optimal weight: 3.9990 chunk 425 optimal weight: 1.9990 chunk 166 optimal weight: 6.9990 chunk 490 optimal weight: 0.8980 chunk 513 optimal weight: 0.7980 chunk 540 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 69 ASN 0 73 ASN 0 174 ASN 1 607 GLN 2 105 GLN 4 45 ASN 4 80 GLN J 396 GLN O 80 GLN Q 45 ASN U 322 GLN U 396 GLN V 322 GLN X 45 ASN X 114 GLN Z 80 GLN Z 101 ASN a 322 GLN ** d 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 216 ASN f 69 ASN f 80 GLN f 174 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 47302 Z= 0.161 Angle : 0.486 10.036 64013 Z= 0.256 Chirality : 0.042 0.164 7270 Planarity : 0.003 0.054 8452 Dihedral : 3.741 31.255 6904 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.84 % Allowed : 18.08 % Favored : 79.08 % 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: 2.43 (0.11), residues: 6089 helix: 3.39 (0.10), residues: 2562 sheet: 0.94 (0.14), residues: 1468 loop : -0.24 (0.14), residues: 2059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP V 429 HIS 0.003 0.001 HIS K 152 PHE 0.037 0.002 PHE K 111 TYR 0.022 0.001 TYR I 143 ARG 0.012 0.000 ARG X 21 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12178 Ramachandran restraints generated. 6089 Oldfield, 0 Emsley, 6089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12178 Ramachandran restraints generated. 6089 Oldfield, 0 Emsley, 6089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 731 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 599 time to evaluate : 5.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 13 MET cc_start: 0.6853 (ttm) cc_final: 0.6212 (tmm) REVERT: 0 21 ARG cc_start: 0.6881 (mtm-85) cc_final: 0.6597 (mtm-85) REVERT: 0 44 GLU cc_start: 0.6478 (tt0) cc_final: 0.5767 (tm-30) REVERT: 0 54 SER cc_start: 0.8591 (t) cc_final: 0.8341 (m) REVERT: 0 74 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8709 (mt) REVERT: 0 80 GLN cc_start: 0.7901 (OUTLIER) cc_final: 0.7605 (tp40) REVERT: 1 609 LEU cc_start: 0.6656 (OUTLIER) cc_final: 0.6239 (mp) REVERT: 4 74 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8366 (mp) REVERT: 4 132 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.7151 (tt0) REVERT: 4 163 ILE cc_start: 0.7644 (mt) cc_final: 0.7360 (mp) REVERT: 4 214 ASP cc_start: 0.8145 (t0) cc_final: 0.7923 (t0) REVERT: 4 225 ILE cc_start: 0.8438 (mt) cc_final: 0.8178 (mm) REVERT: 6 22 LYS cc_start: 0.7891 (mtpt) cc_final: 0.7049 (mmtt) REVERT: 6 147 ILE cc_start: 0.8360 (OUTLIER) cc_final: 0.7933 (pt) REVERT: 8 22 LYS cc_start: 0.7423 (mtmm) cc_final: 0.7113 (pttm) REVERT: 8 33 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8571 (pp) REVERT: 8 149 ASP cc_start: 0.8140 (OUTLIER) cc_final: 0.7488 (m-30) REVERT: 8 156 MET cc_start: 0.8209 (mtm) cc_final: 0.7854 (mtm) REVERT: 8 168 LYS cc_start: 0.7520 (ttmp) cc_final: 0.7128 (ttmm) REVERT: 8 205 VAL cc_start: 0.7837 (m) cc_final: 0.7475 (p) REVERT: 8 216 ASN cc_start: 0.8184 (m-40) cc_final: 0.7932 (t0) REVERT: F 605 LEU cc_start: 0.5383 (OUTLIER) cc_final: 0.5024 (mm) REVERT: F 607 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7330 (tt0) REVERT: I 45 ASN cc_start: 0.7461 (t0) cc_final: 0.6988 (t0) REVERT: I 168 LYS cc_start: 0.7126 (mtpt) cc_final: 0.6664 (mttt) REVERT: J 430 ASN cc_start: 0.7953 (t0) cc_final: 0.7680 (t0) REVERT: J 432 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7536 (mp0) REVERT: K 13 MET cc_start: 0.6392 (mmp) cc_final: 0.5083 (tmm) REVERT: K 14 ARG cc_start: 0.5697 (tpm170) cc_final: 0.5126 (tpm170) REVERT: K 18 GLU cc_start: 0.6787 (tp30) cc_final: 0.6105 (tp30) REVERT: K 