Starting phenix.real_space_refine on Sat Feb 17 11:14:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pxc_13697/02_2024/7pxc_13697_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pxc_13697/02_2024/7pxc_13697.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pxc_13697/02_2024/7pxc_13697.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pxc_13697/02_2024/7pxc_13697.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pxc_13697/02_2024/7pxc_13697_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pxc_13697/02_2024/7pxc_13697_neut_updated.pdb" } resolution = 3.84 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 17 5.49 5 Mg 5 5.21 5 S 179 5.16 5 C 43158 2.51 5 N 12094 2.21 5 O 13355 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 ARG 14": "NH1" <-> "NH2" Residue "0 GLU 15": "OE1" <-> "OE2" Residue "2 GLU 119": "OE1" <-> "OE2" Residue "8 ARG 26": "NH1" <-> "NH2" Residue "A ARG 212": "NH1" <-> "NH2" Residue "A GLU 336": "OE1" <-> "OE2" Residue "A ARG 494": "NH1" <-> "NH2" Residue "A GLU 536": "OE1" <-> "OE2" Residue "B GLU 239": "OE1" <-> "OE2" Residue "B GLU 244": "OE1" <-> "OE2" Residue "B GLU 269": "OE1" <-> "OE2" Residue "B ARG 380": "NH1" <-> "NH2" Residue "B ARG 427": "NH1" <-> "NH2" Residue "B GLU 506": "OE1" <-> "OE2" Residue "B GLU 557": "OE1" <-> "OE2" Residue "C GLU 231": "OE1" <-> "OE2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 378": "NH1" <-> "NH2" Residue "C ARG 427": "NH1" <-> "NH2" Residue "C ARG 494": "NH1" <-> "NH2" Residue "C GLU 554": "OE1" <-> "OE2" Residue "D GLU 269": "OE1" <-> "OE2" Residue "D GLU 280": "OE1" <-> "OE2" Residue "D GLU 344": "OE1" <-> "OE2" Residue "D ASP 441": "OD1" <-> "OD2" Residue "D GLU 489": "OE1" <-> "OE2" Residue "D ARG 543": "NH1" <-> "NH2" Residue "D GLU 557": "OE1" <-> "OE2" Residue "E GLU 336": "OE1" <-> "OE2" Residue "E GLU 346": "OE1" <-> "OE2" Residue "E ARG 378": "NH1" <-> "NH2" Residue "E ARG 380": "NH1" <-> "NH2" Residue "E GLU 455": "OE1" <-> "OE2" Residue "E ARG 494": "NH1" <-> "NH2" Residue "E GLU 497": "OE1" <-> "OE2" Residue "E GLU 559": "OE1" <-> "OE2" Residue "E ARG 580": "NH1" <-> "NH2" Residue "F GLU 145": "OE1" <-> "OE2" Residue "F GLU 262": "OE1" <-> "OE2" Residue "F GLU 344": "OE1" <-> "OE2" Residue "H TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 382": "NH1" <-> "NH2" Residue "H GLU 432": "OE1" <-> "OE2" Residue "H ARG 488": "NH1" <-> "NH2" Residue "I PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 382": "NH1" <-> "NH2" Residue "J ARG 488": "NH1" <-> "NH2" Residue "K PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 132": "OE1" <-> "OE2" Residue "K GLU 173": "OE1" <-> "OE2" Residue "L GLU 432": "OE1" <-> "OE2" Residue "L ARG 488": "NH1" <-> "NH2" Residue "L GLU 512": "OE1" <-> "OE2" Residue "L ARG 515": "NH1" <-> "NH2" Residue "M GLU 434": "OE1" <-> "OE2" Residue "M ARG 488": "NH1" <-> "NH2" Residue "M GLU 512": "OE1" <-> "OE2" Residue "N ARG 382": "NH1" <-> "NH2" Residue "N GLU 434": "OE1" <-> "OE2" Residue "N ARG 488": "NH1" <-> "NH2" Residue "N ARG 515": "NH1" <-> "NH2" Residue "O PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 132": "OE1" <-> "OE2" Residue "O GLU 173": "OE1" <-> "OE2" Residue "P ARG 465": "NH1" <-> "NH2" Residue "P ARG 488": "NH1" <-> "NH2" Residue "P GLU 512": "OE1" <-> "OE2" Residue "Q GLU 18": "OE1" <-> "OE2" Residue "Q PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 357": "NH1" <-> "NH2" Residue "R GLU 434": "OE1" <-> "OE2" Residue "R ARG 488": "NH1" <-> "NH2" Residue "R GLU 512": "OE1" <-> "OE2" Residue "S GLU 433": "OE1" <-> "OE2" Residue "S GLU 434": "OE1" <-> "OE2" Residue "S ARG 488": "NH1" <-> "NH2" Residue "S GLU 512": "OE1" <-> "OE2" Residue "T GLU 15": "OE1" <-> "OE2" Residue "T GLU 18": "OE1" <-> "OE2" Residue "T PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 97": "NH1" <-> "NH2" Residue "T GLU 132": "OE1" <-> "OE2" Residue "U ARG 357": "NH1" <-> "NH2" Residue "U ARG 382": "NH1" <-> "NH2" Residue "U GLU 434": "OE1" <-> "OE2" Residue "U ARG 488": "NH1" <-> "NH2" Residue "U GLU 512": "OE1" <-> "OE2" Residue "U ARG 515": "NH1" <-> "NH2" Residue "V ARG 488": "NH1" <-> "NH2" Residue "W GLU 354": "OE1" <-> "OE2" Residue "W ARG 382": "NH1" <-> "NH2" Residue "W ARG 488": "NH1" <-> "NH2" Residue "W GLU 533": "OE1" <-> "OE2" Residue "X GLU 15": "OE1" <-> "OE2" Residue "X ARG 76": "NH1" <-> "NH2" Residue "X PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 173": "OE1" <-> "OE2" Residue "Y ARG 382": "NH1" <-> "NH2" Residue "Y GLU 432": "OE1" <-> "OE2" Residue "Y ARG 488": "NH1" <-> "NH2" Residue "Y GLU 512": "OE1" <-> "OE2" Residue "Z GLU 132": "OE1" <-> "OE2" Residue "a ARG 382": "NH1" <-> "NH2" Residue "a ARG 388": "NH1" <-> "NH2" Residue "a GLU 434": "OE1" <-> "OE2" Residue "a ARG 488": "NH1" <-> "NH2" Residue "a ARG 509": "NH1" <-> "NH2" Residue "a GLU 512": "OE1" <-> "OE2" Residue "b ARG 382": "NH1" <-> "NH2" Residue "b ARG 488": "NH1" <-> "NH2" Residue "d GLU 18": "OE1" <-> "OE2" Residue "f GLU 18": "OE1" <-> "OE2" Residue "f ARG 21": "NH1" <-> "NH2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 68808 Number of models: 1 Model: "" Number of chains: 42 Chain: "0" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "1" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 42 Classifications: {'peptide': 5} Modifications used: {'COO': 1} Link IDs: {'TRANS': 4} Chain: "2" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "4" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "6" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "8" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "A" Number of atoms: 3665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3665 Classifications: {'peptide': 468} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 444} Chain breaks: 4 Chain: "B" Number of atoms: 3701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3701 Classifications: {'peptide': 473} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 450} Chain breaks: 3 Chain: "C" Number of atoms: 3685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3685 Classifications: {'peptide': 471} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 448} Chain breaks: 3 Chain: "D" Number of atoms: 3584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3584 Classifications: {'peptide': 457} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 433} Chain breaks: 4 Chain: "E" Number of atoms: 3775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3775 Classifications: {'peptide': 483} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 460} Chain breaks: 2 Chain: "F" Number of atoms: 3773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3773 Classifications: {'peptide': 483} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 460} Chain breaks: 2 Chain: "G" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 112 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1636 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1650 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 7, 'TRANS': 206} Chain breaks: 1 Chain: "J" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1640 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 215} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1668 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 7, 'TRANS': 209} Chain breaks: 1 Chain: "L" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1636 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1636 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1636 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "O" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "P" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1640 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 215} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "R" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1636 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1636 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1650 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 7, 'TRANS': 206} Chain breaks: 1 Chain: "U" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1715 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 226} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "V" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1640 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 215} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "W" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1715 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 226} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "X" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1650 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 7, 'TRANS': 206} Chain breaks: 1 Chain: "Y" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1640 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 215} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Z" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "a" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1640 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 215} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "b" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1640 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 215} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "d" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "f" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 26.78, per 1000 atoms: 0.39 Number of scatterers: 68808 At special positions: 0 Unit cell: (139.308, 153.972, 279.838, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 179 16.00 P 17 15.00 Mg 5 11.99 O 13355 8.00 N 12094 7.00 C 43158 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: 20.55 Conformation dependent library (CDL) restraints added in 9.3 seconds 17736 Ramachandran restraints generated. 8868 Oldfield, 0 Emsley, 8868 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16446 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 288 helices and 95 sheets defined 39.7% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.81 Creating SS restraints... Processing helix chain '0' and resid 9 through 25 Processing helix chain '0' and resid 68 through 88 Processing helix chain '0' and resid 91 through 93 No H-bonds generated for 'chain '0' and resid 91 through 93' Processing helix chain '0' and resid 96 through 113 Processing helix chain '0' and resid 160 through 170 Processing helix chain '0' and resid 177 through 189 Processing helix chain '0' and resid 227 through 233 Processing helix chain '2' and resid 9 through 26 Processing helix chain '2' and resid 68 through 88 removed outlier: 4.228A pdb=" N ASN 2 73 " --> pdb=" O ASN 2 69 " (cutoff:3.500A) Processing helix chain '2' and resid 91 through 93 No H-bonds generated for 'chain '2' and resid 91 through 93' Processing helix chain '2' and resid 96 through 113 Processing helix chain '2' and resid 160 through 170 Processing helix chain '2' and resid 177 through 189 Processing helix chain '2' and resid 227 through 233 Processing helix chain '4' and resid 9 through 25 Processing helix chain '4' and resid 68 through 88 Processing helix chain '4' and resid 91 through 93 No H-bonds generated for 'chain '4' and resid 91 through 93' Processing helix chain '4' and resid 96 through 113 Processing helix chain '4' and resid 160 through 170 Processing helix chain '4' and resid 177 through 189 Processing helix chain '4' and resid 227 through 233 Processing helix chain '6' and resid 9 through 25 Processing helix chain '6' and resid 68 through 88 Processing helix chain '6' and resid 91 through 93 No H-bonds generated for 'chain '6' and resid 91 through 93' Processing helix chain '6' and resid 96 through 113 Processing helix chain '6' and resid 160 through 170 Processing helix chain '6' and resid 177 through 189 Processing helix chain '6' and resid 227 through 233 Processing helix chain '8' and resid 9 through 25 removed outlier: 3.770A pdb=" N ARG 8 14 " --> pdb=" O GLU 8 10 " (cutoff:3.500A) Processing helix chain '8' and resid 68 through 88 Processing helix chain '8' and resid 91 through 93 No H-bonds generated for 'chain '8' and resid 91 through 93' Processing helix chain '8' and resid 96 through 113 Processing helix chain '8' and resid 160 through 170 Processing helix chain '8' and resid 177 through 189 Processing helix chain '8' and resid 227 through 233 Processing helix chain 'A' and resid 132 through 134 No H-bonds generated for 'chain 'A' and resid 132 through 134' Processing helix chain 'A' and resid 234 through 239 Processing helix chain 'A' and resid 259 through 273 removed outlier: 3.945A pdb=" N LEU A 270 " --> pdb=" O ASP A 266 " (cutoff:3.500A) Proline residue: A 271 - end of helix Processing helix chain 'A' and resid 276 through 281 removed outlier: 3.623A pdb=" N TYR A 281 " --> pdb=" O LEU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 313 removed outlier: 3.692A pdb=" N ALA A 311 " --> pdb=" O ALA A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 337 No H-bonds generated for 'chain 'A' and resid 335 through 337' Processing helix chain 'A' and resid 347 through 362 Processing helix chain 'A' and resid 389 through 391 No H-bonds generated for 'chain 'A' and resid 389 through 391' Processing helix chain 'A' and resid 393 through 403 Processing helix chain 'A' and resid 423 through 426 No H-bonds generated for 'chain 'A' and resid 423 through 426' Processing helix chain 'A' and resid 442 through 452 removed outlier: 3.502A pdb=" N TYR A 452 " --> pdb=" O ILE A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 467 removed outlier: 3.649A pdb=" N GLU A 466 " --> pdb=" O ASP A 462 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE A 467 " --> pdb=" O ASP A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 487 Processing helix chain 'A' and resid 491 through 493 No H-bonds generated for 'chain 'A' and resid 491 through 493' Processing helix chain 'A' and resid 510 through 513 Processing helix chain 'A' and resid 516 through 536 Processing helix chain 'A' and resid 544 through 559 Processing helix chain 'A' and resid 562 through 564 No H-bonds generated for 'chain 'A' and resid 562 through 564' Processing helix chain 'A' and resid 567 through 577 Processing helix chain 'B' and resid 251 through 253 No H-bonds generated for 'chain 'B' and resid 251 through 253' Processing helix chain 'B' and resid 260 through 273 Proline residue: B 271 - end of helix Processing helix chain 'B' and resid 275 through 281 Processing helix