Starting phenix.real_space_refine on Fri Mar 22 08:01:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fql_29392/03_2024/8fql_29392.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fql_29392/03_2024/8fql_29392.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fql_29392/03_2024/8fql_29392.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fql_29392/03_2024/8fql_29392.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fql_29392/03_2024/8fql_29392.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fql_29392/03_2024/8fql_29392.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 180 5.16 5 C 20592 2.51 5 N 5736 2.21 5 O 6144 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 56": "NH1" <-> "NH2" Residue "A ARG 65": "NH1" <-> "NH2" Residue "A ARG 90": "NH1" <-> "NH2" Residue "A ARG 101": "NH1" <-> "NH2" Residue "A ARG 104": "NH1" <-> "NH2" Residue "A ARG 117": "NH1" <-> "NH2" Residue "A ARG 136": "NH1" <-> "NH2" Residue "A ARG 165": "NH1" <-> "NH2" Residue "A ARG 168": "NH1" <-> "NH2" Residue "A ARG 215": "NH1" <-> "NH2" Residue "A ARG 240": "NH1" <-> "NH2" Residue "A ARG 258": "NH1" <-> "NH2" Residue "A GLU 279": "OE1" <-> "OE2" Residue "A ARG 284": "NH1" <-> "NH2" Residue "A ARG 293": "NH1" <-> "NH2" Residue "A ARG 333": "NH1" <-> "NH2" Residue "A ARG 340": "NH1" <-> "NH2" Residue "A ARG 350": "NH1" <-> "NH2" Residue "A ARG 362": "NH1" <-> "NH2" Residue "A ARG 368": "NH1" <-> "NH2" Residue "A ARG 381": "NH1" <-> "NH2" Residue "A ARG 387": "NH1" <-> "NH2" Residue "A ARG 388": "NH1" <-> "NH2" Residue "B ARG 56": "NH1" <-> "NH2" Residue "B ARG 65": "NH1" <-> "NH2" Residue "B ARG 90": "NH1" <-> "NH2" Residue "B ARG 101": "NH1" <-> "NH2" Residue "B ARG 104": "NH1" <-> "NH2" Residue "B ARG 117": "NH1" <-> "NH2" Residue "B ARG 136": "NH1" <-> "NH2" Residue "B ARG 165": "NH1" <-> "NH2" Residue "B ARG 168": "NH1" <-> "NH2" Residue "B ARG 215": "NH1" <-> "NH2" Residue "B ARG 240": "NH1" <-> "NH2" Residue "B GLU 245": "OE1" <-> "OE2" Residue "B ARG 258": "NH1" <-> "NH2" Residue "B ARG 284": "NH1" <-> "NH2" Residue "B ARG 293": "NH1" <-> "NH2" Residue "B ARG 333": "NH1" <-> "NH2" Residue "B ARG 340": "NH1" <-> "NH2" Residue "B ARG 350": "NH1" <-> "NH2" Residue "B ARG 362": "NH1" <-> "NH2" Residue "B ARG 368": "NH1" <-> "NH2" Residue "B ARG 381": "NH1" <-> "NH2" Residue "B ARG 387": "NH1" <-> "NH2" Residue "B ARG 388": "NH1" <-> "NH2" Residue "C ARG 56": "NH1" <-> "NH2" Residue "C ARG 65": "NH1" <-> "NH2" Residue "C ARG 90": "NH1" <-> "NH2" Residue "C ARG 101": "NH1" <-> "NH2" Residue "C ARG 104": "NH1" <-> "NH2" Residue "C ARG 117": "NH1" <-> "NH2" Residue "C ARG 136": "NH1" <-> "NH2" Residue "C ARG 165": "NH1" <-> "NH2" Residue "C ARG 168": "NH1" <-> "NH2" Residue "C ARG 215": "NH1" <-> "NH2" Residue "C ARG 240": "NH1" <-> "NH2" Residue "C GLU 244": "OE1" <-> "OE2" Residue "C ARG 258": "NH1" <-> "NH2" Residue "C GLU 279": "OE1" <-> "OE2" Residue "C ARG 284": "NH1" <-> "NH2" Residue "C ARG 293": "NH1" <-> "NH2" Residue "C ARG 333": "NH1" <-> "NH2" Residue "C ARG 340": "NH1" <-> "NH2" Residue "C ARG 350": "NH1" <-> "NH2" Residue "C ARG 362": "NH1" <-> "NH2" Residue "C ARG 368": "NH1" <-> "NH2" Residue "C ARG 381": "NH1" <-> "NH2" Residue "C ARG 387": "NH1" <-> "NH2" Residue "C ARG 388": "NH1" <-> "NH2" Residue "D ARG 56": "NH1" <-> "NH2" Residue "D ARG 65": "NH1" <-> "NH2" Residue "D ARG 90": "NH1" <-> "NH2" Residue "D ARG 101": "NH1" <-> "NH2" Residue "D ARG 104": "NH1" <-> "NH2" Residue "D ARG 117": "NH1" <-> "NH2" Residue "D ARG 136": "NH1" <-> "NH2" Residue "D ARG 165": "NH1" <-> "NH2" Residue "D ARG 168": "NH1" <-> "NH2" Residue "D ARG 215": "NH1" <-> "NH2" Residue "D PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 232": "OE1" <-> "OE2" Residue "D ARG 240": "NH1" <-> "NH2" Residue "D ARG 258": "NH1" <-> "NH2" Residue "D GLU 279": "OE1" <-> "OE2" Residue "D ARG 284": "NH1" <-> "NH2" Residue "D ARG 293": "NH1" <-> "NH2" Residue "D ARG 333": "NH1" <-> "NH2" Residue "D ARG 340": "NH1" <-> "NH2" Residue "D ARG 350": "NH1" <-> "NH2" Residue "D ARG 362": "NH1" <-> "NH2" Residue "D ARG 368": "NH1" <-> "NH2" Residue "D ARG 381": "NH1" <-> "NH2" Residue "D ARG 387": "NH1" <-> "NH2" Residue "D ARG 388": "NH1" <-> "NH2" Residue "E ARG 56": "NH1" <-> "NH2" Residue "E ARG 65": "NH1" <-> "NH2" Residue "E ARG 90": "NH1" <-> "NH2" Residue "E ARG 101": "NH1" <-> "NH2" Residue "E ARG 104": "NH1" <-> "NH2" Residue "E ARG 117": "NH1" <-> "NH2" Residue "E ARG 136": "NH1" <-> "NH2" Residue "E ARG 165": "NH1" <-> "NH2" Residue "E ARG 168": "NH1" <-> "NH2" Residue "E ARG 215": "NH1" <-> "NH2" Residue "E ARG 240": "NH1" <-> "NH2" Residue "E ARG 258": "NH1" <-> "NH2" Residue "E GLU 279": "OE1" <-> "OE2" Residue "E ARG 284": "NH1" <-> "NH2" Residue "E ARG 293": "NH1" <-> "NH2" Residue "E ARG 333": "NH1" <-> "NH2" Residue "E ARG 340": "NH1" <-> "NH2" Residue "E ARG 350": "NH1" <-> "NH2" Residue "E ARG 362": "NH1" <-> "NH2" Residue "E ARG 368": "NH1" <-> "NH2" Residue "E ARG 381": "NH1" <-> "NH2" Residue "E ARG 387": "NH1" <-> "NH2" Residue "E ARG 388": "NH1" <-> "NH2" Residue "F ARG 56": "NH1" <-> "NH2" Residue "F ARG 65": "NH1" <-> "NH2" Residue "F ARG 90": "NH1" <-> "NH2" Residue "F ARG 101": "NH1" <-> "NH2" Residue "F ARG 104": "NH1" <-> "NH2" Residue "F ARG 117": "NH1" <-> "NH2" Residue "F ARG 136": "NH1" <-> "NH2" Residue "F ARG 165": "NH1" <-> "NH2" Residue "F ARG 168": "NH1" <-> "NH2" Residue "F ARG 215": "NH1" <-> "NH2" Residue "F PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 232": "OE1" <-> "OE2" Residue "F ARG 240": "NH1" <-> "NH2" Residue "F GLU 245": "OE1" <-> "OE2" Residue "F ARG 258": "NH1" <-> "NH2" Residue "F GLU 279": "OE1" <-> "OE2" Residue "F ARG 284": "NH1" <-> "NH2" Residue "F PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 293": "NH1" <-> "NH2" Residue "F ARG 333": "NH1" <-> "NH2" Residue "F ARG 340": "NH1" <-> "NH2" Residue "F ARG 350": "NH1" <-> "NH2" Residue "F ARG 362": "NH1" <-> "NH2" Residue "F ARG 368": "NH1" <-> "NH2" Residue "F ARG 381": "NH1" <-> "NH2" Residue "F ARG 387": "NH1" <-> "NH2" Residue "F ARG 388": "NH1" <-> "NH2" Residue "G ARG 56": "NH1" <-> "NH2" Residue "G ARG 65": "NH1" <-> "NH2" Residue "G ARG 90": "NH1" <-> "NH2" Residue "G ARG 101": "NH1" <-> "NH2" Residue "G ARG 104": "NH1" <-> "NH2" Residue "G ARG 117": "NH1" <-> "NH2" Residue "G ARG 136": "NH1" <-> "NH2" Residue "G ARG 165": "NH1" <-> "NH2" Residue "G ARG 168": "NH1" <-> "NH2" Residue "G ARG 215": "NH1" <-> "NH2" Residue "G GLU 232": "OE1" <-> "OE2" Residue "G ARG 240": "NH1" <-> "NH2" Residue "G ARG 258": "NH1" <-> "NH2" Residue "G GLU 279": "OE1" <-> "OE2" Residue "G ARG 284": "NH1" <-> "NH2" Residue "G ARG 293": "NH1" <-> "NH2" Residue "G ARG 333": "NH1" <-> "NH2" Residue "G ARG 340": "NH1" <-> "NH2" Residue "G ARG 350": "NH1" <-> "NH2" Residue "G ARG 362": "NH1" <-> "NH2" Residue "G ARG 368": "NH1" <-> "NH2" Residue "G ARG 381": "NH1" <-> "NH2" Residue "G ARG 387": "NH1" <-> "NH2" Residue "G ARG 388": "NH1" <-> "NH2" Residue "H ARG 56": "NH1" <-> "NH2" Residue "H ARG 65": "NH1" <-> "NH2" Residue "H ARG 90": "NH1" <-> "NH2" Residue "H ARG 101": "NH1" <-> "NH2" Residue "H ARG 104": "NH1" <-> "NH2" Residue "H ARG 117": "NH1" <-> "NH2" Residue "H ARG 136": "NH1" <-> "NH2" Residue "H ARG 165": "NH1" <-> "NH2" Residue "H ARG 168": "NH1" <-> "NH2" Residue "H ARG 215": "NH1" <-> "NH2" Residue "H ARG 240": "NH1" <-> "NH2" Residue "H GLU 244": "OE1" <-> "OE2" Residue "H ARG 258": "NH1" <-> "NH2" Residue "H ARG 284": "NH1" <-> "NH2" Residue "H PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 293": "NH1" <-> "NH2" Residue "H ARG 333": "NH1" <-> "NH2" Residue "H ARG 340": "NH1" <-> "NH2" Residue "H ARG 350": "NH1" <-> "NH2" Residue "H ARG 362": "NH1" <-> "NH2" Residue "H ARG 368": "NH1" <-> "NH2" Residue "H ARG 381": "NH1" <-> "NH2" Residue "H ARG 387": "NH1" <-> "NH2" Residue "H ARG 388": "NH1" <-> "NH2" Residue "I ARG 56": "NH1" <-> "NH2" Residue "I ARG 65": "NH1" <-> "NH2" Residue "I ARG 90": "NH1" <-> "NH2" Residue "I ARG 101": "NH1" <-> "NH2" Residue "I ARG 104": "NH1" <-> "NH2" Residue "I ARG 117": "NH1" <-> "NH2" Residue "I ARG 136": "NH1" <-> "NH2" Residue "I ARG 165": "NH1" <-> "NH2" Residue "I ARG 168": "NH1" <-> "NH2" Residue "I ARG 215": "NH1" <-> "NH2" Residue "I ARG 240": "NH1" <-> "NH2" Residue "I GLU 249": "OE1" <-> "OE2" Residue "I ARG 258": "NH1" <-> "NH2" Residue "I GLU 279": "OE1" <-> "OE2" Residue "I ARG 284": "NH1" <-> "NH2" Residue "I ARG 293": "NH1" <-> "NH2" Residue "I ARG 333": "NH1" <-> "NH2" Residue "I ARG 340": "NH1" <-> "NH2" Residue "I ARG 350": "NH1" <-> "NH2" Residue "I ARG 362": "NH1" <-> "NH2" Residue "I ARG 368": "NH1" <-> "NH2" Residue "I ARG 381": "NH1" <-> "NH2" Residue "I ARG 387": "NH1" <-> "NH2" Residue "I ARG 388": "NH1" <-> "NH2" Residue "J ARG 56": "NH1" <-> "NH2" Residue "J ARG 65": "NH1" <-> "NH2" Residue "J ARG 90": "NH1" <-> "NH2" Residue "J ARG 101": "NH1" <-> "NH2" Residue "J ARG 104": "NH1" <-> "NH2" Residue "J ARG 117": "NH1" <-> "NH2" Residue "J ARG 136": "NH1" <-> "NH2" Residue "J ARG 165": "NH1" <-> "NH2" Residue "J ARG 168": "NH1" <-> "NH2" Residue "J ARG 215": "NH1" <-> "NH2" Residue "J PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 240": "NH1" <-> "NH2" Residue "J ARG 258": "NH1" <-> "NH2" Residue "J ARG 284": "NH1" <-> "NH2" Residue "J ARG 293": "NH1" <-> "NH2" Residue "J ARG 333": "NH1" <-> "NH2" Residue "J ARG 340": "NH1" <-> "NH2" Residue "J ARG 350": "NH1" <-> "NH2" Residue "J ARG 362": "NH1" <-> "NH2" Residue "J ARG 368": "NH1" <-> "NH2" Residue "J ARG 381": "NH1" <-> "NH2" Residue "J ARG 387": "NH1" <-> "NH2" Residue "J ARG 388": "NH1" <-> "NH2" Residue "K ARG 56": "NH1" <-> "NH2" Residue "K ARG 65": "NH1" <-> "NH2" Residue "K ARG 90": "NH1" <-> "NH2" Residue "K ARG 101": "NH1" <-> "NH2" Residue "K ARG 104": "NH1" <-> "NH2" Residue "K ARG 117": "NH1" <-> "NH2" Residue "K ARG 136": "NH1" <-> "NH2" Residue "K ARG 165": "NH1" <-> "NH2" Residue "K ARG 168": "NH1" <-> "NH2" Residue "K ARG 215": "NH1" <-> "NH2" Residue "K ARG 240": "NH1" <-> "NH2" Residue "K ARG 258": "NH1" <-> "NH2" Residue "K GLU 279": "OE1" <-> "OE2" Residue "K ARG 284": "NH1" <-> "NH2" Residue "K ARG 293": "NH1" <-> "NH2" Residue "K ARG 333": "NH1" <-> "NH2" Residue "K ARG 340": "NH1" <-> "NH2" Residue "K ARG 350": "NH1" <-> "NH2" Residue "K ARG 362": "NH1" <-> "NH2" Residue "K ARG 368": "NH1" <-> "NH2" Residue "K ARG 381": "NH1" <-> "NH2" Residue "K ARG 387": "NH1" <-> "NH2" Residue "K ARG 388": "NH1" <-> "NH2" Residue "L ARG 56": "NH1" <-> "NH2" Residue "L ARG 65": "NH1" <-> "NH2" Residue "L ARG 90": "NH1" <-> "NH2" Residue "L ARG 101": "NH1" <-> "NH2" Residue "L ARG 104": "NH1" <-> "NH2" Residue "L ARG 117": "NH1" <-> "NH2" Residue "L ARG 136": "NH1" <-> "NH2" Residue "L ARG 165": "NH1" <-> "NH2" Residue "L ARG 168": "NH1" <-> "NH2" Residue "L ARG 215": "NH1" <-> "NH2" Residue "L ARG 240": "NH1" <-> "NH2" Residue "L ARG 258": "NH1" <-> "NH2" Residue "L GLU 279": "OE1" <-> "OE2" Residue "L ARG 284": "NH1" <-> "NH2" Residue "L ARG 293": "NH1" <-> "NH2" Residue "L ARG 333": "NH1" <-> "NH2" Residue "L ARG 340": "NH1" <-> "NH2" Residue "L ARG 350": "NH1" <-> "NH2" Residue "L ARG 362": "NH1" <-> "NH2" Residue "L ARG 368": "NH1" <-> "NH2" Residue "L ARG 381": "NH1" <-> "NH2" Residue "L ARG 387": "NH1" <-> "NH2" Residue "L ARG 388": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 32652 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2721 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 15, 'TRANS': 330} Chain: "B" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2721 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 15, 'TRANS': 330} Chain: "C" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2721 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 15, 'TRANS': 330} Chain: "D" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2721 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 15, 'TRANS': 330} Chain: "E" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2721 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 15, 'TRANS': 330} Chain: "F" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2721 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 15, 'TRANS': 330} Chain: "G" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2721 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 15, 'TRANS': 330} Chain: "H" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2721 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 15, 'TRANS': 330} Chain: "I" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2721 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 15, 'TRANS': 330} Chain: "J" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2721 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 15, 'TRANS': 330} Chain: "K" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2721 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 15, 'TRANS': 330} Chain: "L" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2721 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 15, 'TRANS': 330} Time building chain proxies: 16.44, per 1000 atoms: 0.50 Number of scatterers: 32652 At special positions: 0 Unit cell: (152.28, 154.44, 123.