26 ARG cc_start: 0.6560 (ttm110) cc_final: 0.6203 (ppt90) REVERT: K 216 ASN cc_start: 0.7978 (t0) cc_final: 0.7558 (m-40) REVERT: L 432 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7390 (mp0) REVERT: M 363 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8701 (mp) REVERT: M 364 GLU cc_start: 0.7534 (tt0) cc_final: 0.7218 (tt0) REVERT: M 399 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8810 (tt) REVERT: M 401 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8362 (mp) REVERT: N 395 MET cc_start: 0.7252 (mmm) cc_final: 0.6959 (mmm) REVERT: N 432 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7364 (mp0) REVERT: O 26 ARG cc_start: 0.7409 (ttm110) cc_final: 0.6419 (ppt170) REVERT: O 67 LYS cc_start: 0.7700 (OUTLIER) cc_final: 0.7399 (tttt) REVERT: O 99 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8405 (mt) REVERT: O 105 GLN cc_start: 0.7000 (tp40) cc_final: 0.6582 (tp-100) REVERT: O 113 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6691 (tm-30) REVERT: O 116 LYS cc_start: 0.6676 (tttm) cc_final: 0.6307 (tttm) REVERT: P 424 ASP cc_start: 0.8058 (p0) cc_final: 0.7659 (p0) REVERT: P 430 ASN cc_start: 0.7628 (t0) cc_final: 0.7272 (t0) REVERT: P 432 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.6840 (mp0) REVERT: Q 21 ARG cc_start: 0.6931 (mtm110) cc_final: 0.6625 (ptm160) REVERT: R 509 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.7401 (ttm170) REVERT: S 401 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8487 (mt) REVERT: S 444 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8451 (mp) REVERT: T 52 LYS cc_start: 0.7893 (mtpt) cc_final: 0.7481 (mtmm) REVERT: T 209 GLU cc_start: 0.6872 (tt0) cc_final: 0.6291 (tt0) REVERT: V 345 ILE cc_start: 0.9141 (OUTLIER) cc_final: 0.8831 (mm) REVERT: V 509 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.7221 (ttp-170) REVERT: W 401 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8486 (mp) REVERT: X 21 ARG cc_start: 0.6498 (ttp-110) cc_final: 0.5959 (ttp80) REVERT: Y 324 ASN cc_start: 0.7866 (m-40) cc_final: 0.7647 (t0) REVERT: Z 52 LYS cc_start: 0.8008 (OUTLIER) cc_final: 0.7786 (mtpp) REVERT: b 339 ASP cc_start: 0.7678 (OUTLIER) cc_final: 0.7377 (m-30) REVERT: b 401 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8518 (mp) REVERT: d 51 GLN cc_start: 0.7289 (OUTLIER) cc_final: 0.6651 (mt0) REVERT: d 167 LEU cc_start: 0.7849 (mt) cc_final: 0.7594 (mt) REVERT: f 22 LYS cc_start: 0.7748 (ttpp) cc_final: 0.7380 (tmtt) REVERT: f 214 ASP cc_start: 0.8080 (t0) cc_final: 0.7867 (t0) outliers start: 132 outliers final: 79 residues processed: 682 average time/residue: 1.5074 time to fit residues: 1276.9661 Evaluate side-chains 694 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 585 time to evaluate : 5.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 70 GLU Chi-restraints excluded: chain 0 residue 72 ASP Chi-restraints excluded: chain 0 residue 74 LEU Chi-restraints excluded: chain 0 residue 80 GLN Chi-restraints excluded: chain 0 residue 146 SER Chi-restraints excluded: chain 1 residue 609 LEU Chi-restraints excluded: chain 2 residue 29 SER Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 73 ASN Chi-restraints excluded: chain 2 residue 147 ILE Chi-restraints excluded: chain 2 residue 179 ASP Chi-restraints excluded: chain 2 residue 226 THR Chi-restraints excluded: chain 2 residue 228 SER Chi-restraints excluded: chain 4 residue 74 LEU Chi-restraints excluded: chain 4 residue 102 VAL Chi-restraints excluded: chain 4 residue 132 GLU Chi-restraints excluded: chain 4 residue 147 ILE