chain 'B' and resid 299 through 316 Processing helix chain 'B' and resid 334 through 337 removed outlier: 4.441A pdb=" N LEU B 337 " --> pdb=" O GLY B 334 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 334 through 337' Processing helix chain 'B' and resid 344 through 358 Processing helix chain 'B' and resid 393 through 401 Processing helix chain 'B' and resid 442 through 452 removed outlier: 3.585A pdb=" N TYR B 452 " --> pdb=" O ILE B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 466 removed outlier: 4.013A pdb=" N GLU B 466 " --> pdb=" O ASP B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 486 Processing helix chain 'B' and resid 491 through 493 No H-bonds generated for 'chain 'B' and resid 491 through 493' Processing helix chain 'B' and resid 516 through 536 Processing helix chain 'B' and resid 544 through 560 removed outlier: 4.102A pdb=" N ASP B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 577 Processing helix chain 'C' and resid 132 through 134 No H-bonds generated for 'chain 'C' and resid 132 through 134' Processing helix chain 'C' and resid 190 through 192 No H-bonds generated for 'chain 'C' and resid 190 through 192' Processing helix chain 'C' and resid 236 through 241 Processing helix chain 'C' and resid 258 through 273 removed outlier: 4.607A pdb=" N LEU C 270 " --> pdb=" O ASP C 266 " (cutoff:3.500A) Proline residue: C 271 - end of helix Processing helix chain 'C' and resid 275 through 281 Processing helix chain 'C' and resid 299 through 313 removed outlier: 3.645A pdb=" N ALA C 303 " --> pdb=" O LYS C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 337 No H-bonds generated for 'chain 'C' and resid 335 through 337' Processing helix chain 'C' and resid 344 through 362 removed outlier: 4.450A pdb=" N GLU C 362 " --> pdb=" O GLU C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 400 Proline residue: C 394 - end of helix Processing helix chain 'C' and resid 442 through 452 Processing helix chain 'C' and resid 461 through 466 Processing helix chain 'C' and resid 471 through 486 Processing helix chain 'C' and resid 510 through 512 No H-bonds generated for 'chain 'C' and resid 510 through 512' Processing helix chain 'C' and resid 516 through 537 Processing helix chain 'C' and resid 544 through 553 removed outlier: 3.748A pdb=" N VAL C 552 " --> pdb=" O LEU C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 577 Processing helix chain 'D' and resid 190 through 192 No H-bonds generated for 'chain 'D' and resid 190 through 192' Processing helix chain 'D' and resid 239 through 243 Processing helix chain 'D' and resid 258 through 273 removed outlier: 4.069A pdb=" N LEU D 270 " --> pdb=" O ASP D 266 " (cutoff:3.500A) Proline residue: D 271 - end of helix Processing helix chain 'D' and resid 275 through 281 Processing helix chain 'D' and resid 299 through 313 removed outlier: 4.238A pdb=" N ALA D 303 " --> pdb=" O LYS D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 337 No H-bonds generated for 'chain 'D' and resid 335 through 337' Processing helix chain 'D' and resid 344 through 361 Processing helix chain 'D' and resid 393 through 405 removed outlier: 4.294A pdb=" N GLY D 405 " --> pdb=" O ASP D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 442 through 452 Processing helix chain 'D' and resid 461 through 467 removed outlier: 3.698A pdb=" N GLU D 466 " --> pdb=" O ASP D 462 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N PHE D 467 " --> pdb=" O ASP D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 471 through 486 Processing helix chain 'D' and resid 516 through 536 Processing helix chain 'D' and resid 544 through 561 removed outlier: 4.417A pdb=" N ASP D 560 " --> pdb=" O ALA D 556 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU D 561 " --> pdb=" O GLU D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 577 removed outlier: 4.589A pdb=" N LYS D 576 " --> pdb=" O ARG D 572 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 242 No H-bonds generated for 'chain 'E' and resid 239 through 242' Processing helix chain 'E' and resid 251 through 253 No H-bonds generated for 'chain 'E' and resid 251 through 253' Processing helix chain 'E' and resid 259 through 273 removed outlier: 4.253A pdb=" N LEU E 270 " --> pdb=" O ASP E 266 " (cutoff:3.500A) Proline residue: E 271 - end of helix Processing helix chain 'E' and resid 275 through 280 Processing helix chain 'E' and resid 299 through 317 removed outlier: 3.525A pdb=" N ALA E 307 " --> pdb=" O ALA E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 328 removed outlier: 4.158A pdb=" N TYR E 328 " --> pdb=" O GLU E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 344 through 359 Processing helix chain 'E' and resid 388 through 400 removed outlier: 4.882A pdb=" N VAL E 393 " --> pdb=" O THR E 390 " (cutoff:3.500A) Proline residue: E 394 - end of helix removed outlier: 3.653A pdb=" N ILE E 400 " --> pdb=" O LEU E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 442 through 452 Processing helix chain 'E' and resid 461 through 466 removed outlier: 3.922A pdb=" N GLU E 466 " --> pdb=" O ASP E 462 " (cutoff:3.500A) Processing helix chain 'E' and resid 471 through 486 Processing helix chain 'E' and resid 516 through 537 Processing helix chain 'E' and resid 544 through 557 removed outlier: 3.671A pdb=" N VAL E 552 " --> pdb=" O LEU E 548 " (cutoff:3.500A) Processing helix chain 'E' and resid 570 through 577 Processing helix chain 'F' and resid 190 through 192 No H-bonds generated for 'chain 'F' and resid 190 through 192' Processing helix chain 'F' and resid 236 through 242 removed outlier: 3.545A pdb=" N ASP F 240 " --> pdb=" O ALA F 236 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N LEU F 241 " --> pdb=" O GLU F 237 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 268 Processing helix chain 'F' and resid 270 through 273 No H-bonds generated for 'chain 'F' and resid 270 through 273' Processing helix chain 'F' and resid 275 through 281 Processing helix chain 'F' and resid 300 through 316 Processing helix chain 'F' and resid 324 through 327 No H-bonds generated for 'chain 'F' and resid 324 through 327' Processing helix chain 'F' and resid 335 through 337 No H-bonds generated for 'chain 'F' and resid 335 through 337' Processing helix chain 'F' and resid 344 through 359 Processing helix chain 'F' and resid 373 through 375 No H-bonds generated for 'chain 'F' and resid 373 through 375' Processing helix chain 'F' and resid 388 through 399 removed outlier: 5.224A pdb=" N VAL F 393 " --> pdb=" O THR F 390 " (cutoff:3.500A) Proline residue: F 394 - end of helix Processing helix chain 'F' and resid 418 through 420 No H-bonds generated for 'chain 'F' and resid 418 through 420' Processing helix chain 'F' and resid 423 through 426 No H-bonds generated for 'chain 'F' and resid 423 through 426' Processing helix chain 'F' and resid 442 through 452 removed outlier: 3.522A pdb=" N ASP F 447 " --> pdb=" O GLU F 443 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR F 452 " --> pdb=" O ILE F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 461 through 467 removed outlier: 4.396A pdb=" N GLU F 466 " --> pdb=" O ASP F 462 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N PHE F 467 " --> pdb=" O ASP F 463 " (cutoff:3.500A) Processing helix chain 'F' and resid 471 through 486 Processing helix chain 'F' and resid 491 through 493 No H-bonds generated for 'chain 'F' and resid 491 through 493' Processing helix chain 'F' and resid 510 through 513 Processing helix chain 'F' and resid 516 through 536 Processing helix chain 'F' and resid 544 through 558 removed outlier: 3.741A pdb=" N ASN F 558 " --> pdb=" O GLU F 554 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 577 removed outlier: 5.365A pdb=" N GLY F 575 " --> pdb=" O ALA F 571 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LYS F 576 " --> pdb=" O ARG F 572 " (cutoff:3.500A) Processing helix chain 'H' and resid 349 through 370 Processing helix chain 'H' and resid 376 through 395 removed outlier: 3.520A pdb=" N ASN H 390 " --> pdb=" O MET H 386 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU H 391 " --> pdb=" O VAL H 387 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N ALA H 392 " --> pdb=" O ARG H 388 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ALA H 393 " --> pdb=" O GLY H 389 " (cutoff:3.500A) Processing helix chain 'H' and resid 414 through 416 No H-bonds generated for 'chain 'H' and resid 414 through 416' Processing helix chain 'H' and resid 443 through 456 removed outlier: 4.062A pdb=" N LYS H 452 " --> pdb=" O SER H 448 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N SER H 455 " --> pdb=" O LYS H 451 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N GLN H 456 " --> pdb=" O LYS H 452 " (cutoff:3.500A) Processing helix chain 'H' and resid 460 through 477 Processing helix chain 'H' and resid 507 through 521 Processing helix chain 'I' and resid 9 through 25 Processing helix chain 'I' and resid 68 through 88 Processing helix chain 'I' and resid 91 through 93 No H-bonds generated for 'chain 'I' and resid 91 through 93' Processing helix chain 'I' and resid 96 through 113 Processing helix chain 'I' and resid 160 through 170 Processing helix chain 'I' and resid 177 through 189 Processing helix chain 'I' and resid 205 through 207 No H-bonds generated for 'chain 'I' and resid 205 through 207' Processing helix chain 'I' and resid 227 through 233 Processing helix chain 'J' and resid 349 through 370 Processing helix chain 'J' and resid 376 through 395 removed outlier: 3.591A pdb=" N ASN J 390 " --> pdb=" O MET J 386 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU J 391 " --> pdb=" O VAL J 387 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N ALA J 392 " --> pdb=" O ARG J 388 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ALA J 393 " --> pdb=" O GLY J 389 " (cutoff:3.500A) Processing helix chain 'J' and resid 414 through 416 No H-bonds generated for 'chain 'J' and resid 414 through 416' Processing helix chain 'J' and resid 441 through 456 removed outlier: 4.513A pdb=" N LEU J 444 " --> pdb=" O SER J 441 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET J 450 " --> pdb=" O LYS J 447 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS J 451 " --> pdb=" O SER J 448 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N TYR J 454 " --> pdb=" O LYS J 451 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N SER J 455 " --> pdb=" O LYS J 452 " (cutoff:3.500A) Processing helix chain 'J' and resid 460 through 477 Processing helix chain 'J' and resid 507 through 521 Processing helix chain 'K' and resid 9 through 25 Processing helix chain 'K' and resid 68 through 88 Processing helix chain 'K' and resid 91 through 93 No H-bonds generated for 'chain 'K' and resid 91 through 93' Processing helix chain 'K' and resid 96 through 113 Processing helix chain 'K' and resid 160 through 170 Processing helix chain 'K' and resid 177 through 189 Processing helix chain 'K' and resid 205 through 207 No H-bonds generated for 'chain 'K' and resid 205 through 207' Processing helix chain 'K' and resid 227 through 232 Processing helix chain 'L' and resid 349 through 370 Processing helix chain 'L' and resid 376 through 395 removed outlier: 3.669A pdb=" N LEU L 391 " --> pdb=" O VAL L 387 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ALA L 392 " --> pdb=" O ARG L 388 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ALA L 393 " --> pdb=" O GLY L 389 " (cutoff:3.500A) Processing helix chain 'L' and resid 414 through 416 No H-bonds generated for 'chain 'L' and resid 414 through 416' Processing helix chain 'L' and resid 441 through 456 removed outlier: 4.481A pdb=" N LEU L 444 " --> pdb=" O SER L 441 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS L 451 " --> pdb=" O SER L 448 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N TYR L 454 " --> pdb=" O LYS L 451 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N SER L 455 " --> pdb=" O LYS L 452 " (cutoff:3.500A) Processing helix chain 'L' and resid 460 through 477 Processing helix chain 'L' and resid 507 through 521 Processing helix chain 'M' and resid 349 through 370 Processing helix chain 'M' and resid 376 through 389 Processing helix chain 'M' and resid 391 through 395 Processing helix chain 'M' and resid 414 through 416 No H-bonds generated for 'chain 'M' and resid 414 through 416' Processing helix chain 'M' and resid 443 through 456 removed outlier: 4.009A pdb=" N LYS M 452 " --> pdb=" O SER M 448 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N SER M 455 " --> pdb=" O LYS M 451 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N GLN M 456 " --> pdb=" O LYS M 452 " (cutoff:3.500A) Processing helix chain 'M' and resid 460 through 477 Processing helix chain 'M' and resid 507 through 521 Processing helix chain 'N' and resid 349 through 370 Processing helix chain 'N' and resid 376 through 395 removed outlier: 3.712A pdb=" N LEU N 391 " --> pdb=" O VAL N 387 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ALA N 392 " --> pdb=" O ARG N 388 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N ALA N 393 " --> pdb=" O GLY N 389 " (cutoff:3.500A) Processing helix chain 'N' and resid 414 through 416 No H-bonds generated for 'chain 'N' and resid 414 through 416' Processing helix chain 'N' and resid 443 through 456 removed outlier: 4.094A pdb=" N LYS N 452 " --> pdb=" O SER N 448 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N SER N 455 " --> pdb=" O LYS N 451 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N GLN N 456 " --> pdb=" O LYS N 452 " (cutoff:3.500A) Processing helix chain 'N' and resid 460 through 477 Processing helix chain 'N' and resid 507 through 521 Processing helix chain 'O' and resid 9 through 25 removed outlier: 3.643A pdb=" N ARG O 14 " --> pdb=" O GLU O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 68 through 88 Processing helix chain 'O' and resid 91 through 93 No H-bonds generated for 'chain 'O' and resid 91 through 93' Processing helix chain 'O' and resid 96 through 113 Processing helix chain 'O' and resid 161 through 170 Processing helix chain 'O' and resid 177 through 189 Processing helix chain 'O' and resid 227 through 233 Processing helix chain 'P' and resid 349 through 370 Processing helix chain 'P' and resid 376 through 396 removed outlier: 3.587A pdb=" N ASN P 390 " --> pdb=" O MET P 386 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU P 391 " --> pdb=" O VAL P 387 