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 180 16.00 O 6144 8.00 N 5736 7.00 C 20592 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: 12.43 Conformation dependent library (CDL) restraints added in 6.0 seconds 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7704 Finding SS restraints... Secondary structure from input PDB file: 171 helices and 48 sheets defined 50.9% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.25 Creating SS restraints... Processing helix chain 'A' and resid 53 through 59 Processing helix chain 'A' and resid 60 through 77 Processing helix chain 'A' and resid 97 through 105 Processing helix chain 'A' and resid 112 through 128 Processing helix chain 'A' and resid 195 through 220 removed outlier: 3.823A pdb=" N PHE A 199 " --> pdb=" O SER A 195 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N LYS A 202 " --> pdb=" O ALA A 198 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N SER A 203 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE A 218 " --> pdb=" O GLN A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 247 removed outlier: 4.267A pdb=" N GLU A 244 " --> pdb=" O ARG A 240 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLU A 245 " --> pdb=" O SER A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 296 removed outlier: 3.975A pdb=" N SER A 289 " --> pdb=" O LYS A 285 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU A 290 " --> pdb=" O PHE A 286 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE A 294 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N PHE A 295 " --> pdb=" O LEU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 326 Processing helix chain 'A' and resid 327 through 342 removed outlier: 3.666A pdb=" N ILE A 331 " --> pdb=" O LEU A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 348 Processing helix chain 'A' and resid 357 through 362 Processing helix chain 'A' and resid 364 through 377 Processing helix chain 'A' and resid 382 through 390 removed outlier: 3.780A pdb=" N ASP A 390 " --> pdb=" O MET A 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 59 Processing helix chain 'B' and resid 60 through 77 Processing helix chain 'B' and resid 97 through 105 Processing helix chain 'B' and resid 112 through 128 Processing helix chain 'B' and resid 149 through 151 No H-bonds generated for 'chain 'B' and resid 149 through 151' Processing helix chain 'B' and resid 195 through 220 removed outlier: 3.768A pdb=" N PHE B 199 " --> pdb=" O SER B 195 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N LYS B 202 " --> pdb=" O ALA B 198 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N SER B 203 " --> pdb=" O PHE B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 247 removed outlier: 4.482A pdb=" N VAL B 243 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N GLU B 244 " --> pdb=" O ARG B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 296 removed outlier: 5.176A pdb=" N ARG B 284 " --> pdb=" O MET B 280 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL B 288 " --> pdb=" O ARG B 284 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N SER B 289 " --> pdb=" O LYS B 285 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU B 290 " --> pdb=" O PHE B 286 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE B 294 " --> pdb=" O GLU B 290 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N PHE B 295 " --> pdb=" O LEU B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 303 removed outlier: 3.772A pdb=" N VAL B 302 " --> pdb=" O PRO B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 326 Processing helix chain 'B' and resid 327 through 342 removed outlier: 3.859A pdb=" N ILE B 331 " --> pdb=" O LEU B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 348 Processing helix chain 'B' and resid 357 through 362 Processing helix chain 'B' and resid 364 through 377 removed outlier: 4.284A pdb=" N GLU B 377 " --> pdb=" O LYS B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 390 removed outlier: 3.766A pdb=" N ASP B 390 " --> pdb=" O MET B 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 59 Processing helix chain 'C' and resid 60 through 77 Processing helix chain 'C' and resid 97 through 105 Processing helix chain 'C' and resid 112 through 128 Processing helix chain 'C' and resid 195 through 220 removed outlier: 3.823A pdb=" N PHE C 199 " --> pdb=" O SER C 195 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N LYS C 202 " --> pdb=" O ALA C 198 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N SER C 203 " --> pdb=" O PHE C 199 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE C 218 " --> pdb=" O GLN C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 247 removed outlier: 4.156A pdb=" N GLU C 244 " --> pdb=" O ARG C 240 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLU C 245 " --> pdb=" O SER C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 296 removed outlier: 3.613A pdb=" N VAL C 288 " --> pdb=" O ARG C 284 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER C 289 " --> pdb=" O LYS C 285 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU C 290 " --> pdb=" O PHE C 286 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N PHE C 295 " --> pdb=" O LEU C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 326 Processing helix chain 'C' and resid 327 through 342 removed outlier: 3.666A pdb=" N ILE C 331 " --> pdb=" O LEU C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 348 Processing helix chain 'C' and resid 357 through 362 Processing helix chain 'C' and resid 364 through 377 Processing helix chain 'C' and resid 382 through 390 removed outlier: 3.780A pdb=" N ASP C 390 " --> pdb=" O MET C 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 59 Processing helix chain 'D' and resid 60 through 77 Processing helix chain 'D' and resid 97 through 105 Processing helix chain 'D' and resid 112 through 128 Processing helix chain 'D' and resid 149 through 151 No H-bonds generated for 'chain 'D' and resid 149 through 151' Processing helix chain 'D' and resid 195 through 220 removed outlier: 3.768A pdb=" N PHE D 199 " --> pdb=" O SER D 195 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N LYS D 202 " --> pdb=" O ALA D 198 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N SER D 203 " --> pdb=" O PHE D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 247 removed outlier: 3.663A pdb=" N GLN D 242 " --> pdb=" O GLN D 238 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N VAL D 243 " --> pdb=" O GLN D 239 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLU D 244 " --> pdb=" O ARG D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 296 removed outlier: 5.279A pdb=" N ARG D 284 " --> pdb=" O MET D 280 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL D 288 " --> pdb=" O ARG D 284 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N SER D 289 " --> pdb=" O LYS D 285 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU D 290 " --> pdb=" O PHE D 286 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE D 294 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N PHE D 295 " --> pdb=" O LEU D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 303 removed outlier: 3.772A pdb=" N VAL D 302 " --> pdb=" O PRO D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 326 Processing helix chain 'D' and resid 327 through 342 removed outlier: 3.859A pdb=" N ILE D 331 " --> pdb=" O LEU D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 348 Processing helix chain 'D' and resid 357 through 362 Processing helix chain 'D' and resid 364 through 377 removed outlier: 4.284A pdb=" N GLU D 377 " --> pdb=" O LYS D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 390 removed outlier: 3.766A pdb=" N ASP D 390 " --> pdb=" O MET D 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 59 Processing helix chain 'E' and resid 60 through 77 Processing helix chain 'E' and resid 97 through 105 Processing helix chain 'E' and resid 112 through 128 Processing helix chain 'E' and resid 195 through 220 removed outlier: 3.823A pdb=" N PHE E 199 " --> pdb=" O SER E 195 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N LYS E 202 " --> pdb=" O ALA E 198 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N SER E 203 " --> pdb=" O PHE E 199 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE E 218 " --> pdb=" O GLN E 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 247 removed outlier: 3.663A pdb=" N GLU E 244 " --> pdb=" O ARG E 240 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLU E 245 " --> pdb=" O SER E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 252 removed outlier: 4.042A pdb=" N ALA E 251 " --> pdb=" O LYS E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 296 removed outlier: 3.597A pdb=" N ARG E 284 " --> pdb=" O MET E 280 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL E 288 " --> pdb=" O ARG E 284 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER E 289 " --> pdb=" O LYS E 285 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU E 290 " --> pdb=" O PHE E 286 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE E 294 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N PHE E 295 " --> pdb=" O LEU E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 326 Processing helix chain 'E' and resid 327 through 342 removed outlier: 3.666A pdb=" N ILE E 331 " --> pdb=" O LEU E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 344 through 348 Processing helix chain 'E' and resid 357 through 362 Processing helix chain 'E' and resid 364 through 377 Processing helix chain 'E' and resid 382 through 390 removed outlier: 3.780A pdb=" N ASP E 390 " --> pdb=" O MET E 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 59 Processing helix chain 'F' and resid 60 through 77 Processing helix chain 'F' and resid 97 through 105 Processing helix chain 'F' and resid 112 through 128 Processing helix chain 'F' and resid 149 through 151 No H-bonds generated for 'chain 'F' and resid 149 through 151' Processing helix chain 'F' and resid 195 through 220 removed outlier: 3.768A pdb=" N PHE F 199 " --> pdb=" O SER F 195 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N LYS F 202 " --> pdb=" O ALA F 198 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N SER F 203 " --> pdb=" O PHE F 199 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE F 218 " --> pdb=" O GLN F 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 236 through 246 removed outlier: 4.197A pdb=" N VAL F 243 " --> pdb=" O GLN F 239 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N GLU F 244 " --> pdb=" O ARG F 240 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 296 removed outlier: 5.176A pdb=" N ARG F 284 " --> pdb=" O MET F 280 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL F 288 " --> pdb=" O ARG F 284 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N SER F 289 " --> pdb=" O LYS F 285 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU F 290 " --> pdb=" O PHE F 286 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE F 294 " --> pdb=" O GLU F 290 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N PHE F 295 " --> pdb=" O LEU F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 303 removed outlier: 3.772A pdb=" N VAL F 302 " --> pdb=" O PRO F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 326 Processing helix chain 'F' and resid 327 through 342 removed outlier: 3.860A pdb=" N ILE F 331 " --> pdb=" O LEU F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 344 through 348 Processing helix chain 'F' and resid 357 through 362 Processing helix chain 'F' and resid 364 through 377 removed outlier: 4.284A pdb=" N GLU F 377 " --> pdb=" O LYS F 373 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 390 removed outlier: 3.766A pdb=" N ASP F 390 " --> pdb=" O MET F 386 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 59 Processing helix chain 'G' and resid 60 through 77 Processing helix chain 'G' and resid 97 through 105 Processing helix chain 'G' and resid 112 through 128 Processing helix chain 'G' and resid 195 through 220 removed outlier: 3.823A pdb=" N PHE G 199 " --> pdb=" O SER G 195 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N LYS G 202 " --> pdb=" O ALA G 198 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N SER G 203 " --> pdb=" O PHE G 199 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N PHE G 218 " --> pdb=" O GLN G 214 " (cutoff:3.500A) Processing helix chain 'G' and resid 236 through 247 removed outlier: 3.823A pdb=" N GLU G 244 " --> pdb=" O ARG G 240 " (cutoff:3.500A) Processing helix chain 'G' and resid 248 through 252 removed outlier: 4.189A pdb=" N ALA G 251 " --> pdb=" O LYS G 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 279 through 296 removed outlier: 3.684A pdb=" N ARG G 284 " --> pdb=" O MET G 280 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS G 285 " --> pdb=" O MET G 281 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL G 288 " --> pdb=" O ARG G 284 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N SER G 289 " --> pdb=" O LYS G 285 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU G 290 " --> pdb=" O PHE G 286 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE G 294 " --> pdb=" O GLU G 290 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N PHE G 295 " --> pdb=" O LEU G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 314 through 326 Processing helix chain 'G' and resid 327 through 342 removed outlier: 3.666A pdb=" N ILE G 331 " --> pdb=" O LEU G 327 " (cutoff:3.500A) Processing helix chain 'G' and resid 344 through 348 Processing helix chain 'G' and resid 357 through 362 Processing helix chain 'G' and resid 364 through 377 Processing helix chain 'G' and resid 382 through 390 removed outlier: 3.780A pdb=" N ASP G 390 " --> pdb=" O MET G 386 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 59 Processing helix chain 'H' and resid 60 through 77 Processing helix chain 'H' and resid 97 through 105 Processing helix chain 'H' and resid 112 through 128 Processing helix chain 'H' and resid 149 through 151 No H-bonds generated for 'chain 'H' and resid 149 through 151' Processing helix chain 'H' and resid 195 through 220 removed outlier: 3.768A pdb=" N PHE H 199 " --> pdb=" O SER H 195 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N LYS H 202 " --> pdb=" O ALA H 198 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N SER H 203 " --> pdb=" O PHE H 199 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE H 218 " --> pdb=" O GLN H 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 236 through 246 removed outlier: 4.193A pdb=" N GLU H 244 " --> pdb=" O ARG H 240 " (cutoff:3.500A) Processing helix chain 'H' and resid 278 through 296 removed outlier: 5.685A pdb=" N ARG H 284 " --> pdb=" O MET H 280 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL H 288 " --> pdb=" O ARG H 284 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N SER H 289 " --> pdb=" O LYS H 285 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU H 290 " --> pdb=" O PHE H 286 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE H 294 " --> pdb=" O GLU H 290 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N PHE H 295 " --> pdb=" O LEU H 291 " (cutoff:3.500A) Processing helix chain 'H' and resid 298 through 303 removed outlier: 3.772A pdb=" N VAL H 302 " --> pdb=" O PRO H 298 " (cutoff:3.500A) Processing helix chain 'H' and resid 314 through 326 Processing helix chain 'H' and resid 327 through 342 removed outlier: 3.859A pdb=" N ILE H 331 " --> pdb=" O LEU H 327 " (cutoff:3.500A) Processing helix chain 'H' and resid 344 through 348 Processing helix chain 'H' and resid 357 through 362 Processing helix chain 'H' and resid 364 through 377 removed outlier: 4.284A pdb=" N GLU H 377 " --> pdb=" O LYS H 373 " (cutoff:3.500A) Processing helix chain 'H' and resid 382 through 390 removed outlier: 3.766A pdb=" N ASP H 390 " --> pdb=" O MET H 386 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 59 Processing helix chain 'I' and resid 60 through 77 Processing helix chain 'I' and resid 97 through 105 Processing helix chain 'I' and resid 112 through 128 Processing helix chain 'I' and resid 195 through 220 removed outlier: 3.823A pdb=" N PHE I 199 " --> pdb=" O SER I 195 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N LYS I 202 " --> pdb=" O ALA I 198 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N SER I 203 " --> pdb=" O PHE I 199 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE I 218 " --> pdb=" O GLN I 214 " (cutoff:3.500A) Processing helix chain 'I' and resid 236 through 247 Processing helix chain 'I' and resid 248 through 252 Processing helix chain 'I' and resid 279 through 296 removed outlier: 3.743A pdb=" N ARG I 284 " --> pdb=" O MET I 280 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL I 288 " --> pdb=" O ARG I 284 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N SER I 289 " --> pdb=" O LYS I 285 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU I 290 " --> pdb=" O PHE I 286 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE I 294 " --> pdb=" O GLU I 290 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N PHE I 295 " --> pdb=" O LEU I 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 314 through 326 Processing helix chain 'I' and resid 327 through 342 removed outlier: 3.666A pdb=" N ILE I 331 " --> pdb=" O LEU I 327 " (cutoff:3.500A) Processing helix chain 'I' and resid 344 through 348 Processing helix chain 'I' and resid 357 through 362 Processing helix chain 'I' and resid 364 through 377 Processing helix chain 'I' and resid 382 through 390 removed outlier: 3.780A pdb=" N ASP I 390 " --> pdb=" O MET I 386 " (cutoff:3.500A) Processing helix chain 'J' and resid 53 through 59 Processing helix chain 'J' and resid 60 through 77 Processing helix chain 'J' and resid 97 through 105 Processing helix chain 'J' and resid 112 through 128 Processing helix chain 'J' and resid 149 through 151 No H-bonds generated for 'chain 'J' and resid 149 through 151' Processing helix chain 'J' and resid 195 through 220 removed outlier: 3.768A pdb=" N PHE J 199 " --> pdb=" O SER J 195 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N LYS J 202 " --> pdb=" O ALA J 198 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N SER J 203 " --> pdb=" O PHE J 199 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE J 218 " --> pdb=" O GLN J 214 " (cutoff:3.500A) Processing helix chain 'J' and resid 236 through 247 removed outlier: 3.551A pdb=" N GLN J 242 " --> pdb=" O GLN J 238 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL J 243 " --> pdb=" O GLN J 239 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N GLU J 244 " --> pdb=" O ARG J 240 " (cutoff:3.500A) Processing helix chain 'J' and resid 278 through 296 removed outlier: 5.080A pdb=" N ARG J 284 " --> pdb=" O MET J 280 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL J 288 " --> pdb=" O ARG J 284 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N SER J 289 " --> pdb=" O LYS J 285 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU J 290 " --> pdb=" O PHE J 286 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE J 294 " --> pdb=" O GLU J 290 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N PHE J 295 " --> pdb=" O LEU J 291 " (cutoff:3.500A) Processing helix chain 'J' and resid 298 through 303 removed outlier: 3.772A pdb=" N VAL J 302 " --> pdb=" O PRO J 298 " (cutoff:3.500A) Processing helix chain 'J' and resid 314 through 326 Processing helix chain 'J' and resid 327 through 342 removed outlier: 3.859A pdb=" N ILE J 331 " --> pdb=" O LEU J 327 " (cutoff:3.500A) Processing helix chain 'J' and resid 344 through 348 Processing helix chain 'J' and resid 357 through 362 Processing helix chain 'J' and resid 364 through 377 removed outlier: 4.284A pdb=" N GLU J 377 " --> pdb=" O LYS J 373 " (cutoff:3.500A) Processing helix chain 'J' and resid 382 through 390 removed outlier: 3.766A pdb=" N ASP J 390 " --> pdb=" O MET J 386 " (cutoff:3.500A) Processing helix chain 'K' and resid 53 through 59 Processing helix chain 'K' and resid 60 through 77 Processing helix chain 'K' and resid 97 through 105 Processing helix chain 'K' and resid 112 through 128 Processing helix chain 'K' and resid 195 through 220 removed outlier: 3.823A pdb=" N PHE K 199 " --> pdb=" O SER K 195 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LYS K 202 " --> pdb=" O ALA K 198 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N SER K 203 " --> pdb=" O PHE K 199 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N PHE K 218 " --> pdb=" O GLN K 214 " (cutoff:3.500A) Processing helix chain 'K' and resid 236 through 247 removed outlier: 3.965A pdb=" N GLU K 244 " --> pdb=" O ARG K 240 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU K 245 " --> pdb=" O SER K 241 " (cutoff:3.500A) Processing helix chain 'K' and resid 279 through 296 removed outlier: 3.987A pdb=" N SER K 289 " --> pdb=" O LYS K 285 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU K 290 " --> pdb=" O PHE K 286 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE K 294 " --> pdb=" O GLU K 290 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N PHE K 295 " --> pdb=" O LEU K 291 " (cutoff:3.500A) Processing helix chain 'K' and resid 314 through 326 Processing helix chain 'K' and resid 327 through 342 removed outlier: 3.666A pdb=" N ILE K 331 " --> pdb=" O LEU K 327 " (cutoff:3.500A) Processing helix chain 'K' and resid 344 through 348 Processing helix chain 'K' and resid 357 through 362 Processing helix chain 'K' and resid 364 through 377 Processing helix chain 'K' and resid 382 through 390 removed outlier: 3.780A pdb=" N ASP K 390 " --> pdb=" O MET K 386 " (cutoff:3.500A) Processing helix chain 'L' and resid 53 through 59 Processing helix chain 'L' and resid 60 through 77 Processing helix chain 'L' and resid 97 through 105 Processing helix chain 'L' and resid 112 through 128 Processing helix chain 'L' and resid 149 through 151 No H-bonds generated for 'chain 'L' and resid 149 through 151' Processing helix chain 'L' and resid 195 through 220 removed outlier: 3.768A pdb=" N PHE L 199 " --> pdb=" O SER L 195 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N LYS L 202 " --> pdb=" O ALA L 198 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N SER L 203 " --> pdb=" O PHE L 199 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE L 218 " --> pdb=" O GLN L 214 " (cutoff:3.500A) Processing helix chain 'L' and resid 236 through 247 removed outlier: 3.899A pdb=" N VAL L 243 " --> pdb=" O GLN L 239 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU L 244 " --> pdb=" O ARG L 240 " (cutoff:3.500A) Processing helix chain 'L' and resid 278 through 296 removed outlier: 5.212A pdb=" N ARG L 284 " --> pdb=" O MET L 280 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL L 288 " --> pdb=" O ARG L 284 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N SER L 289 " --> pdb=" O LYS L 285 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU L 290 " --> pdb=" O PHE L 286 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE L 294 " --> pdb=" O GLU L 290 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N PHE L 295 " --> pdb=" O LEU L 291 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 303 removed outlier: 3.772A pdb=" N VAL L 302 " --> pdb=" O PRO L 298 " (cutoff:3.500A) Processing helix chain 'L' and resid 314 through 326 Processing helix chain 'L' and resid 327 through 342 removed outlier: 3.860A pdb=" N ILE L 331 " --> pdb=" O LEU L 327 " (cutoff:3.500A) Processing helix chain 'L' and resid 344 through 348 Processing helix chain 'L' and resid 357 through 362 Processing helix chain 'L' and resid 364 through 377 removed outlier: 4.284A pdb=" N GLU L 377 " --> pdb=" O LYS L 373 " (cutoff:3.500A) Processing helix chain 'L' and resid 382 through 390 removed outlier: 3.766A pdb=" N ASP L 390 " --> pdb=" O MET L 386 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA2, first strand: chain 'A' and resid 131 through 136 removed outlier: 7.436A pdb=" N TYR A 131 " --> pdb=" O PRO A 147 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU A 133 " --> pdb=" O LEU A 145 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU A 145 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASP A 135 " --> pdb=" O ILE A 143 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 153 through 158 Processing sheet with id=AA4, first strand: chain 'A' and resid 226 through 227 removed outlier: 3.528A pdb=" N SER A 269 " --> pdb=" O ILE A 227 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AA6, first strand: chain 'B' and resid 131 through 136 removed outlier: 4.355A pdb=" N TYR B 131 " --> pdb=" O LEU B 148 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 153 through 158 Processing sheet with id=AA8, first strand: chain 'B' and resid 226 through 227 Processing sheet with id=AA9, first strand: chain 'B' and resid 259 through 260 removed outlier: 6.061A pdb=" N LEU B 259 " --> pdb=" O LEU C 228 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 90 through 92 Processing sheet with id=AB2, first strand: chain 'C' and resid 131 through 136 removed outlier: 7.436A pdb=" N TYR C 131 " --> pdb=" O PRO C 147 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU C 133 " --> pdb=" O LEU C 145 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU C 145 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASP C 135 " --> pdb=" O ILE C 143 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 153 through 158 Processing sheet with id=AB4, first strand: chain 'C' and resid 259 through 260 removed outlier: 6.874A pdb=" N LEU C 259 " --> pdb=" O LEU D 228 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'D' and resid 90 through 92 Processing sheet with id=AB6, first strand: chain 'D' and resid 131 through 136 removed outlier: 4.354A pdb=" N TYR D 131 " --> pdb=" O LEU D 148 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 153 through 158 Processing sheet with id=AB8, first strand: chain 'D' and resid 259 through 261 removed outlier: 5.959A pdb=" N LEU D 259 " --> pdb=" O LEU E 228 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 90 through 92 Processing sheet with id=AC1, first strand: chain 'E' and resid 131 through 136 removed outlier: 7.436A pdb=" N TYR E 131 " --> pdb=" O PRO E 147 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU E 133 " --> pdb=" O LEU E 145 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU E 145 " --> pdb=" O LEU E 133 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASP E 135 " --> pdb=" O ILE E 143 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 153 through 158 Processing sheet with id=AC3, first strand: chain 'E' and resid 259 through 260 removed outlier: 6.079A pdb=" N LEU E 259 " --> pdb=" O LEU F 228 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 90 through 92 Processing sheet with id=AC5, first strand: chain 'F' and resid 131 through 136 removed outlier: 4.354A pdb=" N TYR F 131 " --> pdb=" O LEU F 148 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 153 through 158 Processing sheet with id=AC7, first strand: chain 'F' and resid 259 through 261 removed outlier: 5.554A pdb=" N LEU F 259 " --> pdb=" O LEU G 228 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 90 through 92 Processing sheet with id=AC9, first strand: chain 'G' and resid 131 through 136 removed outlier: 7.436A pdb=" N TYR G 131 " --> pdb=" O PRO G 147 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU G 133 " --> pdb=" O LEU G 145 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU G 145 " --> pdb=" O LEU G 133 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASP G 135 " --> pdb=" O ILE G 143 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 153 through 158 Processing sheet with id=AD2, first strand: chain 'G' and resid 259 through 260 removed outlier: 6.157A pdb=" N LEU G 259 " --> pdb=" O LEU H 228 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 90 through 92 Processing sheet with id=AD4, first strand: chain 'H' and resid 131 through 136 removed outlier: 4.355A pdb=" N TYR H 131 " --> pdb=" O LEU H 148 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 153 through 158 Processing sheet with id=AD6, first strand: chain 'H' and resid 259 through 260 removed