Chi-restraints excluded: chain 4 residue 170 SER Chi-restraints excluded: chain 4 residue 176 SER Chi-restraints excluded: chain 6 residue 99 LEU Chi-restraints excluded: chain 6 residue 112 THR Chi-restraints excluded: chain 6 residue 147 ILE Chi-restraints excluded: chain 6 residue 149 ASP Chi-restraints excluded: chain 8 residue 33 LEU Chi-restraints excluded: chain 8 residue 51 GLN Chi-restraints excluded: chain 8 residue 80 GLN Chi-restraints excluded: chain 8 residue 99 LEU Chi-restraints excluded: chain 8 residue 149 ASP Chi-restraints excluded: chain 8 residue 233 LEU Chi-restraints excluded: chain F residue 605 LEU Chi-restraints excluded: chain F residue 607 GLN Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain I residue 174 ASN Chi-restraints excluded: chain J residue 432 GLU Chi-restraints excluded: chain K residue 67 LYS Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 143 TYR Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain L residue 364 GLU Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain L residue 430 ASN Chi-restraints excluded: chain L residue 432 GLU Chi-restraints excluded: chain M residue 330 ASP Chi-restraints excluded: chain M residue 363 LEU Chi-restraints excluded: chain M residue 399 LEU Chi-restraints excluded: chain M residue 401 LEU Chi-restraints excluded: chain M residue 461 ASP Chi-restraints excluded: chain N residue 345 ILE Chi-restraints excluded: chain N residue 432 GLU Chi-restraints excluded: chain N residue 444 LEU Chi-restraints excluded: chain O residue 31 VAL Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain O residue 67 LYS Chi-restraints excluded: chain O residue 99 LEU Chi-restraints excluded: chain O residue 113 GLU Chi-restraints excluded: chain O residue 144 ASP Chi-restraints excluded: chain O residue 146 SER Chi-restraints excluded: chain O residue 176 SER Chi-restraints excluded: chain P residue 395 MET Chi-restraints excluded: chain P residue 409 ILE Chi-restraints excluded: chain P residue 432 GLU Chi-restraints excluded: chain R residue 401 LEU Chi-restraints excluded: chain R residue 476 ASP Chi-restraints excluded: chain R residue 509 ARG Chi-restraints excluded: chain S residue 330 ASP Chi-restraints excluded: chain S residue 401 LEU Chi-restraints excluded: chain S residue 444 LEU Chi-restraints excluded: chain T residue 26 ARG Chi-restraints excluded: chain T residue 49 SER Chi-restraints excluded: chain T residue 147 ILE Chi-restraints excluded: chain T residue 178 THR Chi-restraints excluded: chain T residue 207 SER Chi-restraints excluded: chain U residue 313 VAL Chi-restraints excluded: chain U residue 348 THR Chi-restraints excluded: chain U residue 401 LEU Chi-restraints excluded: chain V residue 345 ILE Chi-restraints excluded: chain V residue 504 ASP Chi-restraints excluded: chain V residue 509 ARG Chi-restraints excluded: chain W residue 330 ASP Chi-restraints excluded: chain W residue 401 LEU Chi-restraints excluded: chain W residue 412 SER Chi-restraints excluded: chain W residue 416 SER Chi-restraints excluded: chain W residue 522 SER Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 49 SER Chi-restraints excluded: chain X residue 146 SER Chi-restraints excluded: chain X residue 228 SER Chi-restraints excluded: chain Y residue 391 LEU Chi-restraints excluded: chain Y residue 409 ILE Chi-restraints excluded: chain Y residue 503 VAL Chi-restraints excluded: chain Z residue 52 LYS Chi-restraints excluded: chain Z residue 74 LEU Chi-restraints excluded: chain Z residue 83 ASP Chi-restraints excluded: chain Z residue 