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ALA P 392 " --> pdb=" O ARG P 388 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ALA P 393 " --> pdb=" O GLY P 389 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN P 396 " --> pdb=" O ALA P 392 " (cutoff:3.500A) Processing helix chain 'P' and resid 414 through 416 No H-bonds generated for 'chain 'P' and resid 414 through 416' Processing helix chain 'P' and resid 441 through 456 removed outlier: 4.412A pdb=" N LEU P 444 " --> pdb=" O SER P 441 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET P 450 " --> pdb=" O LYS P 447 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS P 451 " --> pdb=" O SER P 448 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N TYR P 454 " --> pdb=" O LYS P 451 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N SER P 455 " --> pdb=" O LYS P 452 " (cutoff:3.500A) Processing helix chain 'P' and resid 460 through 477 Processing helix chain 'P' and resid 507 through 522 Processing helix chain 'Q' and resid 9 through 25 Processing helix chain 'Q' and resid 68 through 88 Processing helix chain 'Q' and resid 91 through 93 No H-bonds generated for 'chain 'Q' and resid 91 through 93' Processing helix chain 'Q' and resid 96 through 113 Processing helix chain 'Q' and resid 161 through 170 Processing helix chain 'Q' and resid 177 through 189 Processing helix chain 'Q' and resid 205 through 207 No H-bonds generated for 'chain 'Q' and resid 205 through 207' Processing helix chain 'Q' and resid 227 through 233 Processing helix chain 'R' and resid 349 through 370 Processing helix chain 'R' and resid 376 through 395 removed outlier: 3.617A pdb=" N LEU R 391 " --> pdb=" O VAL R 387 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ALA R 392 " --> pdb=" O ARG R 388 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N ALA R 393 " --> pdb=" O GLY R 389 " (cutoff:3.500A) Processing helix chain 'R' and resid 414 through 416 No H-bonds generated for 'chain 'R' and resid 414 through 416' Processing helix chain 'R' and resid 441 through 456 removed outlier: 4.486A pdb=" N LEU R 444 " --> pdb=" O SER R 441 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS R 451 " --> pdb=" O SER R 448 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N TYR R 454 " --> pdb=" O LYS R 451 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N SER R 455 " --> pdb=" O LYS R 452 " (cutoff:3.500A) Processing helix chain 'R' and resid 460 through 477 Processing helix chain 'R' and resid 507 through 521 Processing helix chain 'S' and resid 349 through 370 Processing helix chain 'S' and resid 376 through 389 Processing helix chain 'S' and resid 391 through 395 Processing helix chain 'S' and resid 414 through 416 No H-bonds generated for 'chain 'S' and resid 414 through 416' Processing helix chain 'S' and resid 443 through 456 removed outlier: 4.024A pdb=" N LYS S 452 " --> pdb=" O SER S 448 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N SER S 455 " --> pdb=" O LYS S 451 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N GLN S 456 " --> pdb=" O LYS S 452 " (cutoff:3.500A) Processing helix chain 'S' and resid 460 through 477 Processing helix chain 'S' and resid 507 through 521 Processing helix chain 'T' and resid 9 through 25 Processing helix chain 'T' and resid 68 through 88 Processing helix chain 'T' and resid 91 through 93 No H-bonds generated for 'chain 'T' and resid 91 through 93' Processing helix chain 'T' and resid 96 through 113 Processing helix chain 'T' and resid 161 through 170 Processing helix chain 'T' and resid 177 through 189 Processing helix chain 'T' and resid 205 through 207 No H-bonds generated for 'chain 'T' and resid 205 through 207' Processing helix chain 'T' and resid 227 through 232 Processing helix chain 'U' and resid 349 through 370 Processing helix chain 'U' and resid 376 through 395 removed outlier: 3.512A pdb=" N LEU U 391 " --> pdb=" O VAL U 387 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ALA U 392 " --> pdb=" O ARG U 388 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N ALA U 393 " --> pdb=" O GLY U 389 " (cutoff:3.500A) Processing helix chain 'U' and resid 414 through 416 No H-bonds generated for 'chain 'U' and resid 414 through 416' Processing helix chain 'U' and resid 441 through 456 removed outlier: 4.565A pdb=" N LEU U 444 " --> pdb=" O SER U 441 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS U 451 " --> pdb=" O SER U 448 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N TYR U 454 " --> pdb=" O LYS U 451 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N SER U 455 " --> pdb=" O LYS U 452 " (cutoff:3.500A) Processing helix chain 'U' and resid 460 through 477 Processing helix chain 'U' and resid 507 through 527 Processing helix chain 'V' and resid 349 through 370 Processing helix chain 'V' and resid 376 through 395 removed outlier: 3.769A pdb=" N LEU V 391 " --> pdb=" O VAL V 387 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N ALA V 392 " --> pdb=" O ARG V 388 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N ALA V 393 " --> pdb=" O GLY V 389 " (cutoff:3.500A) Processing helix chain 'V' and resid 414 through 416 No H-bonds generated for 'chain 'V' and resid 414 through 416' Processing helix chain 'V' and resid 443 through 456 removed outlier: 4.082A pdb=" N LYS V 452 " --> pdb=" O SER V 448 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N SER V 455 " --> pdb=" O LYS V 451 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N GLN V 456 " --> pdb=" O LYS V 452 " (cutoff:3.500A) Processing helix chain 'V' and resid 460 through 477 Processing helix chain 'V' and resid 507 through 522 Processing helix chain 'W' and resid 349 through 370 Processing helix chain 'W' and resid 376 through 395 removed outlier: 3.522A pdb=" N ASN W 390 " --> pdb=" O MET W 386 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU W 391 " --> pdb=" O VAL W 387 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ALA W 392 " --> pdb=" O ARG W 388 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ALA W 393 " --> pdb=" O GLY W 389 " (cutoff:3.500A) Processing helix chain 'W' and resid 414 through 416 No H-bonds generated for 'chain 'W' and resid 414 through 416' Processing helix chain 'W' and resid 443 through 456 removed outlier: 4.097A pdb=" N LYS W 452 " --> pdb=" O SER W 448 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N SER W 455 " --> pdb=" O LYS W 451 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N GLN W 456 " --> pdb=" O LYS W 452 " (cutoff:3.500A) Processing helix chain 'W' and resid 460 through 477 Processing helix chain 'W' and resid 507 through 527 Processing helix chain 'X' and resid 9 through 25 removed outlier: 3.544A pdb=" N ARG X 14 " --> pdb=" O GLU X 10 " (cutoff:3.500A) Processing helix chain 'X' and resid 68 through 88 Processing helix chain 'X' and resid 91 through 93 No H-bonds generated for 'chain 'X' and resid 91 through 93' Processing helix chain 'X' and resid 96 through 113 Processing helix chain 'X' and resid 160 through 170 Processing helix chain 'X' and resid 177 through 189 Processing helix chain 'X' and resid 227 through 232 Processing helix chain 'Y' and resid 349 through 370 Processing helix chain 'Y' and resid 376 through 395 removed outlier: 3.611A pdb=" N LEU Y 391 " --> pdb=" O VAL Y 387 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ALA Y 392 " --> pdb=" O ARG Y 388 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ALA Y 393 " --> pdb=" O GLY Y 389 " (cutoff:3.500A) Processing helix chain 'Y' and resid 414 through 416 No H-bonds generated for 'chain 'Y' and resid 414 through 416' Processing helix chain 'Y' and resid 441 through 456 removed outlier: 4.548A pdb=" N LEU Y 444 " --> pdb=" O SER Y 441 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET Y 450 " --> pdb=" O LYS Y 447 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS Y 451 " --> pdb=" O SER Y 448 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N TYR Y 454 " --> pdb=" O LYS Y 451 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N SER Y 455 " --> pdb=" O LYS Y 452 " (cutoff:3.500A) Processing helix chain 'Y' and resid 460 through 477 Processing helix chain 'Y' and resid 507 through 522 Processing helix chain 'Z' and resid 9 through 25 removed outlier: 4.151A pdb=" N MET Z 13 " --> pdb=" O PRO Z 9 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG Z 14 " --> pdb=" O GLU Z 10 " (cutoff:3.500A) Processing helix chain 'Z' and resid 68 through 88 Processing helix chain 'Z' and resid 91 through 93 No H-bonds generated for 'chain 'Z' and resid 91 through 93' Processing helix chain 'Z' and resid 96 through 113 Processing helix chain 'Z' and resid 161 through 170 Processing helix chain 'Z' and resid 177 through 189 Processing helix chain 'Z' and resid 205 through 207 No H-bonds generated for 'chain 'Z' and resid 205 through 207' Processing helix chain 'Z' and resid 227 through 232 Processing helix chain 'a' and resid 349 through 370 Processing helix chain 'a' and resid 376 through 395 removed outlier: 3.634A pdb=" N ASN a 390 " --> pdb=" O MET a 386 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU a 391 " --> pdb=" O VAL a 387 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N ALA a 392 " --> pdb=" O ARG a 388 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N ALA a 393 " --> pdb=" O GLY a 389 " (cutoff:3.500A) Processing helix chain 'a' and resid 414 through 416 No H-bonds generated for 'chain 'a' and resid 414 through 416' Processing helix chain 'a' and resid 441 through 456 removed outlier: 4.515A pdb=" N LEU a 444 " --> pdb=" O SER a 441 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET a 450 " --> pdb=" O LYS a 447 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS a 451 " --> pdb=" O SER a 448 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N TYR a 454 " --> pdb=" O LYS a 451 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N SER a 455 " --> pdb=" O LYS a 452 " (cutoff:3.500A) Processing helix chain 'a' and resid 460 through 477 Processing helix chain 'a' and resid 507 through 522 Processing helix chain 'b' and resid 349 through 370 Processing helix chain 'b' and resid 376 through 395 removed outlier: 3.799A pdb=" N LEU b 391 " --> pdb=" O VAL b 387 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N ALA b 392 " --> pdb=" O ARG b 388 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ALA b 393 " --> pdb=" O GLY b 389 " (cutoff:3.500A) Processing helix chain 'b' and resid 414 through 416 No H-bonds generated for 'chain 'b' and resid 414 through 416' Processing helix chain 'b' and resid 443 through 456 removed outlier: 4.078A pdb=" N LYS b 452 " --> pdb=" O SER b 448 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N SER b 455 " --> pdb=" O LYS b 451 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N GLN b 456 " --> pdb=" O LYS b 452 " (cutoff:3.500A) Processing helix chain 'b' and resid 460 through 477 Processing helix chain 'b' and resid 507 through 521 Processing helix chain 'd' and resid 9 through 13 Processing helix chain 'd' and resid 15 through 25 Processing helix chain 'd' and resid 68 through 88 Processing helix chain 'd' and resid 91 through 93 No H-bonds generated for 'chain 'd' and resid 91 through 93' Processing helix chain 'd' and resid 96 through 113 Processing helix chain 'd' and resid 160 through 170 Processing helix chain 'd' and resid 177 through 189 Processing helix chain 'd' and resid 227 through 233 Processing helix chain 'f' and resid 9 through 24 Processing helix chain 'f' and resid 68 through 88 Processing helix chain 'f' and resid 91 through 93 No H-bonds generated for 'chain 'f' and resid 91 through 93' Processing helix chain 'f' and resid 96 through 113 removed outlier: 3.687A pdb=" N PHE f 111 " --> pdb=" O LEU f 107 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR f 112 " --> pdb=" O GLY f 108 " (cutoff:3.500A) Processing helix chain 'f' and resid 160 through 170 Processing helix chain 'f' and resid 177 through 189 Processing helix chain 'f' and resid 227 through 233 Processing sheet with id= A, first strand: chain '0' and resid 153 through 156 Processing sheet with id= B, first strand: chain '0' and resid 147 through 150 removed outlier: 3.740A pdb=" N LEU 0 138 " --> pdb=" O GLU 0 150 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N PHE 0 62 " --> pdb=" O GLU 0 55 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N GLU 0 55 " --> pdb=" O PHE 0 62 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ALA 0 64 " --> pdb=" O ILE 0 53 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ILE 0 53 " --> pdb=" O ALA 0 64 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain '2' and resid 153 through 156 Processing sheet with id= D, first strand: chain '2' and resid 147 through 150 removed outlier: 3.726A pdb=" N LEU 2 138 " --> pdb=" O GLU 2 150 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N PHE 2 62 " --> pdb=" O GLU 2 55 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N GLU 2 55 " --> pdb=" O PHE 2 62 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N ALA 2 64 " --> pdb=" O ILE 2 53 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ILE 2 53 " --> pdb=" O ALA 2 64 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain '4' and resid 153 through 156 Processing sheet with id= F, first strand: chain '4' and resid 147 through 150 removed outlier: 3.713A pdb=" N LEU 4 138 " --> pdb=" O GLU 4 150 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N PHE 4 62 " --> pdb=" O GLU 4 55 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N GLU 4 55 " --> pdb=" O PHE 4 62 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ALA 4 64 " --> pdb=" O ILE 4 53 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ILE 4 53 " --> pdb=" O ALA 4 64 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain '6' and resid 153 through 156 Processing sheet with id= H, first strand: chain '6' and resid 147 through 150 removed outlier: 3.676A pdb=" N LEU 6 138 " --> pdb=" O GLU 6 150 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N PHE 6 62 " --> pdb=" O GLU 6 55 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N GLU 6 55 " --> pdb=" O PHE 6 62 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ALA 6 64 " --> pdb=" O ILE 6 53 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ILE 6 53 " --> pdb=" O ALA 6 64 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain '8' and resid 153 through 156 Processing sheet with id= J, first strand: chain '8' and resid 147 through 150 removed outlier: 3.666A pdb=" N LEU 8 138 " --> pdb=" O GLU 8 150 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N PHE 8 62 " --> pdb=" O GLU 8 55 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N GLU 8 55 " --> pdb=" O PHE 8 62 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ALA 8 64 " --> pdb=" O ILE 8 53 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ILE 8 53 " --> pdb=" O ALA 8 64 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 140 through 142 removed outlier: 6.553A pdb=" N ASP A 114 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N THR A 107 " --> pdb=" O THR A 112 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N THR A 112 " --> pdb=" O THR A 107 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 219 through 222 removed outlier: 6.811A pdb=" N LEU A 175 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ILE A 167 " --> pdb=" O ARG A 173 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N ARG A 173 " --> pdb=" O ILE A 167 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 433 through 437 removed outlier: 8.805A pdb=" N VAL A 289 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL A 411 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N LEU A 291 " --> pdb=" O VAL A 411 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N GLY A 413 " --> pdb=" O LEU A 291 " (cutoff:3.500A) removed outlier: 8.817A pdb=" N GLY A 293 " --> pdb=" O GLY A 413 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N SER A 415 " --> pdb=" O GLY A 293 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N VAL A 366 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ILE A 412 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N VAL A 368 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ALA A 414 " --> pdb=" O VAL A 368 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N PHE A 370 " --> pdb=" O ALA A 414 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N TYR A 328 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N PHE A 369 " --> pdb=" O TYR A 328 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N LEU A 330 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N ASP A 371 " --> pdb=" O LEU A 330 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N ILE A 332 " --> pdb=" O ASP A 371 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 583 through 586 removed outlier: 3.799A pdb=" N TYR A 583 " --> pdb=" O THR A 499 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N MET A 508 " --> pdb=" O PHE A 495 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLU A 497 " --> pdb=" O GLU A 506 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N GLU A 506 " --> pdb=" O GLU A 497 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 140 through 142 removed outlier: 6.466A pdb=" N ASP B 114 " --> pdb=" O LEU B 105 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 183 through 187 removed outlier: 6.556A pdb=" N VAL B 177 " --> pdb=" O LEU B 164 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N LEU B 164 " --> pdb=" O VAL B 177 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N SER B 219 " --> pdb=" O ILE B 233 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU B 231 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ASP B 223 " --> pdb=" O ALA B 229 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ALA B 229 " --> pdb=" O ASP B 223 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 433 through 437 removed outlier: 8.087A pdb=" N VAL B 289 " --> pdb=" O VAL B 409 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N VAL B 411 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N LEU B 291 " --> pdb=" O VAL B 411 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N GLY B 413 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N GLY B 293 " --> pdb=" O GLY B 413 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL B 366 " --> pdb=" O ILE B 410 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N ILE B 412 " --> pdb=" O VAL B 366 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL B 368 " --> pdb=" O ILE B 412 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N ALA B 414 " --> pdb=" O VAL B 368 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N PHE B 370 " --> pdb=" O ALA B 414 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 505 through 509 Processing sheet with id= S, first strand: chain 'C' and resid 101 through 103 Processing sheet with id= T, first strand: chain 'C' and resid 112 through 117 Processing sheet with id= U, first strand: chain 'C' and resid 183 through 187 removed outlier: 6.112A pdb=" N VAL C 177 " --> pdb=" O LEU C 164 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N LEU C 164 " --> pdb=" O VAL C 177 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU C 231 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ASP C 223 " --> pdb=" O ALA C 229 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ALA C 229 " --> pdb=" O ASP C 223 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 433 through 437 removed outlier: 8.310A pdb=" N VAL C 289 " --> pdb=" O VAL C 409 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL C 411 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N LEU C 291 " --> pdb=" O VAL C 411 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N GLY C 413 " --> pdb=" O LEU C 291 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N GLY C 293 " --> pdb=" O GLY C 413 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N SER C 415 " --> pdb=" O GLY C 293 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL C 366 " --> pdb=" O ILE C 410 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ILE C 412 " --> pdb=" O VAL C 366 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL C 368 " --> pdb=" O ILE C 412 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N ALA C 414 " --> pdb=" O VAL C 368 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N PHE C 370 " --> pdb=" O ALA C 414 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N TYR C 328 " --> pdb=" O ILE C 367 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N PHE C 369 " --> pdb=" O TYR C 328 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU C 330 " --> pdb=" O PHE C 369 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ASP C 371 " --> pdb=" O LEU C 330 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ILE C 332 " --> pdb=" O ASP C 371 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 505 through 509 Processing sheet with id= X, first strand: chain 'D' and resid 140 through 142 removed outlier: 6.819A pdb=" N ASP D 114 " --> pdb=" O LEU D 105 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 183 through 187 removed outlier: 5.967A pdb=" N VAL D 177 " --> pdb=" O LEU D 164 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N LEU D 164 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU D 160 " --> pdb=" O VAL D 222 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N SER D 219 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU D 231 " --> pdb=" O LEU D 221 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ASP D 223 " --> pdb=" O ALA D 229 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ALA D 229 " --> pdb=" O ASP D 223 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 433 through 436 removed outlier: 6.560A pdb=" N VAL D 411 " --> pdb=" O VAL D 289 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N LEU D 291 " --> pdb=" O VAL D 411 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLY D 413 " --> pdb=" O LEU D 291 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N TYR D 328 " --> pdb=" O ILE D 367 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N PHE D 369 " --> pdb=" O TYR D 328 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU D 330 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ASP D 371 " --> pdb=" O LEU D 330 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ILE D 332 " --> pdb=" O ASP D 371 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'D' and resid 506 through 508 removed outlier: 3.864A pdb=" N LEU D 496 " --> pdb=" O MET D 508 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 140 through 142 removed outlier: 6.568A pdb=" N ASP E 114 " --> pdb=" O LEU E 105 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N THR E 107 " --> pdb=" O THR E 112 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N THR E 112 " --> pdb=" O THR E 107 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'E' and resid 219 through 222 removed outlier: 3.526A pdb=" N GLU E 160 " --> pdb=" O VAL E 222 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LEU E 175 " --> pdb=" O ARG E 165 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N ILE E 167 " --> pdb=" O ARG E 173 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ARG E 173 " --> pdb=" O ILE E 167 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'E' and resid 433 through 437 removed outlier: 7.849A pdb=" N VAL E 289 " --> pdb=" O VAL E 409 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL E 411 " --> pdb=" O VAL E 289 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N LEU E 291 " --> pdb=" O VAL E 411 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLY E 413 " --> pdb=" O LEU E 291 " (cutoff:3.500A) removed outlier: 8.705A pdb=" N GLY E 293 " --> pdb=" O GLY E 413 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N SER E 415 " --> pdb=" O GLY E 293 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N VAL E 366 " --> pdb=" O ILE E 410 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ILE E 412 " --> pdb=" O VAL E 366 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N VAL E 368 " --> pdb=" O ILE E 412 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ALA E 414 " --> pdb=" O VAL E 368 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N PHE E 370 " --> pdb=" O ALA E 414 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'E' and resid 583 through 586 removed outlier: 6.363A pdb=" N MET E 508 " --> pdb=" O PHE E 495 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLU E 497 " --> pdb=" O GLU E 506 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N GLU E 506 " --> pdb=" O GLU E 497 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'F' and resid 140 through 142 removed outlier: 6.742A pdb=" N ASP F 114 " --> pdb=" O LEU F 105 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N THR F 107 " --> pdb=" O THR F 112 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N THR F 112 " --> pdb=" O THR F 107 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'F' and resid 183 through 187 removed outlier: 3.805A pdb=" N GLU F 166 " --> pdb=" O LEU F 175 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL F 177 " --> pdb=" O LEU F 164 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N LEU F 164 " --> pdb=" O VAL F 177 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLU F 231 " --> pdb=" O LEU F 221 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N ASP F 223 " --> pdb=" O ALA F 229 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ALA F 229 " --> pdb=" O ASP F 223 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'F' and resid 433 through 437 removed outlier: 3.651A pdb=" N GLY F 293 " --> pdb=" O SER F 415 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL F 366 " --> pdb=" O ILE F 410 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N ILE F 412 " --> pdb=" O VAL F 366 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N VAL F 368 " --> pdb=" O ILE F 412 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N ALA F 414 " --> pdb=" O VAL F 368 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N PHE F 370 " --> pdb=" O ALA F 414 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LEU F 330 " --> pdb=" O PHE F 369 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'F' and resid 506 through 509 Processing sheet with id= AJ, first strand: chain 'H' and resid 436 through 440 Processing sheet with id= AK, first strand: chain 'H' and resid 341 through 347 removed outlier: 3.676A pdb=" N PHE H 423 " --> pdb=" O PRO H 402 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'H' and resid 320 through 322 removed outlier: 6.496A pdb=" N GLN H 322 " --> pdb=" O ILE H 326 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N ILE H 326 " --> pdb=" O GLN H 322 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'I' and resid 153 through 156 Processing sheet with id= AN, first strand: chain 'I' and resid 147 through 150 removed outlier: 3.876A pdb=" N LEU I 138 " --> pdb=" O GLU I 150 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N PHE I 62 " --> pdb=" O GLU I 55 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N GLU I 55 " --> pdb=" O PHE I 62 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ALA I 64 " --> pdb=" O ILE I 53 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N ILE I 53 " --> pdb=" O ALA I 64 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'J' and resid 436 through 440 Processing sheet with id= AP, first strand: chain 'J' and resid 429 through 431 removed outlier: 3.750A pdb=" N PHE J 423 " --> pdb=" O PRO J 402 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP J 338 " --> pdb=" O THR J 341 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N THR J 343 " --> pdb=" O ILE J 336 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N ILE J 336 " --> pdb=" O THR J 343 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ILE J 345 " --> pdb=" O VAL J 334 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL J 334 " --> pdb=" O ILE J 345 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'J' and resid 320 through 322 removed outlier: 6.296A pdb=" N GLN J 322 " --> pdb=" O ILE J 326 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ILE J 326 " --> pdb=" O GLN J 322 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'K' and resid 153 through 156 Processing sheet with id= AS, first strand: chain 'K' and resid 147 through 150 removed outlier: 3.940A pdb=" N LEU K 138 " --> pdb=" O GLU K 150 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N PHE K 62 " --> pdb=" O GLU K 55 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N GLU K 55 " --> pdb=" O PHE K 62 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ALA K 64 " --> pdb=" O ILE K 53 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ILE K 53 " --> pdb=" O ALA K 64 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'L' and resid 436 through 440 Processing sheet with id= AU, first