outlier: 6.036A pdb=" N LEU H 259 " --> pdb=" O LEU I 228 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 90 through 92 Processing sheet with id=AD8, first strand: chain 'I' and resid 131 through 136 removed outlier: 7.436A pdb=" N TYR I 131 " --> pdb=" O PRO I 147 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU I 133 " --> pdb=" O LEU I 145 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU I 145 " --> pdb=" O LEU I 133 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASP I 135 " --> pdb=" O ILE I 143 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 153 through 158 Processing sheet with id=AE1, first strand: chain 'I' and resid 259 through 260 removed outlier: 6.459A pdb=" N LEU I 259 " --> pdb=" O LEU J 228 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 90 through 92 Processing sheet with id=AE3, first strand: chain 'J' and resid 131 through 136 removed outlier: 4.354A pdb=" N TYR J 131 " --> pdb=" O LEU J 148 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 153 through 158 Processing sheet with id=AE5, first strand: chain 'J' and resid 259 through 260 removed outlier: 6.125A pdb=" N LEU J 259 " --> pdb=" O LEU K 228 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 90 through 92 Processing sheet with id=AE7, first strand: chain 'K' and resid 131 through 136 removed outlier: 7.436A pdb=" N TYR K 131 " --> pdb=" O PRO K 147 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU K 133 " --> pdb=" O LEU K 145 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU K 145 " --> pdb=" O LEU K 133 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASP K 135 " --> pdb=" O ILE K 143 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 153 through 158 Processing sheet with id=AE9, first strand: chain 'K' and resid 259 through 260 removed outlier: 6.424A pdb=" N LEU K 259 " --> pdb=" O LEU L 228 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 90 through 92 Processing sheet with id=AF2, first strand: chain 'L' and resid 131 through 136 removed outlier: 4.354A pdb=" N TYR L 131 " --> pdb=" O LEU L 148 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 153 through 158 1549 hydrogen bonds defined for protein. 4461 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: 9.98 Time building geometry restraints manager: 13.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9842 1.33 - 1.45: 5439 1.45 - 1.58: 17707 1.58 - 1.70: 0 1.70 - 1.82: 312 Bond restraints: 33300 Sorted by residual: bond pdb=" CZ ARG E 387 " pdb=" NH2 ARG E 387 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.30e-02 5.92e+03 9.81e+00 bond pdb=" CZ ARG K 387 " pdb=" NH2 ARG K 387 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.30e-02 5.92e+03 9.81e+00 bond pdb=" CZ ARG A 387 " pdb=" NH2 ARG A 387 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.30e-02 5.92e+03 9.72e+00 bond pdb=" CZ ARG G 387 " pdb=" NH2 ARG G 387 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.30e-02 5.92e+03 9.72e+00 bond pdb=" CZ ARG C 387 " pdb=" NH2 ARG C 387 " ideal model delta sigma weight residual 1.330 1.290 0.040 1.30e-02 5.92e+03 9.70e+00 ... (remaining 33295 not shown) Histogram of bond angle deviations from ideal: 95.78 - 103.59: 448 103.59 - 111.40: 11485 111.40 - 119.20: 14850 119.20 - 127.01: 17631 127.01 - 134.82: 562 Bond angle restraints: 44976 Sorted by residual: angle pdb=" CA TRP J 260 " pdb=" CB TRP J 260 " pdb=" CG TRP J 260 " ideal model delta sigma weight residual 113.60 125.01 -11.41 1.90e+00 2.77e-01 3.61e+01 angle pdb=" OE1 GLN A 214 " pdb=" CD GLN A 214 " pdb=" NE2 GLN A 214 " ideal model delta sigma weight residual 122.60 116.79 5.81 1.00e+00 1.00e+00 3.37e+01 angle pdb=" OE1 GLN C 214 " pdb=" CD GLN C 214 " pdb=" NE2 GLN C 214 " ideal model delta sigma weight residual 122.60 116.86 5.74 1.00e+00 1.00e+00 3.30e+01 angle pdb=" OE1 GLN K 214 " pdb=" CD GLN K 214 " pdb=" NE2 GLN K 214 " ideal model delta sigma weight residual 122.60 116.89 5.71 1.00e+00 1.00e+00 3.26e+01 angle pdb=" C SER K 229 " pdb=" N THR K 230 " pdb=" CA THR K 230 " ideal model delta sigma weight residual 121.54 132.20 -10.66 1.91e+00 2.74e-01 3.11e+01 ... (remaining 44971 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.02: 18446 18.02 - 36.03: 1265 36.03 - 54.05: 309 54.05 - 72.06: 110 72.06 - 90.07: 66 Dihedral angle restraints: 20196 sinusoidal: 8244 harmonic: 11952 Sorted by residual: dihedral pdb=" C LYS F 248 " pdb=" N LYS F 248 " pdb=" CA LYS F 248 " pdb=" CB LYS F 248 " ideal model delta harmonic sigma weight residual -122.60 -139.00 16.40 0 2.50e+00 1.60e-01 4.30e+01 dihedral pdb=" C LYS L 248 " pdb=" N LYS L 248 " pdb=" CA LYS L 248 " pdb=" CB LYS L 248 " ideal model delta harmonic sigma weight residual -122.60 -137.88 15.28 0 2.50e+00 1.60e-01 3.74e+01 dihedral pdb=" C LYS B 248 " pdb=" N LYS B 248 " pdb=" CA LYS B 248 " pdb=" CB LYS B 248 " ideal model delta harmonic sigma weight residual -122.60 -137.86 15.26 0 2.50e+00 1.60e-01 3.73e+01 ... (remaining 20193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 3970 0.118 - 0.236: 844 0.236 - 0.353: 60 0.353 - 0.471: 11 0.471 - 0.589: 11 Chirality restraints: 4896 Sorted by residual: chirality pdb=" CA LYS F 248 " pdb=" N LYS F 248 " pdb=" C LYS F 248 " pdb=" CB LYS F 248 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.59 2.00e-01 2.50e+01 8.67e+00 chirality pdb=" CA LYS L 248 " pdb=" N LYS L 248 " pdb=" C LYS L 248 " pdb=" CB LYS L 248 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.88e+00 chirality pdb=" CA LYS B 248 " pdb=" N LYS B 248 " pdb=" C LYS B 248 " pdb=" CB LYS B 248 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.39e+00 ... (remaining 4893 not shown) Planarity restraints: 5904 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR I 172 " 0.179 2.00e-02 2.50e+03 9.19e-02 1.69e+02 pdb=" CG TYR I 172 " -0.079 2.00e-02 2.50e+03 pdb=" CD1 TYR I 172 " -0.076 2.00e-02 2.50e+03 pdb=" CD2 TYR I 172 " -0.086 2.00e-02 2.50e+03 pdb=" CE1 TYR I 172 " -0.039 2.00e-02 2.50e+03 pdb=" CE2 TYR I 172 " -0.031 2.00e-02 2.50e+03 pdb=" CZ TYR I 172 " 0.018 2.00e-02 2.50e+03 pdb=" OH TYR I 172 " 0.115 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 172 " -0.179 2.00e-02 2.50e+03 9.19e-02 1.69e+02 pdb=" CG TYR C 172 " 0.079 2.00e-02 2.50e+03 pdb=" CD1 TYR C 172 " 0.076 2.00e-02 2.50e+03 pdb=" CD2 TYR C 172 " 0.086 2.00e-02 2.50e+03 pdb=" CE1 TYR C 172 " 0.039 2.00e-02 2.50e+03 pdb=" CE2 TYR C 172 " 0.031 2.00e-02 2.50e+03 pdb=" CZ TYR C 172 " -0.018 2.00e-02 2.50e+03 pdb=" OH TYR C 172 " -0.115 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR K 172 " 0.179 2.00e-02 2.50e+03 9.17e-02 1.68e+02 pdb=" CG TYR K 172 " -0.079 2.00e-02 2.50e+03 pdb=" CD1 TYR K 172 " -0.076 2.00e-02 2.50e+03 pdb=" CD2 TYR K 172 " -0.086 2.00e-02 2.50e+03 pdb=" CE1 TYR K 172 " -0.039 2.00e-02 2.50e+03 pdb=" CE2 TYR K 172 " -0.031 2.00e-02 2.50e+03 pdb=" CZ TYR K 172 " 0.018 2.00e-02 2.50e+03 pdb=" OH TYR K 172 " 0.115 2.00e-02 2.50e+03 ... (remaining 5901 not shown) Histogram of nonbonded interaction distances: 1.26 - 1.99: 42 1.99 - 2.72: 575 2.72 - 3.44: 51039 3.44 - 4.17: 78344 4.17 - 4.90: 138801 Nonbonded interactions: 268801 Sorted by model distance: nonbonded pdb=" CE LYS H 307 " pdb=" CB SER I 308 " model vdw 1.258 3.840 nonbonded pdb=" CE LYS B 307 " pdb=" CB SER C 308 " model vdw 1.258 3.840 nonbonded pdb=" CE LYS D 307 " pdb=" CB SER E 308 " model vdw 1.259 3.840 nonbonded pdb=" CE LYS J 307 " pdb=" CB SER K 308 " model vdw 1.259 3.840 nonbonded pdb=" CB SER A 308 " pdb=" CE LYS L 307 " model vdw 1.259 3.840 ... (remaining 268796 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.080 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: 15.600 Check model and map are aligned: 0.470 Set scattering table: 0.270 Process input model: 79.480 Find NCS groups from input model: 2.170 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6765 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 : 0.012 0.041 33300 Z= 0.773 Angle : 1.783 11.414 44976 Z= 1.169 Chirality : 0.095 0.589 4896 Planarity : 0.016 0.150 5904 Dihedral : 15.334 90.075 12492 Min Nonbonded Distance : 1.258 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 2.57 % Allowed : 6.64 % Favored : 90.79 % Rotamer: Outliers : 2.01 % Allowed : 6.94 % Favored : 91.04 % Cbeta Deviations : 0.39 % 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 (0.12), residues: 4128 helix: -1.37 (0.10), residues: 1744 sheet: 0.26 (0.24), residues: 424 loop : -2.27 (0.14), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.118 0.021 TRP F 260 HIS 0.013 0.004 HIS J 300 PHE 0.069 0.017 PHE K 218 TYR 0.179 0.022 TYR I 172 ARG 0.011 0.001 ARG B 258 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1193 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 1122 time to evaluate : 3.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASP cc_start: 0.6114 (OUTLIER) cc_final: 0.5586 (m-30) REVERT: A 89 ASN cc_start: 0.6561 (m-40) cc_final: 0.5740 (m-40) REVERT: A 244 GLU cc_start: 0.5844 (OUTLIER) cc_final: 0.5285 (mm-30) REVERT: B 195 SER cc_start: 0.7796 (t) cc_final: 0.7547 (p) REVERT: B 232 GLU cc_start: 0.3631 (OUTLIER) cc_final: 0.3307 (pm20) REVERT: C 382 THR cc_start: 0.8621 (p) cc_final: 0.8178 (p) REVERT: D 88 ASP cc_start: 0.5990 (t0) cc_final: 0.5634 (t0) REVERT: D 220 ASN cc_start: 0.7524 (m-40) cc_final: 0.6933 (m110) REVERT: D 364 ASP cc_start: 0.4987 (OUTLIER) cc_final: 0.4442 (p0) REVERT: E 248 LYS cc_start: 0.6120 (OUTLIER) cc_final: 0.4968 (ttpp) REVERT: E 320 LEU cc_start: 0.8479 (mt) cc_final: 0.8207 (mt) REVERT: F 118 GLU cc_start: 0.7185 (tt0) cc_final: 0.6903 (tt0) REVERT: G 106 SER cc_start: 0.7910 (t) cc_final: 0.7223 (p) REVERT: H 280 MET cc_start: 0.7069 (tpp) cc_final: 0.6756 (tpp) REVERT: I 279 GLU cc_start: 0.5144 (OUTLIER) cc_final: 0.4716 (tt0) REVERT: J 223 LYS cc_start: 0.8345 (mtmt) cc_final: 0.7975 (mtpp) REVERT: K 333 ARG cc_start: 0.5947 (mtt-85) cc_final: 0.5693 (mtm-85) REVERT: L 341 TRP cc_start: 0.8169 (m100) cc_final: 0.7732 (m100) outliers start: 71 outliers final: 20 residues processed: 1178 average time/residue: 0.4699 time to fit residues: 853.2716 Evaluate side-chains 648 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 622 time to evaluate : 3.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 248 LYS Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 327 LEU Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain I residue 279 GLU Chi-restraints excluded: chain J residue 229 SER Chi-restraints excluded: chain J residue 245 GLU Chi-restraints excluded: chain J residue 327 LEU Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 228 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 10.0000 chunk 309 optimal weight: 8.9990 chunk 171 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 208 optimal weight: 0.7980 chunk 165 optimal weight: 4.9990 chunk 319 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 chunk 194 optimal weight: 2.9990 chunk 238 optimal weight: 4.9990 chunk 370 optimal weight: 8.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 ASN B 86 GLN B 182 HIS B 214 GLN B 226 GLN B 318 GLN C 86 GLN C 89 ASN C 182 HIS C 226 GLN C 246 ASN ** D 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 318 GLN D 352 HIS E 86 GLN E 89 ASN E 324 GLN ** F 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 318 GLN G 86 GLN ** G 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 242 GLN H 86 GLN H 149 GLN H 226 GLN I 86 GLN ** I 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 167 GLN I 220 ASN I 318 GLN J 86 GLN ** J 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 226 GLN K 86 GLN K 220 ASN L 86 GLN L 89 ASN L 123 GLN ** L 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 318 GLN ** L 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.4191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 33300 Z= 0.279 Angle : 0.779 10.052 44976 Z= 0.410 Chirality : 0.045 0.167 4896 Planarity : 0.005 0.039 5904 Dihedral : 7.304 83.545 4565 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.87 % Allowed : 5.86 % Favored : 93.27 % Rotamer: Outliers : 4.00 % Allowed : 14.00 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.13), residues: 4128 helix: 0.51 (0.12), residues: 1772 sheet: -0.86 (0.19), residues: 688 loop : -1.51 (0.16), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP H 311 HIS 0.006 0.001 HIS I 355 PHE 0.034 0.003 PHE H 186 TYR 0.018 0.002 TYR H 105 ARG 0.009 0.001 ARG I 362 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 853 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 712 time to evaluate : 3.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASP cc_start: 0.6593 (OUTLIER) cc_final: 0.5994 (m-30) REVERT: C 153 MET cc_start: 0.8519 (tpp) cc_final: 0.8273 (tpp) REVERT: C 215 ARG cc_start: 0.7574 (ttt-90) cc_final: 0.7307 (ttp80) REVERT: C 283 SER cc_start: 0.7337 (t) cc_final: 0.6777 (t) REVERT: D 216 ASP cc_start: 0.6704 (m-30) cc_final: 0.6145 (m-30) REVERT: D 220 ASN cc_start: 0.7452 (m-40) cc_final: 0.7101 (m110) REVERT: D 283 SER cc_start: 0.6880 (OUTLIER) cc_final: 0.6267 (p) REVERT: D 347 ASP cc_start: 0.6834 (m-30) cc_final: 0.6591 (m-30) REVERT: E 248 LYS cc_start: 0.7146 (OUTLIER) cc_final: 0.6398 (ttpp) REVERT: F 111 MET cc_start: 0.7035 (mtt) cc_final: 0.6803 (mtt) REVERT: F 283 SER cc_start: 0.6313 (OUTLIER) cc_final: 0.6059 (p) REVERT: F 316 GLU cc_start: 0.7382 (tt0) cc_final: 0.7021 (tt0) REVERT: F 335 GLU cc_start: 0.7238 (mt-10) cc_final: 0.7009 (mt-10) REVERT: G 72 THR cc_start: 0.8577 (m) cc_final: 0.8064 (p) REVERT: G 76 CYS cc_start: 0.7983 (m) cc_final: 0.7429 (m) REVERT: G 392 MET cc_start: 0.6662 (mmm) cc_final: 0.6020 (mmm) REVERT: I 168 ARG cc_start: 0.6203 (tpt170) cc_final: 0.5908 (tmt170) REVERT: I 215 ARG cc_start: 0.7541 (OUTLIER) cc_final: 0.7115 (ttt90) REVERT: I 279 GLU cc_start: 0.5747 (OUTLIER) cc_final: 0.5311 (tp30) REVERT: I 318 GLN cc_start: 0.6410 (OUTLIER) cc_final: 0.5957 (mt0) REVERT: J 335 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7327 (mt-10) REVERT: K 153 MET cc_start: 0.8040 (tpp) cc_final: 0.7591 (mmm) REVERT: K 311 TRP cc_start: 0.3624 (OUTLIER) cc_final: 0.2820 (p90) REVERT: K 318 GLN cc_start: 0.8133 (tm-30) cc_final: 0.7793 (tm-30) REVERT: L 318 GLN cc_start: 0.6978 (mm-40) cc_final: 0.6756 (mm-40) REVERT: L 331 ILE cc_start: 0.8836 (mm) cc_final: 0.8607 (mt) outliers start: 141 outliers final: 69 residues processed: 818 average time/residue: 0.4194 time to fit residues: 547.5041 Evaluate side-chains 608 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 531 time to evaluate : 3.