99 LEU Chi-restraints excluded: chain Z residue 147 ILE Chi-restraints excluded: chain Z residue 178 THR Chi-restraints excluded: chain a residue 307 LYS Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain b residue 339 ASP Chi-restraints excluded: chain b residue 355 PHE Chi-restraints excluded: chain b residue 401 LEU Chi-restraints excluded: chain d residue 51 GLN Chi-restraints excluded: chain d residue 149 ASP Chi-restraints excluded: chain d residue 160 THR Chi-restraints excluded: chain f residue 133 THR Chi-restraints excluded: chain f residue 146 SER Chi-restraints excluded: chain f residue 149 ASP Chi-restraints excluded: chain f residue 228 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 356 optimal weight: 8.9990 chunk 573 optimal weight: 9.9990 chunk 350 optimal weight: 0.9990 chunk 272 optimal weight: 8.9990 chunk 398 optimal weight: 3.9990 chunk 601 optimal weight: 10.0000 chunk 553 optimal weight: 1.9990 chunk 479 optimal weight: 0.6980 chunk 49 optimal weight: 5.9990 chunk 370 optimal weight: 9.9990 chunk 293 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 69 ASN 0 73 ASN 0 174 ASN 1 607 GLN 2 105 GLN 4 45 ASN 4 80 GLN J 396 GLN L 410 HIS O 80 GLN Q 45 ASN U 322 GLN U 396 GLN V 322 GLN ** Y 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 80 GLN Z 101 ASN a 322 GLN ** d 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 216 ASN f 69 ASN f 80 GLN f 174 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 47302 Z= 0.205 Angle : 0.510 11.154 64013 Z= 0.268 Chirality : 0.043 0.170 7270 Planarity : 0.004 0.052 8452 Dihedral : 3.827 29.419 6904 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.75 % Allowed : 18.40 % Favored : 78.84 % 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: 2.34 (0.11), residues: 6089 helix: 3.26 (0.10), residues: 2577 sheet: 0.91 (0.14), residues: 1468 loop : -0.25 (0.14), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP V 429 HIS 0.003 0.001 HIS S 365 PHE 0.031 0.002 PHE 6 71 TYR 0.021 0.001 TYR I 143 ARG 0.011 0.000 ARG X 21 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12178 Ramachandran restraints generated. 6089 Oldfield, 0 Emsley, 6089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12178 Ramachandran restraints generated. 6089 Oldfield, 0 Emsley, 6089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 590 time to evaluate : 6.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 13 MET cc_start: 0.6873 (ttm) cc_final: 0.6227 (tmm) REVERT: 0 21 ARG cc_start: 0.6872 (mtm-85) cc_final: 0.6583 (mtm-85) REVERT: 0 44 GLU cc_start: 0.6487 (tt0) cc_final: 0.5773 (tm-30) REVERT: 0 54 SER cc_start: 0.8599 (t) cc_final: 0.8344 (m) REVERT: 0 74 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8715 (mt) REVERT: 0 80 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.7597 (tp40) REVERT: 1 609 LEU cc_start: 0.6643 (OUTLIER) cc_final: 0.6209 (mp) REVERT: 4 74 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8367 (mp) REVERT: 4 132 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.7186 (tt0) REVERT: 4 163 ILE cc_start: 0.7662 (mt) cc_final: 0.7373 (mp) REVERT: 4 214 ASP cc_start: 0.8242 (t0) cc_final: 0.8011 (t0) REVERT: 4 225 ILE cc_start: 0.8447 (mt) cc_final: 0.8186 (mm) REVERT: 6 22 LYS cc_start: 0.7887 (mtpt) cc_final: 0.7079 (mmtt) REVERT: 6 147 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.7937 (pt) REVERT: 8 22 LYS cc_start: 0.7431 (mtmm) cc_final: 0.7132 (pttm) REVERT: 8 33 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8571 (pp) REVERT: 8 149 ASP cc_start: 0.8148 (OUTLIER) cc_final: 