strand: chain 'L' and resid 429 through 431 removed outlier: 3.713A pdb=" N PHE L 423 " --> pdb=" O PRO L 402 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N THR L 343 " --> pdb=" O ILE L 336 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ILE L 336 " --> pdb=" O THR L 343 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ILE L 345 " --> pdb=" O VAL L 334 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL L 334 " --> pdb=" O ILE L 345 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'L' and resid 320 through 322 removed outlier: 6.348A pdb=" N GLN L 322 " --> pdb=" O ILE L 326 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ILE L 326 " --> pdb=" O GLN L 322 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'M' and resid 436 through 440 Processing sheet with id= AX, first strand: chain 'M' and resid 341 through 347 removed outlier: 3.718A pdb=" N PHE M 423 " --> pdb=" O PRO M 402 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'M' and resid 320 through 322 removed outlier: 6.492A pdb=" N GLN M 322 " --> pdb=" O ILE M 326 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N ILE M 326 " --> pdb=" O GLN M 322 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'N' and resid 436 through 439 Processing sheet with id= BA, first strand: chain 'N' and resid 429 through 431 removed outlier: 3.722A pdb=" N PHE N 423 " --> pdb=" O PRO N 402 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N THR N 343 " --> pdb=" O ILE N 336 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ILE N 336 " --> pdb=" O THR N 343 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N ILE N 345 " --> pdb=" O VAL N 334 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL N 334 " --> pdb=" O ILE N 345 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'N' and resid 320 through 322 removed outlier: 6.553A pdb=" N GLN N 322 " --> pdb=" O ILE N 326 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ILE N 326 " --> pdb=" O GLN N 322 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'O' and resid 153 through 156 Processing sheet with id= BD, first strand: chain 'O' and resid 147 through 150 removed outlier: 3.950A pdb=" N LEU O 138 " --> pdb=" O GLU O 150 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N PHE O 62 " --> pdb=" O GLU O 55 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N GLU O 55 " --> pdb=" O PHE O 62 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N ALA O 64 " --> pdb=" O ILE O 53 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ILE O 53 " --> pdb=" O ALA O 64 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'P' and resid 436 through 440 Processing sheet with id= BF, first strand: chain 'P' and resid 429 through 431 removed outlier: 3.719A pdb=" N PHE P 423 " --> pdb=" O PRO P 402 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N THR P 343 " --> pdb=" O ILE P 336 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ILE P 336 " --> pdb=" O THR P 343 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ILE P 345 " --> pdb=" O VAL P 334 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VAL P 334 " --> pdb=" O ILE P 345 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'P' and resid 320 through 322 removed outlier: 6.351A pdb=" N GLN P 322 " --> pdb=" O ILE P 326 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ILE P 326 " --> pdb=" O GLN P 322 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'Q' and resid 153 through 156 Processing sheet with id= BI, first strand: chain 'Q' and resid 147 through 150 removed outlier: 3.955A pdb=" N LEU Q 138 " --> pdb=" O GLU Q 150 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N PHE Q 62 " --> pdb=" O GLU Q 55 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N GLU Q 55 " --> pdb=" O PHE Q 62 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ALA Q 64 " --> pdb=" O ILE Q 53 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N ILE Q 53 " --> pdb=" O ALA Q 64 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'R' and resid 436 through 440 Processing sheet with id= BK, first strand: chain 'R' and resid 429 through 431 removed outlier: 3.746A pdb=" N PHE R 423 " --> pdb=" O PRO R 402 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N THR R 343 " --> pdb=" O ILE R 336 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N ILE R 336 " --> pdb=" O THR R 343 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ILE R 345 " --> pdb=" O VAL R 334 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL R 334 " --> pdb=" O ILE R 345 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'R' and resid 320 through 322 removed outlier: 6.311A pdb=" N GLN R 322 " --> pdb=" O ILE R 326 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ILE R 326 " --> pdb=" O GLN R 322 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'S' and resid 436 through 440 Processing sheet with id= BN, first strand: chain 'S' and resid 429 through 431 removed outlier: 3.666A pdb=" N PHE S 423 " --> pdb=" O PRO S 402 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N THR S 343 " --> pdb=" O ILE S 336 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N ILE S 336 " --> pdb=" O THR S 343 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ILE S 345 " --> pdb=" O VAL S 334 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL S 334 " --> pdb=" O ILE S 345 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'S' and resid 320 through 322 removed outlier: 6.475A pdb=" N GLN S 322 " --> pdb=" O ILE S 326 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N ILE S 326 " --> pdb=" O GLN S 322 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'T' and resid 153 through 156 Processing sheet with id= BQ, first strand: chain 'T' and resid 147 through 150 removed outlier: 3.955A pdb=" N LEU T 138 " --> pdb=" O GLU T 150 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N PHE T 62 " --> pdb=" O GLU T 55 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N GLU T 55 " --> pdb=" O PHE T 62 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N ALA T 64 " --> pdb=" O ILE T 53 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ILE T 53 " --> pdb=" O ALA T 64 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'U' and resid 436 through 440 Processing sheet with id= BS, first strand: chain 'U' and resid 429 through 432 removed outlier: 4.750A pdb=" N ILE U 420 " --> pdb=" O GLU U 432 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE U 423 " --> pdb=" O PRO U 402 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N THR U 343 " --> pdb=" O ILE U 336 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ILE U 336 " --> pdb=" O THR U 343 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ILE U 345 " --> pdb=" O VAL U 334 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL U 334 " --> pdb=" O ILE U 345 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain 'U' and resid 320 through 322 removed outlier: 6.288A pdb=" N GLN U 322 " --> pdb=" O ILE U 326 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ILE U 326 " --> pdb=" O GLN U 322 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'V' and resid 436 through 439 Processing sheet with id= BV, first strand: chain 'V' and resid 429 through 431 removed outlier: 3.672A pdb=" N PHE V 423 " --> pdb=" O PRO V 402 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N THR V 343 " --> pdb=" O ILE V 336 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N ILE V 336 " --> pdb=" O THR V 343 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ILE V 345 " --> pdb=" O VAL V 334 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL V 334 " --> pdb=" O ILE V 345 " (cutoff:3.500A) Processing sheet with id= BW, first strand: chain 'V' and resid 320 through 322 removed outlier: 6.462A pdb=" N GLN V 322 " --> pdb=" O ILE V 326 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N ILE V 326 " --> pdb=" O GLN V 322 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 'W' and resid 436 through 440 Processing sheet with id= BY, first strand: chain 'W' and resid 341 through 347 removed outlier: 3.677A pdb=" N PHE W 423 " --> pdb=" O PRO W 402 " (cutoff:3.500A) Processing sheet with id= BZ, first strand: chain 'W' and resid 320 through 322 removed outlier: 6.496A pdb=" N GLN W 322 " --> pdb=" O ILE W 326 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N ILE W 326 " --> pdb=" O GLN W 322 " (cutoff:3.500A) Processing sheet with id= CA, first strand: chain 'X' and resid 153 through 156 Processing sheet with id= CB, first strand: chain 'X' and resid 147 through 150 removed outlier: 3.953A pdb=" N LEU X 138 " --> pdb=" O GLU X 150 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N PHE X 62 " --> pdb=" O GLU X 55 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N GLU X 55 " --> pdb=" O PHE X 62 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N ALA X 64 " --> pdb=" O ILE X 53 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N ILE X 53 " --> pdb=" O ALA X 64 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain 'Y' and resid 436 through 440 Processing sheet with id= CD, first strand: chain 'Y' and resid 429 through 431 removed outlier: 3.737A pdb=" N PHE Y 423 " --> pdb=" O PRO Y 402 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASP Y 338 " --> pdb=" O THR Y 341 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N THR Y 343 " --> pdb=" O ILE Y 336 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ILE Y 336 " --> pdb=" O THR Y 343 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ILE Y 345 " --> pdb=" O VAL Y 334 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N VAL Y 334 " --> pdb=" O ILE Y 345 " (cutoff:3.500A) Processing sheet with id= CE, first strand: chain 'Y' and resid 320 through 322 removed outlier: 6.303A pdb=" N GLN Y 322 " --> pdb=" O ILE Y 326 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ILE Y 326 " --> pdb=" O GLN Y 322 " (cutoff:3.500A) Processing sheet with id= CF, first strand: chain 'Z' and resid 153 through 156 Processing sheet with id= CG, first strand: chain 'Z' and resid 147 through 150 removed outlier: 3.930A pdb=" N LEU Z 138 " --> pdb=" O GLU Z 150 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N PHE Z 62 " --> pdb=" O GLU Z 55 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N GLU Z 55 " --> pdb=" O PHE Z 62 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ALA Z 64 " --> pdb=" O ILE Z 53 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ILE Z 53 " --> pdb=" O ALA Z 64 " (cutoff:3.500A) Processing sheet with id= CH, first strand: chain 'a' and resid 436 through 440 Processing sheet with id= CI, first strand: chain 'a' and resid 429 through 431 removed outlier: 3.732A pdb=" N PHE a 423 " --> pdb=" O PRO a 402 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASP a 338 " --> pdb=" O THR a 341 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N THR a 343 " --> pdb=" O ILE a 336 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N ILE a 336 " --> pdb=" O THR a 343 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ILE a 345 " --> pdb=" O VAL a 334 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL a 334 " --> pdb=" O ILE a 345 " (cutoff:3.500A) Processing sheet with id= CJ, first strand: chain 'a' and resid 320 through 322 removed outlier: 6.396A pdb=" N GLN a 322 " --> pdb=" O ILE a 326 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ILE a 326 " --> pdb=" O GLN a 322 " (cutoff:3.500A) Processing sheet with id= CK, first strand: chain 'b' and resid 436 through 440 Processing sheet with id= CL, first strand: chain 'b' and resid 341 through 347 removed outlier: 3.712A pdb=" N PHE b 423 " --> pdb=" O PRO b 402 " (cutoff:3.500A) Processing sheet with id= CM, first strand: chain 'b' and resid 320 through 322 removed outlier: 6.509A pdb=" N GLN b 322 " --> pdb=" O ILE b 326 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ILE b 326 " --> pdb=" O GLN b 322 " (cutoff:3.500A) Processing sheet with id= CN, first strand: chain 'd' and resid 153 through 156 Processing sheet with id= CO, first strand: chain 'd' and resid 147 through 150 removed outlier: 3.707A pdb=" N LEU d 138 " --> pdb=" O GLU d 150 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N PHE d 62 " --> pdb=" O GLU d 55 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N GLU d 55 " --> pdb=" O PHE d 62 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N ALA d 64 " --> pdb=" O ILE d 53 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ILE d 53 " --> pdb=" O ALA d 64 " (cutoff:3.500A) Processing sheet with id= CP, first strand: chain 'f' and resid 153 through 156 Processing sheet with id= CQ, first strand: chain 'f' and resid 147 through 150 removed outlier: 3.740A pdb=" N LEU f 138 " --> pdb=" O GLU f 150 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N PHE f 62 " --> pdb=" O GLU f 55 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N GLU f 55 " --> pdb=" O PHE f 62 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ALA f 64 " --> pdb=" O ILE f 53 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ILE f 53 " --> pdb=" O ALA f 64 " (cutoff:3.500A) 3514 hydrogen bonds defined for protein. 