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 283 SER Chi-restraints excluded: chain E residue 53 ASN Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 149 GLN Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain E residue 248 LYS Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 283 SER Chi-restraints excluded: chain F residue 389 THR Chi-restraints excluded: chain F residue 390 ASP Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain G residue 311 TRP Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 109 GLN Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain I residue 88 ASP Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 215 ARG Chi-restraints excluded: chain I residue 279 GLU Chi-restraints excluded: chain I residue 318 GLN Chi-restraints excluded: chain I residue 320 LEU Chi-restraints excluded: chain I residue 389 THR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 122 MET Chi-restraints excluded: chain J residue 144 SER Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain J residue 389 THR Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 228 LEU Chi-restraints excluded: chain K residue 268 THR Chi-restraints excluded: chain K residue 302 VAL Chi-restraints excluded: chain K residue 311 TRP Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 112 THR Chi-restraints excluded: chain L residue 313 SER Chi-restraints excluded: chain L residue 327 LEU Chi-restraints excluded: chain L residue 388 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 3.9990 chunk 114 optimal weight: 9.9990 chunk 308 optimal weight: 4.9990 chunk 252 optimal weight: 9.9990 chunk 102 optimal weight: 10.0000 chunk 371 optimal weight: 1.9990 chunk 400 optimal weight: 10.0000 chunk 330 optimal weight: 6.9990 chunk 368 optimal weight: 0.9980 chunk 126 optimal weight: 0.8980 chunk 297 optimal weight: 8.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 214 GLN B 352 HIS C 86 GLN C 276 GLN C 318 GLN D 86 GLN D 214 GLN D 239 GLN D 276 GLN D 318 GLN F 214 GLN ** F 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 300 HIS ** G 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 220 ASN G 242 GLN H 182 HIS H 242 GLN I 129 ASN I 182 HIS I 214 GLN ** I 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 ASN L 89 ASN L 182 HIS L 352 HIS L 391 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.5372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 33300 Z= 0.245 Angle : 0.677 10.105 44976 Z= 0.357 Chirality : 0.044 0.163 4896 Planarity : 0.004 0.044 5904 Dihedral : 6.157 73.951 4540 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.80 % Allowed : 6.30 % Favored : 92.90 % Rotamer: Outliers : 4.39 % Allowed : 16.16 % Favored : 79.45 % 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: -0.40 (0.13), residues: 4128 helix: 0.96 (0.12), residues: 1752 sheet: -0.46 (0.21), residues: 588 loop : -1.44 (0.15), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP H 311 HIS 0.007 0.002 HIS L 352 PHE 0.033 0.002 PHE E 186 TYR 0.018 0.002 TYR J 164 ARG 0.009 0.001 ARG J 362 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 737 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 582 time to evaluate : 3.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASP cc_start: 0.6698 (p0) cc_final: 0.6293 (m-30) REVERT: B 227 ILE cc_start: 0.7407 (tp) cc_final: 0.7182 (tt) REVERT: B 280 MET cc_start: 0.7288 (tpt) cc_final: 0.7073 (tpt) REVERT: C 122 MET cc_start: 0.7759 (mmm) cc_final: 0.7439 (tpt) REVERT: C 392 MET cc_start: 0.6989 (mmp) cc_final: 0.6624 (mmt) REVERT: D 216 ASP cc_start: 0.6399 (m-30) cc_final: 0.6016 (m-30) REVERT: D 220 ASN cc_start: 0.7457 (m-40) cc_final: 0.7237 (m110) REVERT: D 232 GLU cc_start: 0.4543 (OUTLIER) cc_final: 0.4020 (pm20) REVERT: D 250 ILE cc_start: 0.1982 (OUTLIER) cc_final: 0.1683 (mm) REVERT: E 242 GLN cc_start: 0.7692 (mm-40) cc_final: 0.7425 (tp40) REVERT: E 248 LYS cc_start: 0.7204 (OUTLIER) cc_final: 0.6570 (ttpp) REVERT: F 197 ILE cc_start: 0.8480 (OUTLIER) cc_final: 0.8216 (tp) REVERT: G 72 THR cc_start: 0.8734 (m) cc_final: 0.8033 (p) REVERT: G 76 CYS cc_start: 0.8201 (m) cc_final: 0.7685 (m) REVERT: G 80 ASP cc_start: 0.6800 (m-30) cc_final: 0.6405 (m-30) REVERT: G 214 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.7891 (tm-30) REVERT: G 356 ASN cc_start: 0.7562 (p0) cc_final: 0.6894 (p0) REVERT: G 392 MET cc_start: 0.7023 (mmm) cc_final: 0.6717 (mmm) REVERT: H 76 CYS cc_start: 0.7121 (m) cc_final: 0.6838 (m) REVERT: H 153 MET cc_start: 0.6751 (tpp) cc_final: 0.6497 (tpp) REVERT: H 388 ARG cc_start: 0.6504 (ttt180) cc_final: 0.6303 (ttt180) REVERT: H 393 PRO cc_start: 0.7545 (Cg_exo) cc_final: 0.7213 (Cg_endo) REVERT: I 136 ARG cc_start: 0.6884 (ptp-170) cc_final: 0.6654 (ptp-110) REVERT: I 215 ARG cc_start: 0.7266 (OUTLIER) cc_final: 0.6869 (ttt90) REVERT: K 311 TRP cc_start: 0.3880 (OUTLIER) cc_final: 0.2828 (p90) REVERT: K 318 GLN cc_start: 0.8091 (tm-30) cc_final: 0.7821 (tm-30) REVERT: K 375 MET cc_start: 0.7094 (mmt) cc_final: 0.6754 (mmt) REVERT: L 184 LYS cc_start: 0.7590 (ttpt) cc_final: 0.7321 (ttpp) REVERT: L 318 GLN cc_start: 0.6973 (mm-40) cc_final: 0.6772 (mm-40) outliers start: 155 outliers final: 91 residues processed: 697 average time/residue: 0.4428 time to fit residues: 497.5398 Evaluate side-chains 615 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 517 time to evaluate : 3.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 125 CYS Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain E residue 53 ASN Chi-restraints excluded: chain E residue 92 LYS Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 248 LYS Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 197 ILE Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 243 VAL Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 389 THR Chi-restraints excluded: chain F residue 390 ASP Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain G residue 214 GLN Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 311 TRP Chi-restraints excluded: chain G residue 316 GLU Chi-restraints excluded: chain G residue 345 SER Chi-restraints excluded: chain G residue 382 THR Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 229 SER Chi-restraints excluded: chain H residue 234 VAL Chi-restraints excluded: chain H residue 247 PHE Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain I residue 88 ASP Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 215 ARG Chi-restraints excluded: chain I residue 273 VAL Chi-restraints excluded: chain I residue 279 GLU Chi-restraints excluded: chain I residue 280 MET Chi-restraints excluded: chain I residue 389 THR Chi-restraints excluded: chain J residue 84 THR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 122 MET Chi-restraints excluded: chain J residue 144 SER Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain J residue 302 VAL Chi-restraints excluded: chain J residue 360 LEU Chi-restraints excluded: chain J residue 389 THR Chi-restraints excluded: chain J residue 390 ASP Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 125 CYS Chi-restraints excluded: chain K residue 176 SER Chi-restraints excluded: chain K residue 228 LEU Chi-restraints excluded: chain K residue 255 VAL Chi-restraints excluded: chain K residue 268 THR Chi-restraints excluded: chain K residue 302 VAL Chi-restraints excluded: chain K residue 311 TRP Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 110 TYR Chi-restraints excluded: chain L residue 112 THR Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain L residue 274 THR Chi-restraints excluded: chain L residue 283 SER Chi-restraints excluded: chain L residue 313 SER Chi-restraints excluded: chain L residue 327 LEU Chi-restraints excluded: chain L residue 389 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 8.9990 chunk 279 optimal weight: 7.9990 chunk 192 optimal weight: 8.9990 chunk 41 optimal weight: 6.9990 chunk 177 optimal weight: 3.9990 chunk 249 optimal weight: 10.0000 chunk 372 optimal weight: 3.9990 chunk 394 optimal weight: 9.9990 chunk 194 optimal weight: 0.0070 chunk 353 optimal weight: 1.9990 chunk 106 optimal weight: 0.4980 overall best weight: 2.1004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 GLN B 214 GLN C 86 GLN D 239 GLN F 87 ASN ** F 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 GLN ** G 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 242 GLN ** H 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 220 ASN I 226 GLN I 318 GLN ** I 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 246 ASN J 352 HIS K 89 ASN K 287 GLN ** K 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 352 HIS L 391 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.5989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 33300 Z= 0.204 Angle : 0.621 8.952 44976 Z= 0.324 Chirality : 0.042 0.158 4896 Planarity : 0.004 0.061 5904 Dihedral : 5.805 85.364 4532 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.73 % Allowed : 5.67 % Favored : 93.60 % Rotamer: Outliers : 4.45 % Allowed : 17.38 % Favored : 78.17 % 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: -0.27 (0.13), residues: 4128 helix: 1.02 (0.13), residues: 1783 sheet: -0.39 (0.20), residues: 651 loop : -1.38 (0.16), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 311 HIS 0.008 0.001 HIS L 352 PHE 0.023 0.002 PHE A 186 TYR 0.016 0.001 TYR H 325 ARG 0.006 0.000 ARG B 165 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 728 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 571 time to evaluate : 3.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASP cc_start: 0.6929 (p0) cc_final: 0.6315 (m-30) REVERT: B 227 ILE cc_start: 0.7542 (tp) cc_final: 0.7302 (tt) REVERT: B 356 ASN cc_start: 0.7365 (OUTLIER) cc_final: 0.7065 (t0) REVERT: C 392 MET cc_start: 0.7238 (mmp) cc_final: 0.6926 (mmt) REVERT: D 120 MET cc_start: 0.7853 (tpp) cc_final: 0.7459 (mmm) REVERT: D 122 MET cc_start: 0.7951 (tpp) cc_final: 0.7430 (tpp) REVERT: D 213 GLN cc_start: 0.8700 (tm-30) cc_final: 0.8405 (tm-30) REVERT: D 216 ASP cc_start: 0.6366 (m-30) cc_final: 0.6078 (m-30) REVERT: D 220 ASN cc_start: 0.7396 (m-40) cc_final: 0.7174 (m-40) REVERT: D 232 GLU cc_start: 0.4376 (OUTLIER) cc_final: 0.3340 (mt-10) REVERT: E 248 LYS cc_start: 0.6980 (OUTLIER) cc_final: 0.6511 (ttpp) REVERT: F 197 ILE cc_start: 0.8232 (OUTLIER) cc_final: 0.7951 (tp) REVERT: F 335 GLU cc_start: 0.7556 (mt-10) cc_final: 0.7271 (mt-10) REVERT: G 72 THR cc_start: 0.8793 (m) cc_final: 0.7987 (p) REVERT: G 76 CYS cc_start: 0.8141 (m) cc_final: 0.7444 (m) REVERT: G 153 MET cc_start: 0.7360 (tpp) cc_final: 0.6636 (tpp) REVERT: G 214 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.8104 (tm-30) REVERT: G 356 ASN cc_start: 0.7769 (p0) cc_final: 0.6902 (p0) REVERT: G 392 MET cc_start: 0.7222 (mmm) cc_final: 0.6798 (mmm) REVERT: H 76 CYS cc_start: 0.6912 (m) cc_final: 0.6400 (m) REVERT: I 215 ARG cc_start: 0.7393 (OUTLIER) cc_final: 0.6967 (ttt90) REVERT: I 335 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.7026 (mt-10) REVERT: I 362 ARG cc_start: 0.8742 (ptm160) cc_final: 0.8356 (ptm160) REVERT: J 111 MET cc_start: 0.8210 (mtt) cc_final: 0.7903 (mtt) REVERT: K 153 MET cc_start: 0.8055 (tpp) cc_final: 0.7822 (mmm) REVERT: K 311 TRP cc_start: 0.3688 (OUTLIER) cc_final: 0.2600 (p90) REVERT: K 318 GLN cc_start: 0.8202 (tm-30) cc_final: 0.7764 (tm-30) REVERT: K 375 MET cc_start: 0.7036 (mmt) cc_final: 0.6742 (mmt) outliers start: 157 outliers final: 99 residues processed: 686 average time/residue: 0.4347 time to fit residues: 478.5563 Evaluate side-chains 625 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 518 time to evaluate : 3.