0.7496 (m-30) REVERT: 8 168 LYS cc_start: 0.7486 (ttmp) cc_final: 0.7078 (ttmm) REVERT: 8 205 VAL cc_start: 0.7869 (m) cc_final: 0.7510 (p) REVERT: 8 216 ASN cc_start: 0.8182 (m-40) cc_final: 0.7934 (t0) REVERT: F 605 LEU cc_start: 0.5425 (OUTLIER) cc_final: 0.5035 (mm) REVERT: F 607 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7319 (tt0) REVERT: I 45 ASN cc_start: 0.7552 (t0) cc_final: 0.7070 (t0) REVERT: J 430 ASN cc_start: 0.7966 (t0) cc_final: 0.7689 (t0) REVERT: J 432 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7518 (mp0) REVERT: K 13 MET cc_start: 0.6380 (mmp) cc_final: 0.5066 (tmm) REVERT: K 14 ARG cc_start: 0.5684 (tpm170) cc_final: 0.5111 (tpm170) REVERT: K 18 GLU cc_start: 0.6798 (tp30) cc_final: 0.6086 (tp30) REVERT: K 26 ARG cc_start: 0.6565 (ttm110) cc_final: 0.6189 (ppt90) REVERT: K 154 VAL cc_start: 0.6618 (t) cc_final: 0.6323 (m) REVERT: K 156 MET cc_start: 0.7177 (mtm) cc_final: 0.6963 (mmm) REVERT: K 216 ASN cc_start: 0.7976 (t0) cc_final: 0.7549 (m-40) REVERT: L 432 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7305 (mp0) REVERT: M 363 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8739 (mp) REVERT: M 364 GLU cc_start: 0.7564 (tt0) cc_final: 0.7246 (tt0) REVERT: M 399 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8818 (tt) REVERT: M 401 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8373 (mp) REVERT: N 395 MET cc_start: 0.7296 (mmm) cc_final: 0.7008 (mmm) REVERT: N 432 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7356 (mp0) REVERT: O 26 ARG cc_start: 0.7477 (ttm110) cc_final: 0.6463 (ppt170) REVERT: O 67 LYS cc_start: 0.7827 (OUTLIER) cc_final: 0.7558 (tttt) REVERT: O 99 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8386 (mt) REVERT: O 105 GLN cc_start: 0.7017 (tp40) cc_final: 0.6600 (tp-100) REVERT: O 113 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6686 (tm-30) REVERT: P 424 ASP cc_start: 0.8094 (p0) cc_final: 0.7661 (p0) REVERT: P 430 ASN cc_start: 0.7646 (t0) cc_final: 0.7294 (t0) REVERT: P 432 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.6859 (mp0) REVERT: Q 21 ARG cc_start: 0.6870 (mtm110) cc_final: 0.6576 (ptm160) REVERT: R 509 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.7405 (ttm170) REVERT: S 401 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8487 (mt) REVERT: S 444 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8471 (mp) REVERT: T 52 LYS cc_start: 0.7894 (mtpt) cc_final: 0.7477 (mtmm) REVERT: T 209 GLU cc_start: 0.6884 (tt0) cc_final: 0.6298 (tt0) REVERT: V 345 ILE cc_start: 0.9163 (OUTLIER) cc_final: 0.8843 (mm) REVERT: V 509 ARG cc_start: 0.7714 (OUTLIER) cc_final: 0.7245 (ttp-170) REVERT: W 401 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8499 (mp) REVERT: X 21 ARG cc_start: 0.6494 (ttp-110) cc_final: 0.5959 (ttp80) REVERT: X 101 ASN cc_start: 0.8234 (m-40) cc_final: 0.7895 (m-40) REVERT: Y 324 ASN cc_start: 0.7922 (m-40) cc_final: 0.7671 (t0) REVERT: Z 52 LYS cc_start: 0.8022 (OUTLIER) cc_final: 0.7788 (mtpp) REVERT: b 339 ASP cc_start: 0.7681 (OUTLIER) cc_final: 0.7388 (m-30) REVERT: b 401 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8537 (mp) REVERT: d 51 GLN cc_start: 0.7302 (OUTLIER) cc_final: 0.6677 (mt0) REVERT: d 167 LEU cc_start: 0.7864 (mt) cc_final: 0.7598 (mt) REVERT: f 22 LYS cc_start: 0.7729 (ttpp) cc_final: 0.7339 (tmtt) REVERT: f 214 ASP cc_start: 0.8073 (t0) cc_final: 0.7863 (t0) outliers start: 128 outliers final: 88 residues processed: 669 average time/residue: 1.5172 time to fit residues: 1260.8036 Evaluate side-chains 701 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 583 time to evaluate : 5.