9891 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: 27.87 Time building geometry restraints manager: 22.63 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: 16061 1.33 - 1.45: 14747 1.45 - 1.58: 38700 1.58 - 1.70: 30 1.70 - 1.83: 326 Bond restraints: 69864 Sorted by residual: bond pdb=" C4 ATP A 701 " pdb=" C5 ATP A 701 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.81e+01 bond pdb=" CA TYR Z 89 " pdb=" C TYR Z 89 " ideal model delta sigma weight residual 1.517 1.465 0.052 6.30e-03 2.52e+04 6.76e+01 bond pdb=" C4 ATP F 701 " pdb=" C5 ATP F 701 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.76e+01 bond pdb=" C4 ATP B 701 " pdb=" C5 ATP B 701 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.69e+01 bond pdb=" C4 ATP E 701 " pdb=" C5 ATP E 701 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.64e+01 ... (remaining 69859 not shown) Histogram of bond angle deviations from ideal: 99.65 - 106.92: 1853 106.92 - 114.19: 39884 114.19 - 121.46: 36390 121.46 - 128.74: 16213 128.74 - 136.01: 226 Bond angle restraints: 94566 Sorted by residual: angle pdb=" PB ATP E 701 " pdb=" O3B ATP E 701 " pdb=" PG ATP E 701 " ideal model delta sigma weight residual 139.87 118.13 21.74 1.00e+00 1.00e+00 4.72e+02 angle pdb=" PB ATP B 701 " pdb=" O3B ATP B 701 " pdb=" PG ATP B 701 " ideal model delta sigma weight residual 139.87 118.61 21.26 1.00e+00 1.00e+00 4.52e+02 angle pdb=" PB ATP F 701 " pdb=" O3B ATP F 701 " pdb=" PG ATP F 701 " ideal model delta sigma weight residual 139.87 118.78 21.09 1.00e+00 1.00e+00 4.45e+02 angle pdb=" PB ATP A 701 " pdb=" O3B ATP A 701 " pdb=" PG ATP A 701 " ideal model delta sigma weight residual 139.87 119.34 20.53 1.00e+00 1.00e+00 4.22e+02 angle pdb=" PB ATP C 701 " pdb=" O3B ATP C 701 " pdb=" PG ATP C 701 " ideal model delta sigma weight residual 139.87 120.35 19.52 1.00e+00 1.00e+00 3.81e+02 ... (remaining 94561 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.00: 40925 28.00 - 55.99: 1235 55.99 - 83.99: 179 83.99 - 111.98: 38 111.98 - 139.98: 2 Dihedral angle restraints: 42379 sinusoidal: 16646 harmonic: 25733 Sorted by residual: dihedral pdb=" CA ARG F 378 " pdb=" C ARG F 378 " pdb=" N THR F 379 " pdb=" CA THR F 379 " ideal model delta harmonic sigma weight residual 180.00 137.57 42.43 0 5.00e+00 4.00e-02 7.20e+01 dihedral pdb=" C5' ADP D 701 " pdb=" O5' ADP D 701 " pdb=" PA ADP D 701 " pdb=" O2A ADP D 701 " ideal model delta sinusoidal sigma weight residual -60.00 79.98 -139.98 1 2.00e+01 2.50e-03 4.24e+01 dihedral pdb=" O1B ADP D 701 " pdb=" O3A ADP D 701 " pdb=" PB ADP D 701 " pdb=" PA ADP D 701 " ideal model delta sinusoidal sigma weight residual 300.00 167.11 132.89 1 2.00e+01 2.50e-03 4.03e+01 ... (remaining 42376 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 8640 0.062 - 0.123: 1832 0.123 - 0.185: 243 0.185 - 0.247: 27 0.247 - 0.308: 6 Chirality restraints: 10748 Sorted by residual: chirality pdb=" CA GLU d 18 " pdb=" N GLU d 18 " pdb=" C GLU d 18 " pdb=" CB GLU d 18 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" CA ARG 0 26 " pdb=" N ARG 0 26 " pdb=" C ARG 0 26 " pdb=" CB ARG 0 26 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CA TYR 8 103 " pdb=" N TYR 8 103 " pdb=" C TYR 8 103 " pdb=" CB TYR 8 103 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.92e+00 ... (remaining 10745 not shown) Planarity restraints: 12421 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 576 " -0.016 2.00e-02 2.50e+03 3.34e-02 1.11e+01 pdb=" C LYS A 576 " 0.058 2.00e-02 2.50e+03 pdb=" O LYS A 576 " -0.022 2.00e-02 2.50e+03 pdb=" N LYS A 577 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU W 401 " 0.050 5.00e-02 4.00e+02 7.58e-02 9.19e+00 pdb=" N PRO W 402 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO W 402 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO W 402 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU M 401 " -0.045 5.00e-02 4.00e+02 6.77e-02 7.33e+00 pdb=" N PRO M 402 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO M 402 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO M 402 " -0.036 5.00e-02 4.00e+02 ... (remaining 12418 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 284 2.54 - 3.13: 53613 3.13 - 3.72: 105368 3.72 - 4.31: 150958 4.31 - 4.90: 248545 Nonbonded interactions: 558768 Sorted by model distance: nonbonded pdb=" O2B ATP E 701 " pdb="MG MG E 702 " model vdw 1.952 2.170 nonbonded pdb=" O2B ATP B 701 " pdb="MG MG B 702 " model vdw 1.983 2.170 nonbonded pdb=" O1B ATP F 701 " pdb="MG MG F 702 " model vdw 2.051 2.170 nonbonded pdb=" O1B ATP A 701 " pdb="MG MG A 702 " model vdw 2.055 2.170 nonbonded pdb=" OG1 THR F 300 " pdb="MG MG F 702 " model vdw 2.095 2.170 ... (remaining 558763 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain '0' and (resid 8 through 190 or resid 204 through 234)) selection = (chain '2' and (resid 8 through 190 or resid 204 through 234)) selection = (chain '4' and (resid 8 through 190 or resid 204 through 234)) selection = (chain '6' and (resid 8 through 190 or resid 204 through 234)) selection = (chain '8' and (resid 8 through 190 or resid 204 through 234)) selection = chain 'I' selection = (chain 'K' and (resid 8 through 190 or resid 204 through 234)) selection = (chain 'O' and (resid 8 through 190 or resid 204 through 234)) selection = (chain 'Q' and (resid 8 through 190 or resid 204 through 234)) selection = chain 'T' selection = chain 'X' selection = (chain 'Z' and (resid 8 through 190 or resid 204 through 234)) selection = (chain 'd' and (resid 8 through 190 or resid 204 through 234)) selection = (chain 'f' and (resid 8 through 190 or resid 204 through 234)) } ncs_group { reference = (chain 'A' and (resid 97 through 377 or resid 390 through 587 or resid 605 throu \ gh 609)) selection = (chain 'B' and (resid 97 through 315 or resid 326 through 377 or resid 390 throu \ gh 587 or resid 605 through 609)) selection = (chain 'C' and (resid 97 through 377 or resid 390 through 587 or resid 605 throu \ gh 609)) selection = (chain 'D' and resid 97 through 609) selection = (chain 'E' and (resid 97 through 315 or resid 326 through 377 or resid 390 throu \ gh 587 or resid 605 through 609)) selection = (chain 'F' and (resid 97 through 315 or resid 326 through 377 or resid 390 throu \ gh 587 or resid 605 through 609)) } ncs_group { reference = chain 'H' selection = (chain 'J' and resid 301 through 522) selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = (chain 'P' and resid 301 through 522) selection = chain 'R' selection = chain 'S' selection = (chain 'U' and resid 301 through 522) selection = (chain 'V' and resid 301 through 522) selection = (chain 'W' and resid 301 through 522) selection = (chain 'Y' and resid 301 through 522) selection = (chain 'a' and resid 301 through 522) selection = (chain 'b' and resid 301 through 522) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.530 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: 0.090 Extract box with map and model: 11.350 Check model and map are aligned: 0.780 Set scattering table: 0.530 Process input model: 143.120 Find NCS groups from input model: 4.370 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 166.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6799 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 : 0.006 0.108 69864 Z= 0.415 Angle : 0.907 21.735 94566 Z= 0.581 Chirality : 0.051 0.308 10748 Planarity : 0.005 0.076 12421 Dihedral : 13.699 139.977 25933 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.66 % Favored : 96.20 % Rotamer: Outliers : 3.95 % Allowed : 6.27 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.84 (0.09), residues: 8868 helix: -0.46 (0.08), residues: 3515 sheet: -0.25 (0.11), residues: 2046 loop : -0.60 (0.11), residues: 3307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP Y 429 HIS 0.007 0.001 HIS V 365 PHE 0.034 0.003 PHE K 71 TYR 0.022 0.002 TYR 6 130 ARG 0.006 0.001 ARG b 465 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17736 Ramachandran restraints generated. 8868 Oldfield, 0 Emsley, 8868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17736 Ramachandran restraints generated. 8868 Oldfield, 0 Emsley, 8868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1851 residues out of total 7050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 278 poor density : 1573 time to evaluate : 5.980 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: 0 29 SER cc_start: 0.7132 (m) cc_final: 0.6763 (p) REVERT: 0 44 GLU cc_start: 0.6187 (tt0) cc_final: 0.5859 (tm-30) REVERT: 0 54 SER cc_start: 0.7388 (t) cc_final: 0.7035 (m) REVERT: 0 69 ASN cc_start: 0.7466 (OUTLIER) cc_final: 0.7212 (p0) REVERT: 0 101 ASN cc_start: 0.7161 (t0) cc_final: 0.6941 (m-40) REVERT: 0 233 LEU cc_start: 0.7078 (mp) cc_final: 0.6801 (mm) REVERT: 1 609 LEU cc_start: 0.6003 (mt) cc_final: 0.5727 (mt) REVERT: 2 11 GLN cc_start: 0.4736 (mt0) cc_final: 0.4064 (tm-30) REVERT: 2 22 LYS cc_start: 0.6851 (ptpp) cc_final: 0.6455 (tptt) REVERT: 2 28 LYS cc_start: 0.7326 (mmtt) cc_final: 0.7098 (mmtt) REVERT: 2 116 LYS cc_start: 0.7086 (ttpp) cc_final: 0.5759 (ttpp) REVERT: 2 149 ASP cc_start: 0.7865 (t0) cc_final: 0.7650 (m-30) REVERT: 4 21 ARG cc_start: 0.6131 (ttp80) cc_final: 0.5918 (ttp80) REVERT: 4 44 GLU cc_start: 0.6727 (tt0) cc_final: 0.6203 (pt0) REVERT: 4 51 GLN cc_start: 0.6352 (mt0) cc_final: 0.5941 (mm-40) REVERT: 4 97 ARG cc_start: 0.6523 (ttt-90) cc_final: 0.6155 (ttm-80) REVERT: 4 101 ASN cc_start: 0.7092 (t0) cc_final: 0.6629 (m-40) REVERT: 4 163 ILE cc_start: 0.6828 (mt) cc_final: 0.6548 (mt) REVERT: 4 171 TYR cc_start: 0.6333 (t80) cc_final: 0.5768 (t80) REVERT: 6 11 GLN cc_start: 0.4185 (OUTLIER) cc_final: 0.3921 (mm-40) REVERT: 6 28 LYS cc_start: 0.7490 (mmtt) cc_final: 0.6878 (mmtt) REVERT: 6 44 GLU cc_start: 0.7612 (tt0) cc_final: 0.6928 (tm-30) REVERT: 6 97 ARG cc_start: 0.6384 (ttt-90) cc_final: 0.6115 (ttt-90) REVERT: 6 101 ASN cc_start: 0.7205 (t0) cc_final: 0.6924 (m-40) REVERT: 6 113 GLU cc_start: 0.7138 (mm-30) cc_final: 0.6360 (tt0) REVERT: 6 168 LYS cc_start: 0.7316 (mttt) cc_final: 0.6639 (tttt) REVERT: 6 182 ARG cc_start: 0.5019 (OUTLIER) cc_final: 0.4778 (mtm-85) REVERT: 6 233 LEU cc_start: 0.7436 (mp) cc_final: 0.6948 (mt) REVERT: 6 234 LEU cc_start: 0.5543 (OUTLIER) cc_final: 0.4834 (pt) REVERT: 8 69 ASN cc_start: 0.7221 (OUTLIER) cc_final: 0.6662 (p0) REVERT: 8 73 ASN cc_start: 0.6775 (OUTLIER) cc_final: 0.6042 (m-40) REVERT: 8 74 LEU cc_start: 0.7543 (OUTLIER) cc_final: 0.7303 (mt) REVERT: 8 97 ARG cc_start: 0.7197 (ttt-90) cc_final: 0.6769 (ttt90) REVERT: 8 156 MET cc_start: 0.8015 (mtm) cc_final: 0.7635 (mtm) REVERT: 8 159 THR cc_start: 0.7088 (p) cc_final: 0.6372 (t) REVERT: 8 163 ILE cc_start: 0.7003 (mt) cc_final: 0.6554 (mt) REVERT: 8 168 LYS cc_start: 0.6588 (mttt) cc_final: 0.6374 (mtpp) REVERT: A 492 ASP cc_start: 0.8131 (OUTLIER) cc_final: 0.7206 (t0) REVERT: B 143 LEU cc_start: 0.8809 (mm) cc_final: 0.8538 (mm) REVERT: B 545 GLN cc_start: 0.8594 (tp40) cc_final: 0.8195 (pm20) REVERT: C 281 TYR cc_start: 0.8078 (OUTLIER) cc_final: 0.7219 (t80) REVERT: C 297 CYS cc_start: 0.9072 (m) cc_final: 0.8783 (m) REVERT: C 395 GLN cc_start: 0.7718 (tp40) cc_final: 0.7213 (tp40) REVERT: C 496 LEU cc_start: 0.6787 (tp) cc_final: 0.6543 (tp) REVERT: C 508 MET cc_start: 0.8171 (mmt) cc_final: 0.7905 (mmp) REVERT: C 536 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7290 (tt0) REVERT: D 187 TRP cc_start: 0.7110 (m-10) cc_final: 0.6271 (m-90) REVERT: D 283 LEU cc_start: 0.7171 (OUTLIER) cc_final: 0.6637 (tp) REVERT: E 352 ILE cc_start: 0.9301 (mt) cc_final: 0.8677 (mp) REVERT: F 297 CYS cc_start: 0.8327 (m) cc_final: 0.7864 (m) REVERT: F 317 VAL cc_start: 0.8067 (t) cc_final: 0.7833 (t) REVERT: F 378 ARG cc_start: 0.4812 (OUTLIER) cc_final: 0.4481 (mmp80) REVERT: F 390 THR cc_start: 0.8669 (m) cc_final: 0.8300 (m) REVERT: H 345 ILE cc_start: 0.7419 (OUTLIER) cc_final: 0.7163 (mm) REVERT: H 363 LEU cc_start: 0.6398 (OUTLIER) cc_final: 0.6147 (mp) REVERT: H 388 ARG cc_start: 0.6379 (tpt-90) cc_final: 0.6096 (ttm170) REVERT: H 450 MET cc_start: 0.7599 (mtm) cc_final: 0.7383 (mtp) REVERT: I 18 GLU cc_start: 0.6516 (mm-30) cc_final: 0.6262 (tp30) REVERT: I 105 GLN cc_start: 0.7299 (tt0) cc_final: 0.7066 (tm-30) REVERT: I 121 GLU cc_start: 0.6849 (tt0) cc_final: 0.6546 (tp30) REVERT: I 153 PHE cc_start: 0.5436 (p90) cc_final: 0.4994 (p90) REVERT: I 209 GLU cc_start: 0.5124 (tt0) cc_final: 0.4597 (tt0) REVERT: I 233 LEU cc_start: 0.5994 (mm) cc_final: 0.5490 (tp) REVERT: J 325 MET cc_start: 0.8157 (mtm) cc_final: 0.7699 (ttp) REVERT: J 354 GLU cc_start: 0.6792 (OUTLIER) cc_final: 0.6588 (mt-10) REVERT: J 364 GLU cc_start: 0.7632 (tt0) cc_final: 0.7317 (pt0) REVERT: J 431 ILE cc_start: 0.7889 (mt) cc_final: 0.7586 (mt) REVERT: J 507 GLU cc_start: 0.7779 (tt0) cc_final: 0.7426 (tp30) REVERT: K 18 GLU cc_start: 0.7252 (mm-30) cc_final: 0.6142 (mm-30) REVERT: K 26 ARG cc_start: 0.6451 (OUTLIER) cc_final: 0.6095 (ptt90) REVERT: K 67 LYS cc_start: 0.7564 (tttm) cc_final: 0.7267 (ttpt) REVERT: K 89 TYR cc_start: 0.7906 (m-80) cc_final: 0.7568 (m-80) REVERT: K 112 THR cc_start: 0.7464 (m) cc_final: 0.7183 (p) REVERT: K 116 LYS cc_start: 0.6658 (ttpp) cc_final: 0.6269 (ttpt) REVERT: K 119 GLU cc_start: 0.7471 (mt-10) cc_final: 0.6786 (mp0) REVERT: K 146 SER cc_start: 0.7903 (m) cc_final: 0.7398 (p) REVERT: K 209 GLU cc_start: 0.5608 (tt0) cc_final: 0.5393 (tt0) REVERT: K 216 ASN cc_start: 0.7369 (t0) cc_final: 0.6531 (m-40) REVERT: L 325 MET cc_start: 0.8145 (mtm) cc_final: 0.7047 (ttm) REVERT: L 332 ARG cc_start: 0.7411 (mtt-85) cc_final: 0.6599 (mtt180) REVERT: L 361 VAL cc_start: 0.7989 (OUTLIER) cc_final: 0.7590 (t) REVERT: L 364 GLU cc_start: 0.8083 (tt0) cc_final: 0.7565 (pt0) REVERT: L 388 ARG cc_start: 0.6589 (tpt-90) cc_final: 0.6086 (ttm-80) REVERT: L 477 ASP cc_start: 0.6245 (m-30) cc_final: 0.6034 (m-30) REVERT: M 307 LYS cc_start: 0.7794 (mtpt) cc_final: 0.7518 (mtmm) REVERT: M 322 GLN cc_start: 0.8515 (mt0) cc_final: 0.8291 (mt0) REVERT: M 325 MET cc_start: 0.8092 (mtm) cc_final: 0.7530 (ttm) REVERT: M 432 GLU cc_start: 0.6696 (tp30) cc_final: 0.6285 (mm-30) REVERT: N 325 MET cc_start: 0.7836 (mtm) cc_final: 0.7304 (ttp) REVERT: N 364 GLU cc_start: 0.7964 (tt0) cc_final: 0.7636 (pt0) REVERT: N 432 GLU cc_start: 0.6570 (tp30) cc_final: 0.5894 (mm-30) REVERT: N 434 GLU cc_start: 0.7042 (mt-10) cc_final: 0.6691 (pm20) REVERT: N 447 LYS cc_start: 0.7972 (mtmt) cc_final: 0.7690 (mtpp) REVERT: N 477 ASP cc_start: 0.7245 (m-30) cc_final: 0.6972 (m-30) REVERT: N 509 ARG cc_start: 0.6170 (OUTLIER) cc_final: 0.5929 (tpt-90) REVERT: N 512 GLU cc_start: 0.6573 (tt0) cc_final: 0.6367 (tm-30) REVERT: N 519 GLU cc_start: 0.7377 (mt-10) cc_final: 0.7173 (mm-30) REVERT: O 26 ARG cc_start: 0.7253 (OUTLIER) cc_final: 0.6541 (ppt170) REVERT: O 33 LEU cc_start: 0.6966 (OUTLIER) cc_final: 0.6639 (pp) REVERT: O 74 LEU cc_start: 0.7254 (OUTLIER) cc_final: 0.6811 (mt) REVERT: O 101 ASN cc_start: 0.7230 (t0) cc_final: 0.6932 (m-40) REVERT: O 116 LYS cc_start: 0.6842 (ttpp) cc_final: 0.6439 (mttt) REVERT: O 137 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7278 (mt-10) REVERT: O 143 TYR cc_start: 0.5549 (p90) cc_final: 0.5119 (p90) REVERT: O 146 SER cc_start: 0.6871 (m) cc_final: 0.6650 (t) REVERT: O 165 ASN cc_start: 0.5655 (m-40) cc_final: 0.5388 (m-40) REVERT: O 174 ASN cc_start: 0.6917 (t0) cc_final: 0.6589 (t0) REVERT: O 178 THR cc_start: 0.5702 (m) cc_final: 0.5469 (p) REVERT: O 181 LEU cc_start: 0.5991 (tp) cc_final: 0.5780 (tt) REVERT: O 216 ASN cc_start: 0.7609 (t0) cc_final: 0.7354 (m-40) REVERT: O 228 SER cc_start: 0.5018 (p) cc_final: 0.4734 (p) REVERT: P 325 MET cc_start: 0.8126 (mtm) cc_final: 0.7338 (ttp) REVERT: P 364 GLU cc_start: 0.8045 (tt0) cc_final: 0.7757 (pt0) REVERT: P 388 ARG cc_start: 0.6297 (tpt-90) cc_final: 0.5650 (ttm110) REVERT: P 503 VAL cc_start: 0.7524 (m) cc_final: 0.7292 (p) REVERT: P 509 ARG cc_start: 0.6882 (ttp80) cc_final: 0.6319 (tpt90) REVERT: Q 10 GLU cc_start: 0.4382 (OUTLIER) cc_final: 0.4125 (mp0) REVERT: Q 74 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7495 (mt) REVERT: Q 121 GLU cc_start: 0.7461 (tt0) cc_final: 0.7242 (mm-30) REVERT: Q 135 ARG cc_start: 0.6879 (ttm110) cc_final: 0.6648 (ttm110) REVERT: Q 146 SER cc_start: 0.7011 (m) cc_final: 0.6708 (p) REVERT: Q 155 VAL cc_start: 0.6577 (t) cc_final: 0.6054 (m) REVERT: Q 156 MET cc_start: 0.6824 (mtm) cc_final: 0.6307 (mtm) REVERT: Q 159 THR cc_start: 0.3870 (p) cc_final: 0.3360 (m) REVERT: Q 228 SER cc_start: 0.6870 (p) cc_final: 0.6513 (p) REVERT: Q 234 LEU cc_start: 0.6744 (OUTLIER) cc_final: 0.6060 (tp) REVERT: R 322 GLN cc_start: 0.8109 (mt0) cc_final: 0.7824 (mt0) REVERT: R 325 MET cc_start: 0.7726 (mtm) cc_final: 0.6714 (ttp) REVERT: R 354 GLU cc_start: 0.7685 (tt0) cc_final: 0.7222 (tp30) REVERT: R 507 GLU cc_start: 0.7920 (tt0) cc_final: 0.6840 (tp30) REVERT: R 519 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7644 (tp30) REVERT: S 345 ILE cc_start: 0.7347 (OUTLIER) cc_final: 0.7033 (mt) REVERT: S 364 GLU cc_start: 0.8681 (tt0) cc_final: 0.8380 (tt0) REVERT: S 519 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7632 (tm-30) REVERT: T 49 SER cc_start: 0.7214 (m) cc_final: 0.6896 (m) REVERT: T 85 ARG cc_start: 0.7695 (mmt90) cc_final: 0.7473 (tpp80) REVERT: T 97 ARG cc_start: 0.5748 (ttp80) cc_final: 0.5126 (ttt180) REVERT: T 106 THR cc_start: 0.6494 (m) cc_final: 0.6292 (t) REVERT: T 111 PHE cc_start: 0.6923 (t80) cc_final: 0.6635 (t80) REVERT: T 112 THR cc_start: 0.7268 (m) cc_final: 0.6724 (p) REVERT: T 119 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7519 (mp0) REVERT: T 121 GLU cc_start: 0.7148 (tt0) cc_final: 0.6557 (tp30) REVERT: T 134 LYS cc_start: 0.7343 (ttpt) cc_final: 0.6837 (ttpt) REVERT: T 178 THR cc_start: 0.5804 (m) cc_final: 0.5541 (p) REVERT: T 207 SER cc_start: 0.5431 (p) cc_final: 0.5228 (t) REVERT: T 216 ASN cc_start: 0.7540 (t0) cc_final: 0.6882 (m110) REVERT: T 228 SER cc_start: 0.6004 (p) cc_final: 0.5728 (t) REVERT: U 314 MET cc_start: 0.8719 (ttm) cc_final: 0.8282 (ttm) REVERT: U 330 ASP cc_start: 0.7443 (OUTLIER) cc_final: 0.7128 (p0) REVERT: U 447 LYS cc_start: 0.7279 (mtmt) cc_final: 0.6955 (mtmt) REVERT: U 509 ARG cc_start: 0.7437 (tpt170) cc_final: 0.6996 (ttp80) REVERT: V 307 LYS cc_start: 0.7429 (mtpt) cc_final: 0.7222 (mtpp) REVERT: V 325 MET cc_start: 0.7650 (mtm) cc_final: 0.7219 (ttp) REVERT: V 364 GLU cc_start: 0.7874 (tt0) cc_final: 0.7601 (pt0) REVERT: V 432 GLU cc_start: 0.5736 (mm-30) cc_final: 0.5223 (mm-30) REVERT: V 509 ARG cc_start: 0.6366 (OUTLIER) cc_final: 0.5815 (ttt180) REVERT: V 519 GLU cc_start: 0.7677 (tt0) cc_final: 0.7471 (tp30) REVERT: W 307 LYS cc_start: 0.7591 (mtpt) cc_final: 0.7266 (mtpt) REVERT: W 354 GLU cc_start: 0.6968 (OUTLIER) cc_final: 0.6573 (tt0) REVERT: W 364 GLU cc_start: 0.7797 (tt0) cc_final: 0.7322 (pt0) REVERT: W 509 ARG cc_start: 0.6787 (tpt170) cc_final: 0.6258 (ttp-170) REVERT: W 519 GLU cc_start: 0.6869 (mt-10) cc_final: 0.6536 (mm-30) REVERT: W 522 SER cc_start: 0.6056 (t) cc_final: 0.5737 (m) REVERT: X 24 ILE cc_start: 0.6746 (mt) cc_final: 0.6466 (mt) REVERT: X 44 GLU cc_start: 0.5645 (tt0) cc_final: 0.5096 (tt0) REVERT: X 49 SER cc_start: 0.7769 (m) cc_final: 0.7474 (m) REVERT: X 52 LYS cc_start: 0.6958 (mtpt) cc_final: 0.6670 (mtmm) REVERT: X 69 ASN cc_start: 0.7121 (OUTLIER) cc_final: 0.6692 (p0) REVERT: X 80 GLN cc_start: 0.7626 (tp-100) cc_final: 0.7391 (tp-100) REVERT: X 101 ASN cc_start: 0.6855 (t0) cc_final: 0.6578 (m-40) REVERT: X 119 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7703 (mp0) REVERT: X 130 TYR cc_start: 0.7549 (t80) cc_final: 0.6477 (t80) REVERT: X 156 MET cc_start: 0.5513 (mtm) cc_final: 0.5114 (mtm) REVERT: X 163 ILE cc_start: 0.6641 (mt) cc_final: 0.6338 (mt) REVERT: X 216 ASN cc_start: 0.7374 (t0) cc_final: 0.6750 (t0) REVERT: X 233 LEU cc_start: 0.6688 (mp) cc_final: 0.6216 (mm) REVERT: Y 314 MET cc_start: 0.8515 (ttm) cc_final: 0.8313 (ttm) REVERT: Y 325 MET cc_start: 0.7898 (mtm) cc_final: 0.7052 (ttm) REVERT: Y 430 ASN cc_start: 0.7842 (t0) cc_final: 0.7093 (t0) REVERT: Y 432 GLU cc_start: 0.6206 (tp30) cc_final: 0.5852 (mm-30) REVERT: Y 450 MET cc_start: 0.7383 (mtm) cc_final: 0.7028 (mtm) REVERT: Y 509 ARG cc_start: 0.7470 (tpt170) cc_final: 0.6407 (ttt180) REVERT: Z 28 LYS cc_start: 0.7368 (mmtt) cc_final: 0.7124 (mmtp) REVERT: Z 33 LEU cc_start: 0.6750 (OUTLIER) cc_final: 0.6385 (pt) REVERT: Z 52 LYS cc_start: 0.7371 (mtpt) cc_final: 0.6757 (mttm) REVERT: Z 101 ASN cc_start: 0.7641 (t0) cc_final: 0.7243 (m-40) REVERT: Z 121 GLU cc_start: 0.7762 (tt0) cc_final: 0.7446 (tt0) REVERT: Z 138 LEU cc_start: 0.7807 (mt) cc_final: 0.7492 (mp) REVERT: Z 150 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7923 (mp0) REVERT: Z 178 THR cc_start: 0.5270 (m) cc_final: 0.5007 (p) REVERT: Z 181 LEU cc_start: 0.6682 (tp) cc_final: 0.6433 (tt) REVERT: Z 216 ASN cc_start: 0.8186 (t0) cc_final: 0.7396 (m-40) REVERT: a 325 MET cc_start: 0.7805 (mtm) cc_final: 0.7135 (ttp) REVERT: a 345 ILE cc_start: 0.7194 (OUTLIER) cc_final: 0.6952 (mt) REVERT: a 354 GLU cc_start: 0.7238 (tt0) cc_final: 0.6889 (mt-10) REVERT: b 354 GLU cc_start: 0.6864 (tt0) cc_final: 0.6446 (mm-30) REVERT: b 355 PHE cc_start: 0.7361 (m-10) cc_final: 0.7041 (m-80) REVERT: b 461 ASP cc_start: 0.6304 (t70) cc_final: 0.6037 (t0) REVERT: b 519 GLU cc_start: 0.6854 (mt-10) cc_final: 0.6565 (mm-30) REVERT: d 13 MET cc_start: 0.5910 (mtp) cc_final: 0.5434 (mmm) REVERT: d 19 LEU cc_start: 0.7504 (tt) cc_final: 0.7197 (mt) REVERT: d 101 ASN cc_start: 0.7530 (t0) cc_final: 0.7091 (m110) REVERT: d 118 TYR cc_start: 0.7727 (m-10) cc_final: 0.7354 (m-10) REVERT: d 143 TYR cc_start: 0.6028 (p90) cc_final: 0.5803 (p90) REVERT: d 179 ASP cc_start: 0.7011 (m-30) cc_final: 0.6625 (t0) REVERT: d 234 LEU cc_start: 0.6046 (OUTLIER) cc_final: 0.5659 (pt) REVERT: f 22 LYS cc_start: 0.5297 (tppp) cc_final: 0.5051 (tptp) REVERT: f 44 GLU cc_start: 0.7251 (tt0) cc_final: 0.6766 (tm-30) REVERT: f 69 ASN cc_start: 0.7151 (OUTLIER) cc_final: 0.6651 (m-40) REVERT: f 101 ASN cc_start: 0.6969 (t0) cc_final: 0.6733 (m-40) REVERT: f 146 SER cc_start: 0.7829 (p) cc_final: 0.7357 (p) REVERT: f 149 ASP cc_start: 0.7774 (t0) cc_final: 0.7348 (p0) REVERT: f 163 ILE cc_start: 0.6517 (mt) cc_final: 0.6058 (mm) REVERT: f 165 ASN cc_start: 0.5749 (m-40) cc_final: 0.5508 (m110) REVERT: f 234 LEU cc_start: 0.7039 (OUTLIER) cc_final: 0.6669 (pt) outliers start: 278 outliers final: 58 residues processed: 1788 average time/residue: 0.7306 time to fit residues: 2168.8587 Evaluate side-chains 1011 residues out of total 7050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 919 time to evaluate : 6.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 69 ASN Chi-restraints excluded: chain 0 residue 205 VAL Chi-restraints excluded: chain 0 residue 234 LEU Chi-restraints excluded: chain 2 residue 234 LEU Chi-restraints excluded: chain 4 residue 205 VAL Chi-restraints excluded: chain 4 residue 234 LEU Chi-restraints excluded: chain 6 residue 11 GLN Chi-restraints excluded: chain 6 residue 182 ARG Chi-restraints excluded: chain 6 residue 205 VAL Chi-restraints excluded: chain 6 residue 234 LEU Chi-restraints excluded: chain 8 residue 69 ASN Chi-restraints excluded: chain 8 residue 73 ASN Chi-restraints excluded: chain 8 residue 74 LEU Chi-restraints excluded: chain 8 residue 99 LEU Chi-restraints excluded: chain 8 residue 234 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 430 ARG Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain D residue 244 GLU Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 300 THR Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 408 ASN Chi-restraints excluded: chain E residue 581 ILE Chi-restraints excluded: chain E residue 588 VAL Chi-restraints excluded: chain F residue 378 ARG Chi-restraints excluded: chain H residue 345 ILE Chi-restraints excluded: chain H residue 363 LEU Chi-restraints excluded: chain I residue 74 LEU Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain J residue 345 ILE Chi-restraints excluded: chain J residue 354 GLU Chi-restraints excluded: chain J residue 486 LEU Chi-restraints excluded: chain K residue 26 ARG Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain L residue 345 ILE Chi-restraints excluded: chain L residue 361 VAL Chi-restraints excluded: chain L residue 441 SER Chi-restraints excluded: chain L residue 444 LEU Chi-restraints excluded: chain M residue 503 VAL Chi-restraints excluded: chain N residue 345 ILE Chi-restraints excluded: chain N residue 444 LEU Chi-restraints excluded: chain N residue 509 ARG Chi-restraints excluded: chain O residue 26 ARG Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 74 LEU Chi-restraints excluded: chain O residue 123 CYS Chi-restraints excluded: chain P residue 444 LEU Chi-restraints excluded: chain Q residue 10 GLU Chi-restraints excluded: chain Q residue 74 LEU Chi-restraints excluded: chain Q residue 123 CYS Chi-restraints excluded: chain Q residue 234 LEU Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 361 VAL Chi-restraints excluded: chain R residue 363 LEU Chi-restraints excluded: chain S residue 345 ILE Chi-restraints excluded: chain T residue 74 LEU Chi-restraints excluded: chain U residue 330 ASP Chi-restraints excluded: chain U residue 345 ILE Chi-restraints excluded: chain V residue 444 LEU Chi-restraints excluded: chain V residue 509 ARG Chi-restraints excluded: chain W residue 345 ILE Chi-restraints excluded: chain W residue 354 GLU Chi-restraints excluded: chain W residue 363 LEU Chi-restraints excluded: chain X residue 69 ASN Chi-restraints excluded: chain X residue 74 LEU Chi-restraints excluded: chain Y residue 345 ILE Chi-restraints excluded: chain Y residue 361 VAL Chi-restraints excluded: chain Y residue 444 LEU Chi-restraints excluded: chain Z residue 33 LEU Chi-restraints excluded: chain Z residue 123 CYS Chi-restraints excluded: chain Z residue 147 ILE Chi-restraints excluded: chain a residue 345 ILE Chi-restraints excluded: chain d residue 74 LEU Chi-restraints excluded: chain d residue 144 ASP Chi-restraints excluded: chain d residue 205 VAL Chi-restraints excluded: chain d residue 234 LEU Chi-restraints excluded: chain f residue 69 ASN Chi-restraints excluded: chain f residue 234 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 886 random chunks: chunk 748 optimal weight: 5.9990 chunk 671 optimal weight: 0.7980 chunk 372 optimal weight: 0.7980 chunk 229 optimal weight: 6.9990 chunk 452 optimal weight: 9.9990 chunk 358 optimal weight: 3.9990 chunk 694 optimal weight: 0.8980 chunk 268 optimal weight: 4.9990 chunk 422 optimal weight: 9.9990 chunk 516 optimal weight: 0.9980 chunk 804 optimal weight: 4.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 11 GLN 0 69 ASN 0 80 GLN 1 607 GLN 2 11 GLN ** 2 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 114 GLN 4 114 GLN 6 114 GLN 8 11 GLN 8 69 ASN 8 80 GLN 8 114 GLN 8 165 ASN 8 231 GLN ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 HIS ** C 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 HIS D 308 ASN D 546 HIS ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 460 HIS ** F 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 5 GLN H 456 GLN I 45 ASN I 98 GLN I 114 GLN J 456 GLN K 80 GLN K 114 GLN L 322 GLN ** L 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 396 GLN L 456 GLN M 456 GLN N 456 GLN O 51 GLN O 80 GLN O 114 GLN ** P 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 456 GLN Q 11 GLN Q 105 GLN ** Q 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 456 GLN S 456 GLN T 80 GLN U 322 GLN U 456 GLN V 322 GLN V 456 GLN W 456 GLN X 69 ASN X 73 ASN X 80 GLN X 114 GLN X 129 HIS Y 456 GLN Z 98 GLN Z 114 GLN a 396 GLN a 456 GLN b 322 GLN b 456 GLN d 11 GLN ** d 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 114 GLN f 11 GLN f 45 ASN f 69 ASN ** f 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 63 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6923 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.114 69864 Z= 0.238 Angle : 0.593 8.389 94566 Z= 0.310 Chirality : 0.044 0.209 10748 Planarity : 0.005 0.061 12421 Dihedral : 7.186 124.642 10321 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.38 % Favored : 97.61 % Rotamer: Outliers : 2.84 % Allowed : 10.52 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.09), residues: 8868 helix: 1.80 (0.08), residues: 3488 sheet: 0.37 (0.11), residues: 2052 loop : -0.19 (0.11), residues: 3328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 570 HIS 0.014 0.001 HIS T 152 PHE 0.033 0.003 PHE 6 71 TYR 0.043 0.002 TYR T 171 ARG 0.012 0.001 ARG 4 182 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17736 Ramachandran restraints generated. 8868 Oldfield, 0 Emsley, 8868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17736 Ramachandran restraints generated. 