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 311 TRP Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain B residue 111 MET Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 356 ASN Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 354 GLU Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain E residue 53 ASN Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain E residue 248 LYS Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 197 ILE Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 389 THR Chi-restraints excluded: chain F residue 390 ASP Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain G residue 189 THR Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 214 GLN Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 261 ILE Chi-restraints excluded: chain G residue 311 TRP Chi-restraints excluded: chain G residue 316 GLU Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 229 SER Chi-restraints excluded: chain H residue 234 VAL Chi-restraints excluded: chain H residue 247 PHE Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain I residue 88 ASP Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 215 ARG Chi-restraints excluded: chain I residue 279 GLU Chi-restraints excluded: chain I residue 280 MET Chi-restraints excluded: chain I residue 290 GLU Chi-restraints excluded: chain I residue 320 LEU Chi-restraints excluded: chain I residue 335 GLU Chi-restraints excluded: chain I residue 389 THR Chi-restraints excluded: chain J residue 84 THR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 122 MET Chi-restraints excluded: chain J residue 144 SER Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain J residue 183 LEU Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain J residue 302 VAL Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 360 LEU Chi-restraints excluded: chain J residue 389 THR Chi-restraints excluded: chain J residue 390 ASP Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 125 CYS Chi-restraints excluded: chain K residue 176 SER Chi-restraints excluded: chain K residue 228 LEU Chi-restraints excluded: chain K residue 255 VAL Chi-restraints excluded: chain K residue 261 ILE Chi-restraints excluded: chain K residue 268 THR Chi-restraints excluded: chain K residue 302 VAL Chi-restraints excluded: chain K residue 311 TRP Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 110 TYR Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain L residue 290 GLU Chi-restraints excluded: chain L residue 313 SER Chi-restraints excluded: chain L residue 388 ARG Chi-restraints excluded: chain L residue 389 THR Chi-restraints excluded: chain L residue 391 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 7.9990 chunk 223 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 293 optimal weight: 8.9990 chunk 162 optimal weight: 3.9990 chunk 336 optimal weight: 9.9990 chunk 272 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 201 optimal weight: 6.9990 chunk 353 optimal weight: 7.9990 chunk 99 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 GLN A 220 ASN A 318 GLN D 239 GLN ** E 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 ASN F 87 ASN F 182 HIS ** F 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 167 GLN G 182 HIS ** G 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 242 GLN ** I 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 318 GLN ** I 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 391 ASN K 89 ASN ** K 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 246 ASN ** L 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 352 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.6828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 33300 Z= 0.410 Angle : 0.740 10.481 44976 Z= 0.387 Chirality : 0.047 0.227 4896 Planarity : 0.005 0.072 5904 Dihedral : 6.284 102.814 4532 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.75 % Allowed : 7.29 % Favored : 91.96 % Rotamer: Outliers : 5.64 % Allowed : 18.51 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.13), residues: 4128 helix: 0.56 (0.12), residues: 1810 sheet: -0.82 (0.21), residues: 614 loop : -1.45 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 311 HIS 0.009 0.002 HIS H 300 PHE 0.032 0.002 PHE L 186 TYR 0.020 0.002 TYR E 330 ARG 0.008 0.001 ARG F 284 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 741 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 542 time to evaluate : 4.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASP cc_start: 0.7110 (p0) cc_final: 0.6496 (m-30) REVERT: A 89 ASN cc_start: 0.6991 (m-40) cc_final: 0.6017 (m-40) REVERT: B 227 ILE cc_start: 0.7639 (tp) cc_final: 0.7384 (tt) REVERT: C 110 TYR cc_start: 0.8082 (m-80) cc_final: 0.7865 (m-80) REVERT: C 392 MET cc_start: 0.7575 (mmp) cc_final: 0.7326 (mmt) REVERT: D 118 GLU cc_start: 0.7268 (tt0) cc_final: 0.7033 (tt0) REVERT: D 216 ASP cc_start: 0.6528 (m-30) cc_final: 0.6187 (m-30) REVERT: D 220 ASN cc_start: 0.7620 (m-40) cc_final: 0.7310 (m-40) REVERT: D 239 GLN cc_start: 0.5619 (tp-100) cc_final: 0.4534 (pt0) REVERT: D 347 ASP cc_start: 0.6743 (m-30) cc_final: 0.6467 (m-30) REVERT: E 168 ARG cc_start: 0.6308 (tpm170) cc_final: 0.6028 (tpm170) REVERT: F 215 ARG cc_start: 0.7668 (tmm160) cc_final: 0.7461 (tmm160) REVERT: G 76 CYS cc_start: 0.7961 (m) cc_final: 0.7462 (m) REVERT: G 214 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.7984 (tm-30) REVERT: G 356 ASN cc_start: 0.7973 (p0) cc_final: 0.7341 (p0) REVERT: G 392 MET cc_start: 0.7426 (mmm) cc_final: 0.6869 (mmm) REVERT: I 215 ARG cc_start: 0.7367 (OUTLIER) cc_final: 0.6995 (ttt90) REVERT: J 277 ASP cc_start: 0.6116 (t0) cc_final: 0.5745 (t0) REVERT: K 153 MET cc_start: 0.8085 (tpp) cc_final: 0.7796 (mmm) REVERT: K 311 TRP cc_start: 0.4134 (OUTLIER) cc_final: 0.3298 (p-90) REVERT: K 318 GLN cc_start: 0.8550 (tm-30) cc_final: 0.8034 (tm-30) outliers start: 199 outliers final: 139 residues processed: 688 average time/residue: 0.4163 time to fit residues: 461.5494 Evaluate side-chains 624 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 482 time to evaluate : 3.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 311 TRP Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 76 CYS Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 82 PHE Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 125 CYS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 367 SER Chi-restraints excluded: chain E residue 53 ASN Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 126 PHE Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 149 GLN Chi-restraints excluded: chain E residue 177 GLN Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain E residue 242 GLN Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain E residue 337 SER Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 257 LYS Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 389 THR Chi-restraints excluded: chain F residue 390 ASP Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 90 ARG Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain G residue 188 PHE Chi-restraints excluded: chain G residue 214 GLN Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 257 LYS Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 261 ILE Chi-restraints excluded: chain G residue 311 TRP Chi-restraints excluded: chain G residue 345 SER Chi-restraints excluded: chain G residue 382 THR Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 125 CYS Chi-restraints excluded: chain H residue 176 SER Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 229 SER Chi-restraints excluded: chain H residue 234 VAL Chi-restraints excluded: chain H residue 247 PHE Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain I residue 88 ASP Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain I residue 118 GLU Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 215 ARG Chi-restraints excluded: chain I residue 262 LEU Chi-restraints excluded: chain I residue 273 VAL Chi-restraints excluded: chain I residue 279 GLU Chi-restraints excluded: chain I residue 280 MET Chi-restraints excluded: chain I residue 290 GLU Chi-restraints excluded: chain I residue 320 LEU Chi-restraints excluded: chain I residue 375 MET Chi-restraints excluded: chain J residue 84 THR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 122 MET Chi-restraints excluded: chain J residue 144 SER Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain J residue 183 LEU Chi-restraints excluded: chain J residue 302 VAL Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 360 LEU Chi-restraints excluded: chain J residue 389 THR Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 146 LEU Chi-restraints excluded: chain K residue 176 SER Chi-restraints excluded: chain K residue 228 LEU Chi-restraints excluded: chain K residue 255 VAL Chi-restraints excluded: chain K residue 261 ILE Chi-restraints excluded: chain K residue 268 THR Chi-restraints excluded: chain K residue 302 VAL Chi-restraints excluded: chain K residue 311 TRP Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 122 MET Chi-restraints excluded: chain L residue 146 LEU Chi-restraints excluded: chain L residue 150 SER Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain L residue 290 GLU Chi-restraints excluded: chain L residue 313 SER Chi-restraints excluded: chain L residue 388 ARG Chi-restraints excluded: chain L residue 389 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 5.9990 chunk 355 optimal weight: 4.9990 chunk 77 optimal weight: 20.0000 chunk 231 optimal weight: 0.9990 chunk 97 optimal weight: 0.0060 chunk 394 optimal weight: 7.9990 chunk 327 optimal weight: 0.6980 chunk 182 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 130 optimal weight: 0.7980 chunk 207 optimal weight: 6.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 GLN A 220 ASN B 220 ASN C 167 GLN ** D 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 GLN E 384 ASN ** F 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 214 GLN G 242 GLN ** I 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 213 GLN ** J 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 ASN K 384 ASN L 246 ASN ** L 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 352 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.6983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 33300 Z= 0.159 Angle : 0.597 11.122 44976 Z= 0.311 Chirality : 0.041 0.222 4896 Planarity : 0.004 0.062 5904 Dihedral : 5.412 70.793 4525 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.75 % Allowed : 5.77 % Favored : 93.48 % Rotamer: Outliers : 3.17 % Allowed : 20.80 % Favored : 76.02 % 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: -0.19 (0.13), residues: 4128 helix: 1.06 (0.13), residues: 1761 sheet: 0.00 (0.21), residues: 542 loop : -1.37 (0.15), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 311 HIS 0.010 0.001 HIS L 352 PHE 0.019 0.001 PHE A 186 TYR 0.015 0.001 TYR E 110 ARG 0.005 0.000 ARG E 388 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 548 time to evaluate : 3.540 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 ASP cc_start: 0.6977 (p0) cc_final: 0.6439 (m-30) REVERT: A 89 ASN cc_start: 0.6991 (m-40) cc_final: 0.6072 (m-40) REVERT: A 182 HIS cc_start: 0.7593 (t70) cc_final: 0.7390 (t70) REVERT: B 227 ILE cc_start: 0.7617 (tp) cc_final: 0.7358 (tt) REVERT: D 122 MET cc_start: 0.7929 (tpp) cc_final: 0.7444 (tpp) REVERT: D 213 GLN cc_start: 0.8686 (tm-30) cc_final: 0.8398 (tm-30) REVERT: D 216 ASP cc_start: 0.6347 (m-30) cc_final: 0.5978 (m-30) REVERT: D 220 ASN cc_start: 0.7277 (m-40) cc_final: 0.7016 (m-40) REVERT: D 232 GLU cc_start: 0.4046 (OUTLIER) cc_final: 0.3106 (mt-10) REVERT: D 277 ASP cc_start: 0.5376 (OUTLIER) cc_final: 0.4824 (p0) REVERT: E 58 LEU cc_start: 0.8873 (tp) cc_final: 0.8526 (tt) REVERT: E 160 LYS cc_start: 0.6201 (tptt) cc_final: 0.5746 (mttm) REVERT: E 279 GLU cc_start: 0.4894 (OUTLIER) cc_final: 0.3844 (tm-30) REVERT: G 72 THR cc_start: 0.8792 (OUTLIER) cc_final: 0.7838 (p) REVERT: G 76 CYS cc_start: 0.7855 (m) cc_final: 0.7264 (m) REVERT: G 356 ASN cc_start: 0.7873 (p0) cc_final: 0.7082 (p0) REVERT: G 392 MET cc_start: 0.7422 (mmm) cc_final: 0.7080 (mmm) REVERT: H 255 VAL cc_start: 0.5628 (OUTLIER) cc_final: 0.5292 (p) REVERT: I 215 ARG cc_start: 0.7243 (OUTLIER) cc_final: 0.6835 (ttt90) REVERT: I 259 LEU cc_start: 0.6074 (OUTLIER) cc_final: 0.5869 (mt) REVERT: I 318 GLN cc_start: 0.6655 (OUTLIER) cc_final: 0.5897 (mt0) REVERT: I 362 ARG cc_start: 0.8790 (ptm160) cc_final: 0.8517 (ptm160) REVERT: J 111 MET cc_start: 0.8539 (mtt) cc_final: 0.7908 (mtt) REVERT: K 153 MET cc_start: 0.8122 (tpp) cc_final: 0.7884 (mmm) REVERT: K 227 ILE cc_start: 0.7977 (OUTLIER) cc_final: 0.7703 (mp) REVERT: K 311 TRP cc_start: 0.4233 (OUTLIER) cc_final: 0.2861 (p90) REVERT: K 318 GLN cc_start: 0.8394 (tm-30) cc_final: 0.7979 (tm-30) outliers start: 112 outliers final: 74 residues processed: 627 average time/residue: 0.4294 time to fit residues: 433.4211 Evaluate side-chains 584 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 500 time to evaluate : 3.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 311 TRP Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 168 ARG Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 136 ARG Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain E residue 53 ASN Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 126 PHE Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 137 ASN Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 390 ASP Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain G residue 188 PHE Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 261 ILE Chi-restraints excluded: chain G residue 311 TRP Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 176 SER Chi-restraints excluded: chain H residue 247 PHE Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 88 ASP Chi-restraints excluded: chain I residue 118 GLU Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 197 ILE Chi-restraints excluded: chain I residue 215 ARG Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain I residue 279 GLU Chi-restraints excluded: chain I residue 280 MET Chi-restraints excluded: chain I residue 290 GLU Chi-restraints excluded: chain I residue 318 GLN Chi-restraints excluded: chain I residue 320 LEU Chi-restraints excluded: chain I residue 367 SER Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 122 MET Chi-restraints excluded: chain J residue 144 SER Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain J residue 260 TRP Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 360 LEU Chi-restraints excluded: chain J residue 390 ASP Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 227 ILE Chi-restraints excluded: chain K residue 255 VAL Chi-restraints excluded: chain K residue 261 ILE Chi-restraints excluded: chain K residue 268 THR Chi-restraints excluded: chain K residue 302 VAL Chi-restraints excluded: chain K residue 311 TRP Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain L residue 281 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 224 optimal weight: 3.9990 chunk 288 optimal weight: 0.5980 chunk 223 optimal weight: 8.9990 chunk 332 optimal weight: 6.9990 chunk 220 optimal weight: 3.9990 chunk 393 optimal weight: 0.7980 chunk 246 optimal weight: 9.9990 chunk 239 optimal weight: 5.9990 chunk 181 optimal weight: 7.