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 70 GLU Chi-restraints excluded: chain 0 residue 72 ASP Chi-restraints excluded: chain 0 residue 74 LEU Chi-restraints excluded: chain 0 residue 80 GLN Chi-restraints excluded: chain 0 residue 146 SER Chi-restraints excluded: chain 1 residue 609 LEU Chi-restraints excluded: chain 2 residue 29 SER Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 147 ILE Chi-restraints excluded: chain 2 residue 179 ASP Chi-restraints excluded: chain 2 residue 226 THR Chi-restraints excluded: chain 2 residue 228 SER Chi-restraints excluded: chain 4 residue 74 LEU Chi-restraints excluded: chain 4 residue 102 VAL Chi-restraints excluded: chain 4 residue 132 GLU Chi-restraints excluded: chain 4 residue 147 ILE Chi-restraints excluded: chain 4 residue 170 SER Chi-restraints excluded: chain 4 residue 176 SER Chi-restraints excluded: chain 6 residue 99 LEU Chi-restraints excluded: chain 6 residue 112 THR Chi-restraints excluded: chain 6 residue 147 ILE Chi-restraints excluded: chain 6 residue 149 ASP Chi-restraints excluded: chain 8 residue 33 LEU Chi-restraints excluded: chain 8 residue 51 GLN Chi-restraints excluded: chain 8 residue 80 GLN Chi-restraints excluded: chain 8 residue 99 LEU Chi-restraints excluded: chain 8 residue 149 ASP Chi-restraints excluded: chain 8 residue 233 LEU Chi-restraints excluded: chain F residue 605 LEU Chi-restraints excluded: chain F residue 607 GLN Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain I residue 174 ASN Chi-restraints excluded: chain J residue 432 GLU Chi-restraints excluded: chain K residue 67 LYS Chi-restraints excluded: chain K residue 73 ASN Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 143 TYR Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain L residue 325 MET Chi-restraints excluded: chain L residue 364 GLU Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain L residue 409 ILE Chi-restraints excluded: chain L residue 430 ASN Chi-restraints excluded: chain L residue 432 GLU Chi-restraints excluded: chain M residue 330 ASP Chi-restraints excluded: chain M residue 363 LEU Chi-restraints excluded: chain M residue 399 LEU Chi-restraints excluded: chain M residue 401 LEU Chi-restraints excluded: chain N residue 345 ILE Chi-restraints excluded: chain N residue 432 GLU Chi-restraints excluded: chain N residue 444 LEU Chi-restraints excluded: chain O residue 31 VAL Chi-restraints excluded: chain O residue 40 LEU Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain O residue 67 LYS Chi-restraints excluded: chain O residue 99 LEU Chi-restraints excluded: chain O residue 113 GLU Chi-restraints excluded: chain O residue 144 ASP Chi-restraints excluded: chain O residue 146 SER Chi-restraints excluded: chain O residue 176 SER Chi-restraints excluded: chain P residue 395 MET Chi-restraints excluded: chain P residue 409 ILE Chi-restraints excluded: chain P residue 432 GLU Chi-restraints excluded: chain R residue 396 GLN Chi-restraints excluded: chain R residue 401 LEU Chi-restraints excluded: chain R residue 476 ASP Chi-restraints excluded: chain R residue 509 ARG Chi-restraints excluded: chain S residue 325 MET Chi-restraints excluded: chain S residue 330 ASP Chi-restraints excluded: chain S residue 401 LEU Chi-restraints excluded: chain S residue 444 LEU Chi-restraints excluded: chain T residue 26 ARG Chi-restraints excluded: chain T residue 49 SER Chi-restraints excluded: chain T residue 133 THR Chi-restraints excluded: chain T residue 147 ILE Chi-restraints