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 GLN D 336 ASN ** F 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 242 GLN ** I 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 238 GLN ** I 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 391 ASN L 318 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.7242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 33300 Z= 0.253 Angle : 0.633 10.212 44976 Z= 0.329 Chirality : 0.043 0.230 4896 Planarity : 0.004 0.070 5904 Dihedral : 5.416 74.951 4523 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.73 % Allowed : 7.00 % Favored : 92.27 % Rotamer: Outliers : 4.14 % Allowed : 20.52 % Favored : 75.34 % 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: -0.36 (0.13), residues: 4128 helix: 0.89 (0.12), residues: 1803 sheet: -0.23 (0.22), residues: 572 loop : -1.43 (0.15), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 311 HIS 0.008 0.001 HIS H 300 PHE 0.020 0.002 PHE L 186 TYR 0.015 0.002 TYR E 330 ARG 0.005 0.000 ARG A 215 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 516 time to evaluate : 3.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASP cc_start: 0.7069 (p0) cc_final: 0.6528 (m-30) REVERT: A 89 ASN cc_start: 0.6950 (m-40) cc_final: 0.6467 (t0) REVERT: B 227 ILE cc_start: 0.7595 (tp) cc_final: 0.7349 (tt) REVERT: D 122 MET cc_start: 0.7938 (tpp) cc_final: 0.7541 (tpp) REVERT: D 213 GLN cc_start: 0.8707 (tm-30) cc_final: 0.8421 (tm-30) REVERT: D 216 ASP cc_start: 0.6441 (m-30) cc_final: 0.6095 (m-30) REVERT: D 220 ASN cc_start: 0.7302 (m-40) cc_final: 0.7055 (m-40) REVERT: D 232 GLU cc_start: 0.4438 (OUTLIER) cc_final: 0.3406 (mt-10) REVERT: D 277 ASP cc_start: 0.5551 (OUTLIER) cc_final: 0.4830 (p0) REVERT: E 160 LYS cc_start: 0.6213 (tptt) cc_final: 0.5820 (mttm) REVERT: E 188 PHE cc_start: 0.8427 (OUTLIER) cc_final: 0.8137 (t80) REVERT: E 279 GLU cc_start: 0.5418 (OUTLIER) cc_final: 0.4040 (tm-30) REVERT: F 188 PHE cc_start: 0.7542 (OUTLIER) cc_final: 0.7103 (t80) REVERT: G 72 THR cc_start: 0.8865 (OUTLIER) cc_final: 0.8028 (p) REVERT: G 76 CYS cc_start: 0.7876 (m) cc_final: 0.7322 (m) REVERT: G 257 LYS cc_start: 0.6325 (OUTLIER) cc_final: 0.5994 (ptpt) REVERT: G 352 HIS cc_start: 0.6073 (t-170) cc_final: 0.5759 (t70) REVERT: G 356 ASN cc_start: 0.7951 (p0) cc_final: 0.7136 (p0) REVERT: G 392 MET cc_start: 0.7454 (mmm) cc_final: 0.7134 (mmm) REVERT: H 281 MET cc_start: 0.7805 (tpp) cc_final: 0.7567 (mmm) REVERT: I 215 ARG cc_start: 0.7243 (OUTLIER) cc_final: 0.6847 (ttt90) REVERT: I 259 LEU cc_start: 0.6339 (OUTLIER) cc_final: 0.6031 (mt) REVERT: I 318 GLN cc_start: 0.6810 (OUTLIER) cc_final: 0.6024 (mt0) REVERT: J 392 MET cc_start: 0.7406 (mmm) cc_final: 0.7030 (mmm) REVERT: K 153 MET cc_start: 0.8098 (tpp) cc_final: 0.7845 (mmm) REVERT: K 188 PHE cc_start: 0.8322 (OUTLIER) cc_final: 0.7769 (t80) REVERT: K 311 TRP cc_start: 0.4070 (OUTLIER) cc_final: 0.2774 (p90) REVERT: K 318 GLN cc_start: 0.8482 (tm-30) cc_final: 0.8006 (tm-30) outliers start: 146 outliers final: 104 residues processed: 624 average time/residue: 0.4326 time to fit residues: 435.1936 Evaluate side-chains 600 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 484 time to evaluate : 3.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 311 TRP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 125 CYS Chi-restraints excluded: chain C residue 168 ARG Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 136 ARG Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 367 SER Chi-restraints excluded: chain E residue 53 ASN Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 126 PHE Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 177 GLN Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 188 PHE Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 242 GLN Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 188 PHE Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 390 ASP Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain G residue 135 ASP Chi-restraints excluded: chain G residue 188 PHE Chi-restraints excluded: chain G residue 257 LYS Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 261 ILE Chi-restraints excluded: chain G residue 311 TRP Chi-restraints excluded: chain G residue 316 GLU Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 109 GLN Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 120 MET Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 234 VAL Chi-restraints excluded: chain H residue 247 PHE Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain H residue 263 GLU Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 88 ASP Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain I residue 118 GLU Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 197 ILE Chi-restraints excluded: chain I residue 215 ARG Chi-restraints excluded: chain I residue 248 LYS Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain I residue 262 LEU Chi-restraints excluded: chain I residue 279 GLU Chi-restraints excluded: chain I residue 280 MET Chi-restraints excluded: chain I residue 290 GLU Chi-restraints excluded: chain I residue 318 GLN Chi-restraints excluded: chain I residue 320 LEU Chi-restraints excluded: chain I residue 375 MET Chi-restraints excluded: chain J residue 76 CYS Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 122 MET Chi-restraints excluded: chain J residue 144 SER Chi-restraints excluded: chain J residue 260 TRP Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 360 LEU Chi-restraints excluded: chain J residue 390 ASP Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 188 PHE Chi-restraints excluded: chain K residue 255 VAL Chi-restraints excluded: chain K residue 261 ILE Chi-restraints excluded: chain K residue 268 THR Chi-restraints excluded: chain K residue 302 VAL Chi-restraints excluded: chain K residue 311 TRP Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain L residue 388 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 6.9990 chunk 157 optimal weight: 20.0000 chunk 234 optimal weight: 8.9990 chunk 118 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 76 optimal weight: 0.9990 chunk 250 optimal weight: 9.9990 chunk 267 optimal weight: 9.9990 chunk 194 optimal weight: 6.9990 chunk 36 optimal weight: 0.8980 chunk 309 optimal weight: 5.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 GLN ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 391 ASN ** D 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 182 HIS E 214 GLN F 177 GLN ** F 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 226 GLN ** J 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 287 GLN L 318 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.7528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 33300 Z= 0.323 Angle : 0.675 10.876 44976 Z= 0.350 Chirality : 0.045 0.236 4896 Planarity : 0.005 0.075 5904 Dihedral : 5.632 75.636 4522 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.78 % Allowed : 7.19 % Favored : 92.03 % Rotamer: Outliers : 4.39 % Allowed : 20.41 % Favored : 75.20 % 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: -0.55 (0.13), residues: 4128 helix: 0.72 (0.12), residues: 1806 sheet: -0.38 (0.22), residues: 588 loop : -1.51 (0.15), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP G 311 HIS 0.013 0.002 HIS L 352 PHE 0.025 0.002 PHE H 82 TYR 0.016 0.002 TYR E 330 ARG 0.008 0.001 ARG A 215 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 505 time to evaluate : 3.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASP cc_start: 0.7172 (p0) cc_final: 0.6708 (m-30) REVERT: A 89 ASN cc_start: 0.6907 (m-40) cc_final: 0.5923 (m-40) REVERT: D 122 MET cc_start: 0.8050 (tpp) cc_final: 0.7415 (ttp) REVERT: D 213 GLN cc_start: 0.8720 (tm-30) cc_final: 0.8408 (tm-30) REVERT: D 216 ASP cc_start: 0.6469 (m-30) cc_final: 0.6138 (m-30) REVERT: D 220 ASN cc_start: 0.7419 (m-40) cc_final: 0.7146 (m-40) REVERT: D 232 GLU cc_start: 0.4410 (OUTLIER) cc_final: 0.3493 (mt-10) REVERT: D 277 ASP cc_start: 0.5666 (OUTLIER) cc_final: 0.5157 (p0) REVERT: E 58 LEU cc_start: 0.8984 (tp) cc_final: 0.8608 (tt) REVERT: E 160 LYS cc_start: 0.6461 (tptt) cc_final: 0.5863 (mmtp) REVERT: E 188 PHE cc_start: 0.8511 (OUTLIER) cc_final: 0.8114 (t80) REVERT: E 279 GLU cc_start: 0.5371 (OUTLIER) cc_final: 0.4001 (tm-30) REVERT: F 111 MET cc_start: 0.8549 (ptp) cc_final: 0.8310 (ptp) REVERT: F 188 PHE cc_start: 0.7706 (OUTLIER) cc_final: 0.7184 (t80) REVERT: F 277 ASP cc_start: 0.5659 (OUTLIER) cc_final: 0.4687 (t70) REVERT: G 72 THR cc_start: 0.8832 (OUTLIER) cc_final: 0.7869 (p) REVERT: G 76 CYS cc_start: 0.7852 (m) cc_final: 0.7328 (m) REVERT: G 120 MET cc_start: 0.8202 (mmm) cc_final: 0.7893 (tpt) REVERT: G 257 LYS cc_start: 0.6485 (OUTLIER) cc_final: 0.6101 (ptpt) REVERT: G 356 ASN cc_start: 0.7946 (p0) cc_final: 0.7201 (p0) REVERT: I 215 ARG cc_start: 0.7257 (OUTLIER) cc_final: 0.6864 (ttt90) REVERT: I 318 GLN cc_start: 0.6952 (OUTLIER) cc_final: 0.6148 (mt0) REVERT: K 153 MET cc_start: 0.8075 (tpp) cc_final: 0.7786 (mmm) REVERT: K 188 PHE cc_start: 0.8330 (OUTLIER) cc_final: 0.7853 (t80) REVERT: K 311 TRP cc_start: 0.4359 (OUTLIER) cc_final: 0.3498 (p-90) REVERT: K 318 GLN cc_start: 0.8582 (tm-30) cc_final: 0.7990 (tm-30) outliers start: 155 outliers final: 116 residues processed: 620 average time/residue: 0.4752 time to fit residues: 477.4834 Evaluate side-chains 608 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 480 time to evaluate : 3.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 311 TRP Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 82 PHE Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 125 CYS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 367 SER Chi-restraints excluded: chain E residue 53 ASN Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 126 PHE Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 177 GLN Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 188 PHE Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 242 GLN Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain E residue 377 GLU Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 188 PHE Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 277 ASP Chi-restraints excluded: chain F residue 313 SER Chi-restraints excluded: chain F residue 390 ASP Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain G residue 135 ASP Chi-restraints excluded: chain G residue 188 PHE Chi-restraints excluded: chain G residue 257 LYS Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 311 TRP Chi-restraints excluded: chain G residue 316 GLU Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 234 VAL Chi-restraints excluded: chain H residue 247 PHE Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain H residue 263 GLU Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 88 ASP Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain I residue 118 GLU Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 197 ILE Chi-restraints excluded: chain I residue 215 ARG Chi-restraints excluded: chain I residue 248 LYS Chi-restraints excluded: chain I residue 262 LEU Chi-restraints excluded: chain I residue 279 GLU Chi-restraints excluded: chain I residue 280 MET Chi-restraints excluded: chain I residue 290 GLU Chi-restraints excluded: chain I residue 318 GLN Chi-restraints excluded: chain I residue 320 LEU Chi-restraints excluded: chain I residue 375 MET Chi-restraints excluded: chain I residue 389 THR Chi-restraints excluded: chain J residue 76 CYS Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 122 MET Chi-restraints excluded: chain J residue 144 SER Chi-restraints excluded: chain J residue 162 VAL Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain J residue 260 TRP Chi-restraints excluded: chain J residue 302 VAL Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 360 LEU Chi-restraints excluded: chain J residue 389 THR Chi-restraints excluded: chain J residue 390 ASP Chi-restraints excluded: chain K residue 71 SER Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 188 PHE Chi-restraints excluded: chain K residue 255 VAL Chi-restraints excluded: chain K residue 261 ILE Chi-restraints excluded: chain K residue 268 THR Chi-restraints excluded: chain K residue 302 VAL Chi-restraints excluded: chain K residue 311 TRP Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain L residue 281 MET Chi-restraints excluded: chain L residue 318 GLN Chi-restraints excluded: chain L residue 388 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 8.9990 chunk 376 optimal weight: 3.9990 chunk 343 optimal weight: 5.9990 chunk 366 optimal weight: 0.8980 chunk 220 optimal weight: 10.0000 chunk 159 optimal weight: 2.9990 chunk 287 optimal weight: 8.9990 chunk 112 optimal weight: 7.9990 chunk 331 optimal weight: 7.9990 chunk 346 optimal weight: 6.9990 chunk 365 optimal weight: 0.7980 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 GLN ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 214 GLN ** F 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 391 ASN ** I 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 391 ASN L 318 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.7641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 33300 Z= 0.245 Angle : 0.634 11.886 44976 Z= 0.329 Chirality : 0.043 0.233 4896 Planarity : 0.004 0.069 5904 Dihedral : 5.438 74.156 4521 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.73 % Allowed : 7.29 % Favored : 91.98 % Rotamer: Outliers : 4.25 % Allowed : 20.80 % Favored : 74.94 % 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: -0.41 (0.13), residues: 4128 helix: 0.90 (0.13), residues: 1764 sheet: -0.13 (0.21), residues: 612 loop : -1.55 (0.15), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 311 HIS 0.015 0.001 HIS L 352 PHE 0.026 0.002 PHE H 82 TYR 0.016 0.002 TYR F 105 ARG 0.007 0.000 ARG A 215 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 493 time to evaluate : 4.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASP cc_start: 0.7141 (p0) cc_final: 0.6680 (m-30) REVERT: A 89 ASN cc_start: 0.6930 (m-40) cc_final: 0.6017 (m-40) REVERT: C 122 MET cc_start: 0.7788 (tpt) cc_final: 0.7495 (tpt) REVERT: D 122 MET cc_start: 0.8034 (tpp) cc_final: 0.7398 (ttp) REVERT: D 188 PHE cc_start: 0.8283 (OUTLIER) cc_final: 0.7947 (t80) REVERT: D 213 GLN cc_start: 0.8710 (tm-30) cc_final: 0.8466 (tm-30) REVERT: D 216 ASP cc_start: 0.6447 (m-30) cc_final: 0.6132 (m-30) REVERT: D 220 ASN cc_start: 0.7296 (m-40) cc_final: 0.7065 (m-40) REVERT: D 232 GLU cc_start: 0.4253 (OUTLIER) cc_final: 0.3459 (mt-10) REVERT: D 277 ASP cc_start: 0.5460 (OUTLIER) cc_final: 0.4552 (p0) REVERT: E 58 LEU cc_start: 0.8985 (tp) cc_final: 0.8604 (tt) REVERT: E 160 LYS cc_start: 0.6415 (tptt) cc_final: 0.5820 (mmtp) REVERT: E 188 PHE cc_start: 0.8470 (OUTLIER) cc_final: 0.8132 (t80) REVERT: E 279 GLU cc_start: 0.5104 (OUTLIER) cc_final: 0.3759 (tm-30) REVERT: F 188 PHE cc_start: 0.7565 (OUTLIER) cc_final: 0.7165 (t80) REVERT: F 277 ASP cc_start: 0.5667 (OUTLIER) cc_final: 0.4570 (t70) REVERT: G 72 THR cc_start: 0.8824 (OUTLIER) cc_final: 0.7915 (p) REVERT: G 76 CYS cc_start: 0.7801 (m) cc_final: 0.7287 (m) REVERT: G 120 MET cc_start: 0.8200 (mmm) cc_final: 0.7872 (tpt) REVERT: G 257 LYS cc_start: 0.6386 (OUTLIER) cc_final: 0.5895 (ptpt) REVERT: G 356 ASN cc_start: 0.7951 (p0) cc_final: 0.7160 (p0) REVERT: G 392 MET cc_start: 0.7178 (mmm) cc_final: 0.6915 (mmm) REVERT: I 120 MET cc_start: 0.7932 (mmm) cc_final: 0.7402 (tpp) REVERT: I 215 ARG cc_start: 0.7203 (OUTLIER) cc_final: 0.6852 (ttt90) REVERT: I 318 GLN cc_start: 0.6895 (OUTLIER) cc_final: 0.6087 (mt0) REVERT: J 123 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7846 (mt0) REVERT: K 153 MET cc_start: 0.8058 (tpp) cc_final: 0.7756 (mmm) REVERT: K 188 PHE cc_start: 0.8279 (OUTLIER) cc_final: 0.7806 (t80) REVERT: K 311 TRP cc_start: 0.4540 (OUTLIER) cc_final: 0.3029 (p90) REVERT: K 318 GLN cc_start: 0.8532 (tm-30) cc_final: 0.8053 (tm-30) outliers start: 150 outliers final: 117 residues processed: 606 average time/residue: 0.4184 time to fit residues: 408.6705 Evaluate side-chains 608 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 477 time to evaluate : 3.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 311 TRP Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 125 CYS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 188 PHE Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 367 SER Chi-restraints excluded: chain E residue 53 ASN Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 126 PHE Chi-restraints excluded: chain E residue 177 GLN Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 188 PHE Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 242 GLN Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 377 GLU Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 76 CYS Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 188 PHE Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 277 ASP Chi-restraints excluded: chain F residue 389 THR Chi-restraints excluded: chain F residue 390 ASP Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 90 ARG Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain G residue 135 ASP Chi-restraints excluded: chain G residue 188 PHE Chi-restraints excluded: chain G residue 257 LYS Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 311 TRP Chi-restraints excluded: chain G residue 316 GLU Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 229 SER Chi-restraints excluded: chain H residue 234 VAL Chi-restraints excluded: chain H residue 247 PHE Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain H residue 263 GLU Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 88 ASP Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 197 ILE Chi-restraints excluded: chain I residue 215 ARG Chi-restraints excluded: chain I residue 248 LYS Chi-restraints excluded: chain I residue 279 GLU Chi-restraints excluded: chain I residue 280 MET Chi-restraints excluded: chain I residue 290 GLU Chi-restraints excluded: chain I residue 318 GLN Chi-restraints excluded: chain I residue 320 LEU Chi-restraints excluded: chain I residue 375 MET Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 122 MET Chi-restraints excluded: chain J residue 123 GLN Chi-restraints excluded: chain J residue 144 SER Chi-restraints excluded: chain J residue 162 VAL Chi-restraints excluded: chain J residue 260 TRP Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 360 LEU Chi-restraints excluded: chain J residue 390 ASP Chi-restraints excluded: chain K residue 71 SER Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 176 SER Chi-restraints excluded: chain K residue 188 PHE Chi-restraints excluded: chain K residue 255 VAL Chi-restraints excluded: chain K residue 261 ILE Chi-restraints excluded: chain K residue 268 THR Chi-restraints excluded: chain K residue 302 VAL Chi-restraints excluded: chain K residue 311 TRP Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain L residue 281 MET Chi-restraints excluded: chain L residue 318 GLN Chi-restraints excluded: chain L residue 388 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 5.9990 chunk 387 optimal weight: 8.9990 chunk 236 optimal weight: 6.9990 chunk 183 optimal weight: 10.0000 chunk 269 optimal weight: 5.9990 chunk 406 optimal weight: 0.9980 chunk 374 optimal weight: 0.9990 chunk 323 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 250 optimal weight: 6.9990 chunk 198 optimal weight: 4.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 GLN A 220 ASN ** D 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 391 ASN E 214 GLN F 167 GLN ** F 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 391 ASN L 318 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.7790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 33300 Z= 0.292 Angle : 0.664 12.992 44976 Z= 0.344 Chirality : 0.044 0.238 4896 Planarity : 0.005 0.082 5904 Dihedral : 5.509 70.457 4521 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.75 % Allowed : 7.63 % Favored : 91.62 % Rotamer: Outliers : 4.05 % Allowed : 21.51 % Favored : 74.43 % 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: -0.61 (0.13), residues: 4128 helix: 0.72 (0.12), residues: 1806 sheet: -0.48 (0.21), residues: 648 loop : -1.60 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP G 311 HIS 0.016 0.002 HIS L 352 PHE 0.024 0.002 PHE H 82 TYR 0.015 0.002 TYR E 330 ARG 0.009 0.001 ARG C 168 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 482 time to evaluate : 3.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASP cc_start: 0.7166 (p0) cc_final: 0.6740 (m-30) REVERT: A 89 ASN cc_start: 0.6985 (m-40) cc_final: 0.6022 (m-40) REVERT: D 122 MET cc_start: 0.8040 (tpp) cc_final: 0.7428 (ttp) REVERT: D 188 PHE cc_start: 0.8318 (OUTLIER) cc_final: 0.7944 (t80) REVERT: D 213 GLN cc_start: 0.8705 (tm-30) cc_final: 0.8442 (tm-30) REVERT: D 216 ASP cc_start: 0.6462 (m-30) cc_final: 0.6167 (m-30) REVERT: D 220 ASN cc_start: 0.7303 (m-40) cc_final: 0.7072 (m-40) REVERT: D 232 GLU cc_start: 0.4309 (OUTLIER) cc_final: 0.3492 (mt-10) REVERT: D 277 ASP cc_start: 0.5592 (OUTLIER) cc_final: 0.4405 (p0) REVERT: E 160 LYS cc_start: 0.6567 (tptt) cc_final: 0.6045 (mmtp) REVERT: E 188 PHE cc_start: 0.8502 (OUTLIER) cc_final: 0.8170 (t80) REVERT: E 279 GLU cc_start: 0.5212 (OUTLIER) cc_final: 0.3744 (tm-30) REVERT: F 188 PHE cc_start: 0.7682 (OUTLIER) cc_final: 0.7335 (t80) REVERT: F 277 ASP cc_start: 0.5745 (OUTLIER) cc_final: 0.4892 (t0) REVERT: G 72 THR cc_start: 0.8836 (OUTLIER) cc_final: 0.7933 (p) REVERT: G 76 CYS cc_start: 0.7786 (m) cc_final: 0.7289 (m) REVERT: G 120 MET cc_start: 0.8184 (mmm) cc_final: 0.7933 (tpt) REVERT: G 257 LYS cc_start: 0.6408 (OUTLIER) cc_final: 0.5922 (ptpt) REVERT: G 356 ASN cc_start: 0.7946 (p0) cc_final: 0.7187 (p0) REVERT: H 105 TYR cc_start: 0.8303 (t80) cc_final: 0.8049 (t80) REVERT: I 215 ARG cc_start: 0.7255 (OUTLIER) cc_final: 0.6893 (ttt90) REVERT: I 318 GLN cc_start: 0.6980 (OUTLIER) cc_final: 0.6177 (mt0) REVERT: J 123 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7874 (mt0) REVERT: K 153 MET cc_start: 0.8078 (tpp) cc_final: 0.7781 (mmm) REVERT: K 188 PHE cc_start: 0.8341 (OUTLIER) cc_final: 0.7867 (t80) REVERT: K 311 TRP cc_start: 0.4572 (OUTLIER) cc_final: 0.3477 (p-90) REVERT: K 318 GLN cc_start: 0.8564 (tm-30) cc_final: 0.8009 (tm-30) outliers start: 143 outliers final: 125 residues processed: 590 average time/residue: 0.4749 time to fit residues: 455.1627 Evaluate side-chains 618 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 479 time to evaluate : 3.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 311 TRP Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 125 CYS Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 188 PHE Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 367 SER Chi-restraints excluded: chain E residue 53 ASN Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 126 PHE Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 177 GLN Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 188 PHE Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 242 GLN Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 377 GLU Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 76 CYS Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 188 PHE Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 277 ASP Chi-restraints excluded: chain F residue 389 THR Chi-restraints excluded: chain F residue 390 ASP Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 90 ARG Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain G residue 135 ASP Chi-restraints excluded: chain G residue 188 PHE Chi-restraints excluded: chain G residue 257 LYS Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 311 TRP Chi-restraints excluded: chain G residue 316 GLU Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 109 GLN Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 229 SER Chi-restraints excluded: chain H residue 234 VAL Chi-restraints excluded: chain H residue 247 PHE Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 88 ASP Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 197 ILE Chi-restraints excluded: chain I residue 215 ARG Chi-restraints excluded: chain I residue 248 LYS Chi-restraints excluded: chain I residue 279 GLU Chi-restraints excluded: chain I residue 280 MET Chi-restraints excluded: chain I residue 290 GLU Chi-restraints excluded: chain I residue 318 GLN Chi-restraints excluded: chain I residue 320 LEU Chi-restraints excluded: chain I residue 375 MET Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain J residue 110 TYR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 122 MET Chi-restraints excluded: chain J residue 123 GLN Chi-restraints excluded: chain J residue 144 SER Chi-restraints excluded: chain J residue 162 VAL Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain J residue 188 PHE Chi-restraints excluded: chain J residue 260 TRP Chi-restraints excluded: chain J residue 302 VAL Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 360 LEU Chi-restraints excluded: chain J residue 390 ASP Chi-restraints excluded: chain K residue 71 SER Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 176 SER Chi-restraints excluded: chain K residue 188 PHE Chi-restraints excluded: chain K residue 255 VAL Chi-restraints excluded: chain K residue 261 ILE Chi-restraints excluded: chain K residue 268 THR Chi-restraints excluded: chain K residue 302 VAL Chi-restraints excluded: chain K residue 311 TRP Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain L residue 281 MET Chi-restraints excluded: chain L residue 318 GLN Chi-restraints excluded: chain L residue 388 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 8.9990 chunk 344 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 298 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 chunk 89 optimal weight: 40.0000 chunk 324 optimal weight: 9.9990 chunk 135 optimal weight: 7.9990 chunk 332 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 59 optimal weight: 8.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 GLN A 220 ASN D 352 HIS E 214 GLN ** F 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 317 GLN ** I 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 391 ASN ** J 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 391 ASN L 318 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.152076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.125364 restraints weight = 46225.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.128670 restraints weight = 26004.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.130746 restraints weight = 18146.724| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.7876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 33300 Z= 0.247 Angle : 0.642 12.828 44976 Z= 0.331 Chirality : 0.043 0.242 4896 Planarity : 0.005 0.074 5904 Dihedral : 5.392 70.383 4521 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.73 % Allowed : 7.22 % Favored : 92.05 % Rotamer: Outliers : 4.05 % Allowed : 21.54 % Favored : 74.40 % 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: -0.47 (0.13), residues: 4128 helix: 0.89 (0.13), residues: 1764 sheet: -0.18 (0.21), residues: 612 loop : -1.63 (0.15), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 311 HIS 0.017 0.001 HIS L 352 PHE 0.023 0.002 PHE H 82 TYR 0.014 0.001 TYR E 330 ARG 0.009 0.000 ARG A 215 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8107.23 seconds wall clock time: 146 minutes 0.41 seconds (8760.41 seconds total)