excluded: chain T residue 178 THR Chi-restraints excluded: chain T residue 207 SER Chi-restraints excluded: chain U residue 313 VAL Chi-restraints excluded: chain U residue 320 SER Chi-restraints excluded: chain U residue 348 THR Chi-restraints excluded: chain U residue 401 LEU Chi-restraints excluded: chain U residue 520 SER Chi-restraints excluded: chain V residue 345 ILE Chi-restraints excluded: chain V residue 504 ASP Chi-restraints excluded: chain V residue 509 ARG Chi-restraints excluded: chain W residue 330 ASP Chi-restraints excluded: chain W residue 401 LEU Chi-restraints excluded: chain W residue 412 SER Chi-restraints excluded: chain W residue 416 SER Chi-restraints excluded: chain W residue 522 SER Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 49 SER Chi-restraints excluded: chain X residue 146 SER Chi-restraints excluded: chain X residue 228 SER Chi-restraints excluded: chain Y residue 391 LEU Chi-restraints excluded: chain Y residue 409 ILE Chi-restraints excluded: chain Y residue 503 VAL Chi-restraints excluded: chain Z residue 52 LYS Chi-restraints excluded: chain Z residue 74 LEU Chi-restraints excluded: chain Z residue 83 ASP Chi-restraints excluded: chain Z residue 99 LEU Chi-restraints excluded: chain Z residue 146 SER Chi-restraints excluded: chain Z residue 147 ILE Chi-restraints excluded: chain a residue 307 LYS Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain b residue 339 ASP Chi-restraints excluded: chain b residue 355 PHE Chi-restraints excluded: chain b residue 401 LEU Chi-restraints excluded: chain d residue 51 GLN Chi-restraints excluded: chain d residue 149 ASP Chi-restraints excluded: chain d residue 160 THR Chi-restraints excluded: chain f residue 133 THR Chi-restraints excluded: chain f residue 146 SER Chi-restraints excluded: chain f residue 149 ASP Chi-restraints excluded: chain f residue 228 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 380 optimal weight: 0.5980 chunk 510 optimal weight: 9.9990 chunk 146 optimal weight: 4.9990 chunk 441 optimal weight: 8.9990 chunk 70 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 479 optimal weight: 0.9990 chunk 200 optimal weight: 4.9990 chunk 492 optimal weight: 7.9990 chunk 60 optimal weight: 8.9990 chunk 88 optimal weight: 10.0000 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 69 ASN 0 73 ASN 0 174 ASN 1 607 GLN 4 45 ASN J 396 GLN L 410 HIS O 80 GLN Q 45 ASN U 322 GLN U 396 GLN V 322 GLN X 45 ASN Z 80 GLN Z 101 ASN a 322 GLN ** d 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 216 ASN f 69 ASN f 80 GLN f 174 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.130565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.092722 restraints weight = 59805.003| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.77 r_work: 0.2899 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 47302 Z= 0.266 Angle : 0.546 11.021 64013 Z= 0.288 Chirality : 0.044 0.175 7270 Planarity : 0.004 0.052 8452 Dihedral : 4.003 27.494 6904 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.88 % Allowed : 18.21 % Favored : 78.91 % 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: 2.16 (0.11), residues: 6089 helix: 3.05 (0.10), residues: 2600 sheet: 0.82 (0.14), residues: 1474 loop : -0.29 (0.14), residues: 2015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P 429 HIS 0.004 0.001 HIS T 129 PHE 0.031 0.003 PHE 2 71 TYR 0.027 0.002 TYR T 118 ARG 0.014 0.000 ARG O 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20281.14 seconds wall clock time: 356 minutes 0.48 seconds (21360.48 seconds total)