8868 Oldfield, 0 Emsley, 8868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1160 residues out of total 7050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 960 time to evaluate : 6.085 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: 0 13 MET cc_start: 0.7357 (ttm) cc_final: 0.6637 (tmm) REVERT: 0 28 LYS cc_start: 0.7279 (mmtt) cc_final: 0.6918 (mmtm) REVERT: 0 101 ASN cc_start: 0.7403 (t0) cc_final: 0.7170 (m-40) REVERT: 0 114 GLN cc_start: 0.5907 (mp10) cc_final: 0.5377 (mp10) REVERT: 0 143 TYR cc_start: 0.6426 (p90) cc_final: 0.6064 (p90) REVERT: 2 11 GLN cc_start: 0.5317 (mt0) cc_final: 0.4414 (tm-30) REVERT: 2 22 LYS cc_start: 0.6565 (ptpp) cc_final: 0.6345 (tptt) REVERT: 2 135 ARG cc_start: 0.7783 (tpp80) cc_final: 0.6851 (ttm-80) REVERT: 2 234 LEU cc_start: 0.6530 (OUTLIER) cc_final: 0.6227 (pt) REVERT: 4 45 ASN cc_start: 0.7797 (t0) cc_final: 0.6900 (t0) REVERT: 4 51 GLN cc_start: 0.6373 (mt0) cc_final: 0.5896 (mm-40) REVERT: 4 97 ARG cc_start: 0.6755 (ttt-90) cc_final: 0.6499 (ttm110) REVERT: 4 101 ASN cc_start: 0.6948 (t0) cc_final: 0.6490 (m-40) REVERT: 4 173 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.7188 (mm-30) REVERT: 6 11 GLN cc_start: 0.4684 (OUTLIER) cc_final: 0.4445 (mm-40) REVERT: 6 28 LYS cc_start: 0.7441 (mmtt) cc_final: 0.6992 (mmtt) REVERT: 6 44 GLU cc_start: 0.7599 (tt0) cc_final: 0.6911 (tm-30) REVERT: 6 97 ARG cc_start: 0.6645 (ttt-90) cc_final: 0.6327 (ttt-90) REVERT: 6 101 ASN cc_start: 0.7403 (t0) cc_final: 0.7184 (m-40) REVERT: 6 113 GLU cc_start: 0.7087 (mm-30) cc_final: 0.6402 (tt0) REVERT: 6 168 LYS cc_start: 0.7039 (mttt) cc_final: 0.6789 (tttt) REVERT: 6 171 TYR cc_start: 0.6436 (t80) cc_final: 0.6160 (t80) REVERT: 6 183 ILE cc_start: 0.6829 (mm) cc_final: 0.6565 (mp) REVERT: 6 233 LEU cc_start: 0.7557 (mp) cc_final: 0.7120 (mt) REVERT: 6 234 LEU cc_start: 0.6207 (OUTLIER) cc_final: 0.5512 (pt) REVERT: 8 11 GLN cc_start: 0.6548 (mt0) cc_final: 0.6035 (mm110) REVERT: 8 73 ASN cc_start: 0.7013 (OUTLIER) cc_final: 0.6671 (m-40) REVERT: 8 80 GLN cc_start: 0.7819 (tp40) cc_final: 0.7484 (tp40) REVERT: 8 163 ILE cc_start: 0.7139 (mt) cc_final: 0.6879 (mt) REVERT: 8 179 ASP cc_start: 0.7207 (m-30) cc_final: 0.6954 (t0) REVERT: A 492 ASP cc_start: 0.8122 (OUTLIER) cc_final: 0.7206 (t0) REVERT: B 520 GLN cc_start: 0.8314 (tt0) cc_final: 0.7974 (tt0) REVERT: B 545 GLN cc_start: 0.8558 (tp40) cc_final: 0.8141 (pm20) REVERT: C 281 TYR cc_start: 0.8134 (OUTLIER) cc_final: 0.7134 (t80) REVERT: C 297 CYS cc_start: 0.9058 (m) cc_final: 0.8794 (m) REVERT: C 395 GLN cc_start: 0.7959 (tp40) cc_final: 0.7614 (tp40) REVERT: C 508 MET cc_start: 0.8147 (mmt) cc_final: 0.7944 (mmp) REVERT: D 187 TRP cc_start: 0.7153 (m-10) cc_final: 0.6387 (m-90) REVERT: D 283 LEU cc_start: 0.7303 (OUTLIER) cc_final: 0.7031 (tp) REVERT: D 486 MET cc_start: 0.7326 (tmm) cc_final: 0.6672 (tmm) REVERT: E 352 ILE cc_start: 0.9200 (mt) cc_final: 0.8919 (mt) REVERT: F 168 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7947 (mt) REVERT: F 297 CYS cc_start: 0.8399 (m) cc_final: 0.7937 (m) REVERT: F 378 ARG cc_start: 0.4442 (OUTLIER) cc_final: 0.4222 (mmp80) REVERT: F 545 GLN cc_start: 0.7836 (tp-100) cc_final: 0.7623 (tp-100) REVERT: H 388 ARG cc_start: 0.6916 (tpt-90) cc_final: 0.6361 (ttp-170) REVERT: I 73 ASN cc_start: 0.6758 (t0) cc_final: 0.6497 (t0) REVERT: I 105 GLN cc_start: 0.7386 (tt0) cc_final: 0.6974 (tm-30) REVERT: I 121 GLU cc_start: 0.6854 (tt0) cc_final: 0.6611 (tp30) REVERT: I 182 ARG cc_start: 0.5477 (OUTLIER) cc_final: 0.5127 (mpt-90) REVERT: I 233 LEU cc_start: 0.6680 (mm) cc_final: 0.6098 (tp) REVERT: J 325 MET cc_start: 0.8107 (mtm) cc_final: 0.7534 (ttm) REVERT: J 364 GLU cc_start: 0.7697 (tt0) cc_final: 0.7308 (pt0) REVERT: J 507 GLU cc_start: 0.7919 (tt0) cc_final: 0.7555 (tp30) REVERT: J 509 ARG cc_start: 0.6837 (tpt90) cc_final: 0.6436 (ttt180) REVERT: K 26 ARG cc_start: 0.6329 (ttm110) cc_final: 0.6071 (ppt170) REVERT: K 67 LYS cc_start: 0.7483 (tttm) cc_final: 0.7006 (ttpt) REVERT: K 89 TYR cc_start: 0.8208 (m-80) cc_final: 0.7911 (m-80) REVERT: K 112 THR cc_start: 0.7319 (m) cc_final: 0.6926 (p) REVERT: K 135 ARG cc_start: 0.7597 (ttm-80) cc_final: 0.6998 (tpp-160) REVERT: K 146 SER cc_start: 0.7257 (m) cc_final: 0.6747 (p) REVERT: K 150 GLU cc_start: 0.7585 (mm-30) cc_final: 0.6931 (mm-30) REVERT: K 216 ASN cc_start: 0.7257 (t0) cc_final: 0.6441 (m-40) REVERT: K 234 LEU cc_start: 0.6233 (mt) cc_final: 0.6027 (mm) REVERT: L 325 MET cc_start: 0.8043 (mtm) cc_final: 0.7158 (ttp) REVERT: L 332 ARG cc_start: 0.7310 (mtt-85) cc_final: 0.6491 (mtt180) REVERT: M 307 LYS cc_start: 0.8134 (mtpt) cc_final: 0.7855 (mtmm) REVERT: M 325 MET cc_start: 0.8141 (mtm) cc_final: 0.7606 (ttt) REVERT: M 432 GLU cc_start: 0.6163 (tp30) cc_final: 0.5953 (mm-30) REVERT: N 325 MET cc_start: 0.8055 (mtm) cc_final: 0.7541 (ttp) REVERT: N 354 GLU cc_start: 0.7061 (mt-10) cc_final: 0.6581 (mm-30) REVERT: N 364 GLU cc_start: 0.7979 (tt0) cc_final: 0.7619 (pt0) REVERT: N 432 GLU cc_start: 0.6558 (tp30) cc_final: 0.5985 (mm-30) REVERT: N 433 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7985 (mt-10) REVERT: N 434 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7462 (pm20) REVERT: N 447 LYS cc_start: 0.7966 (mtmt) cc_final: 0.7595 (mtpp) REVERT: N 512 GLU cc_start: 0.6977 (tt0) cc_final: 0.6664 (tm-30) REVERT: N 519 GLU cc_start: 0.7080 (mt-10) cc_final: 0.6866 (mm-30) REVERT: O 26 ARG cc_start: 0.7189 (ttm110) cc_final: 0.6481 (ppt170) REVERT: O 116 LYS cc_start: 0.7020 (ttpp) cc_final: 0.6628 (mttt) REVERT: O 143 TYR cc_start: 0.5506 (p90) cc_final: 0.5100 (p90) REVERT: O 146 SER cc_start: 0.6824 (m) cc_final: 0.6561 (t) REVERT: O 174 ASN cc_start: 0.7210 (t0) cc_final: 0.6924 (t0) REVERT: O 216 ASN cc_start: 0.7741 (t0) cc_final: 0.7447 (m-40) REVERT: O 226 THR cc_start: 0.5972 (t) cc_final: 0.5523 (m) REVERT: P 325 MET cc_start: 0.7982 (mtm) cc_final: 0.7139 (ttp) REVERT: P 364 GLU cc_start: 0.7906 (tt0) cc_final: 0.7688 (mt-10) REVERT: P 388 ARG cc_start: 0.6967 (tpt-90) cc_final: 0.6249 (ttm110) REVERT: Q 74 LEU cc_start: 0.7283 (OUTLIER) cc_final: 0.7081 (mt) REVERT: Q 97 ARG cc_start: 0.6240 (ttp80) cc_final: 0.5865 (mtm110) REVERT: Q 113 GLU cc_start: 0.7325 (tp30) cc_final: 0.6634 (tt0) REVERT: Q 134 LYS cc_start: 0.7537 (ttpp) cc_final: 0.7208 (tttm) REVERT: Q 135 ARG cc_start: 0.7133 (ttm110) cc_final: 0.6887 (ttm110) REVERT: Q 146 SER cc_start: 0.7162 (m) cc_final: 0.6745 (p) REVERT: Q 156 MET cc_start: 0.7019 (mtm) cc_final: 0.6485 (mtm) REVERT: Q 228 SER cc_start: 0.6749 (p) cc_final: 0.6498 (p) REVERT: Q 234 LEU cc_start: 0.6526 (OUTLIER) cc_final: 0.5857 (tp) REVERT: R 322 GLN cc_start: 0.7864 (mt0) cc_final: 0.7637 (mt0) REVERT: R 325 MET cc_start: 0.7751 (mtm) cc_final: 0.6802 (ttp) REVERT: R 507 GLU cc_start: 0.7941 (tt0) cc_final: 0.6783 (tp30) REVERT: R 519 GLU cc_start: 0.7481 (mt-10) cc_final: 0.7089 (tp30) REVERT: S 364 GLU cc_start: 0.8470 (tt0) cc_final: 0.8201 (tt0) REVERT: S 395 MET cc_start: 0.6770 (mmm) cc_final: 0.6495 (mmm) REVERT: S 519 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7709 (tm-30) REVERT: T 52 LYS cc_start: 0.7331 (mtpt) cc_final: 0.6990 (mtmm) REVERT: T 113 GLU cc_start: 0.7385 (tp30) cc_final: 0.7089 (tm-30) REVERT: T 121 GLU cc_start: 0.7202 (tt0) cc_final: 0.6703 (mm-30) REVERT: T 134 LYS cc_start: 0.7390 (ttpt) cc_final: 0.7036 (ttpt) REVERT: T 156 MET cc_start: 0.6330 (mtm) cc_final: 0.5947 (mtm) REVERT: T 207 SER cc_start: 0.5883 (p) cc_final: 0.5607 (t) REVERT: T 214 ASP cc_start: 0.6329 (t0) cc_final: 0.5925 (t0) REVERT: T 216 ASN cc_start: 0.7697 (t0) cc_final: 0.6944 (m110) REVERT: U 314 MET cc_start: 0.8647 (ttm) cc_final: 0.8155 (ttm) REVERT: U 433 GLU cc_start: 0.7289 (tm-30) cc_final: 0.7000 (mm-30) REVERT: U 509 ARG cc_start: 0.6926 (tpt170) cc_final: 0.6463 (ttp80) REVERT: V 307 LYS cc_start: 0.7941 (mtpt) cc_final: 0.7649 (mtpp) REVERT: V 325 MET cc_start: 0.7658 (mtm) cc_final: 0.7219 (mmt) REVERT: V 358 LEU cc_start: 0.7355 (tp) cc_final: 0.7126 (mt) REVERT: V 364 GLU cc_start: 0.7734 (tt0) cc_final: 0.7343 (pt0) REVERT: V 395 MET cc_start: 0.6876 (mmp) cc_final: 0.6444 (mtm) REVERT: V 509 ARG cc_start: 0.6564 (OUTLIER) cc_final: 0.6074 (ttt180) REVERT: V 519 GLU cc_start: 0.7733 (tt0) cc_final: 0.7152 (mt-10) REVERT: W 364 GLU cc_start: 0.7611 (tt0) cc_final: 0.7054 (pt0) REVERT: W 509 ARG cc_start: 0.6524 (tpt170) cc_final: 0.6011 (ttt180) REVERT: W 522 SER cc_start: 0.6020 (t) cc_final: 0.5666 (m) REVERT: X 26 ARG cc_start: 0.7396 (ptm-80) cc_final: 0.7106 (ptm-80) REVERT: X 52 LYS cc_start: 0.7399 (mtpt) cc_final: 0.6933 (mtmm) REVERT: X 80 GLN cc_start: 0.7904 (tp40) cc_final: 0.7567 (tp-100) REVERT: X 101 ASN cc_start: 0.6595 (t0) cc_final: 0.6373 (m-40) REVERT: X 119 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7923 (mp0) REVERT: X 130 TYR cc_start: 0.7583 (t80) cc_final: 0.6234 (t80) REVERT: X 216 ASN cc_start: 0.7515 (t0) cc_final: 0.6829 (t0) REVERT: Y 325 MET cc_start: 0.8020 (mtm) cc_final: 0.6940 (ttt) REVERT: Z 14 ARG cc_start: 0.5174 (ptp-110) cc_final: 0.4945 (ptp90) REVERT: Z 28 LYS cc_start: 0.7170 (mmtt) cc_final: 0.6953 (mmtm) REVERT: Z 52 LYS cc_start: 0.7673 (mtpt) cc_final: 0.7024 (mttm) REVERT: Z 130 TYR cc_start: 0.7602 (t80) cc_final: 0.7368 (t80) REVERT: Z 138 LEU cc_start: 0.7658 (mt) cc_final: 0.7319 (mp) REVERT: Z 150 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7763 (mp0) REVERT: Z 152 HIS cc_start: 0.7295 (m-70) cc_final: 0.6885 (m-70) REVERT: Z 216 ASN cc_start: 0.8505 (t0) cc_final: 0.7831 (m-40) REVERT: a 325 MET cc_start: 0.7892 (mtm) cc_final: 0.7053 (ttp) REVERT: a 354 GLU cc_start: 0.7120 (tt0) cc_final: 0.6737 (mt-10) REVERT: b 358 LEU cc_start: 0.7403 (tp) cc_final: 0.7194 (mt) REVERT: d 11 GLN cc_start: 0.6577 (mt0) cc_final: 0.6282 (mt0) REVERT: d 13 MET cc_start: 0.5401 (mtp) cc_final: 0.4770 (mmm) REVERT: d 101 ASN cc_start: 0.7716 (t0) cc_final: 0.7303 (m110) REVERT: d 143 TYR cc_start: 0.6150 (p90) cc_final: 0.5870 (p90) REVERT: d 234 LEU cc_start: 0.6428 (OUTLIER) cc_final: 0.6099 (pt) REVERT: f 44 GLU cc_start: 0.7090 (tt0) cc_final: 0.6567 (tm-30) REVERT: f 69 ASN cc_start: 0.7242 (p0) cc_final: 0.6473 (m-40) REVERT: f 101 ASN cc_start: 0.7226 (t0) cc_final: 0.6777 (m-40) REVERT: f 112 THR cc_start: 0.7942 (OUTLIER) cc_final: 0.7673 (p) REVERT: f 146 SER cc_start: 0.7959 (p) cc_final: 0.7755 (p) REVERT: f 149 ASP cc_start: 0.7756 (t0) cc_final: 0.7405 (p0) outliers start: 200 outliers final: 99 residues processed: 1108 average time/residue: 0.6743 time to fit residues: 1254.1059 Evaluate side-chains 923 residues out of total 7050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 808 time to evaluate : 6.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 51 GLN Chi-restraints excluded: chain 0 residue 70 GLU Chi-restraints excluded: chain 0 residue 147 ILE Chi-restraints excluded: chain 0 residue 226 THR Chi-restraints excluded: chain 2 residue 170 SER Chi-restraints excluded: chain 2 residue 228 SER Chi-restraints excluded: chain 2 residue 234 LEU Chi-restraints excluded: chain 4 residue 173 GLU Chi-restraints excluded: chain 4 residue 219 ARG Chi-restraints excluded: chain 4 residue 234 LEU Chi-restraints excluded: chain 6 residue 11 GLN Chi-restraints excluded: chain 6 residue 147 ILE Chi-restraints excluded: chain 6 residue 234 LEU Chi-restraints excluded: chain 8 residue 73 ASN Chi-restraints excluded: chain 8 residue 147 ILE Chi-restraints excluded: chain 8 residue 205 VAL Chi-restraints excluded: chain 8 residue 226 THR Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 297 CYS Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 430 ARG Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain D residue 244 GLU Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 439 ARG Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain D residue 518 MET Chi-restraints excluded: chain D residue 560 ASP Chi-restraints excluded: chain E residue 139 GLN Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 408 ASN Chi-restraints excluded: chain E residue 581 ILE Chi-restraints excluded: chain E residue 588 VAL Chi-restraints excluded: chain E residue 604 ASN Chi-restraints excluded: chain E residue 605 LEU Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 378 ARG Chi-restraints excluded: chain F residue 459 VAL Chi-restraints excluded: chain H residue 345 ILE Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain I residue 182 ARG Chi-restraints excluded: chain J residue 345 ILE Chi-restraints excluded: chain K residue 69 ASN Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain L residue 399 LEU Chi-restraints excluded: chain L residue 444 LEU Chi-restraints excluded: chain N residue 345 ILE Chi-restraints excluded: chain N residue 399 LEU Chi-restraints excluded: chain N residue 444 LEU Chi-restraints excluded: chain O residue 29 SER Chi-restraints excluded: chain O residue 133 THR Chi-restraints excluded: chain O residue 147 ILE Chi-restraints excluded: chain O residue 176 SER Chi-restraints excluded: chain P residue 399 LEU Chi-restraints excluded: chain P residue 409 ILE Chi-restraints excluded: chain P residue 444 LEU Chi-restraints excluded: chain P residue 486 LEU Chi-restraints excluded: chain Q residue 74 LEU Chi-restraints excluded: chain Q residue 147 ILE Chi-restraints excluded: chain Q residue 234 LEU Chi-restraints excluded: chain R residue 396 GLN Chi-restraints excluded: chain R residue 399 LEU Chi-restraints excluded: chain S residue 345 ILE Chi-restraints excluded: chain S residue 386 MET Chi-restraints excluded: chain S residue 409 ILE Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain T residue 154 VAL Chi-restraints excluded: chain U residue 313 VAL Chi-restraints excluded: chain U residue 520 SER Chi-restraints excluded: chain V residue 412 SER Chi-restraints excluded: chain V residue 444 LEU Chi-restraints excluded: chain V residue 504 ASP Chi-restraints excluded: chain V residue 509 ARG Chi-restraints excluded: chain W residue 331 VAL Chi-restraints excluded: chain W residue 345 ILE Chi-restraints excluded: chain W residue 486 LEU Chi-restraints excluded: chain W residue 512 GLU Chi-restraints excluded: chain X residue 110 ILE Chi-restraints excluded: chain X residue 147 ILE Chi-restraints excluded: chain Y residue 409 ILE Chi-restraints excluded: chain Y residue 444 LEU Chi-restraints excluded: chain Y residue 503 VAL Chi-restraints excluded: chain Z residue 146 SER Chi-restraints excluded: chain Z residue 147 ILE Chi-restraints excluded: chain b residue 447 LYS Chi-restraints excluded: chain d residue 47 SER Chi-restraints excluded: chain d residue 74 LEU Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain d residue 109 THR Chi-restraints excluded: chain d residue 144 ASP Chi-restraints excluded: chain d residue 234 LEU Chi-restraints excluded: chain f residue 74 LEU Chi-restraints excluded: chain f residue 112 THR Chi-restraints excluded: chain f residue 228 SER Chi-restraints excluded: chain f residue 233 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 886 random chunks: chunk 447 optimal weight: 1.9990 chunk 249 optimal weight: 20.0000 chunk 669 optimal weight: 2.9990 chunk 547 optimal weight: 0.6980 chunk 221 optimal weight: 6.9990 chunk 806 optimal weight: 3.9990 chunk 870 optimal weight: 0.8980 chunk 717 optimal weight: 4.9990 chunk 799 optimal weight: 10.0000 chunk 274 optimal weight: 10.0000 chunk 646 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 11 GLN 2 69 ASN 2 114 GLN 6 231 GLN 8 73 ASN ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN B 354 GLN D 546 HIS E 129 ASN E 139 GLN ** F 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 174 ASN J 437 GLN ** L 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 114 GLN T 80 GLN U 322 GLN U 381 ASN Y 390 ASN b 322 GLN d 69 ASN f 114 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 69864 Z= 0.232 Angle : 0.549 9.227 94566 Z= 0.288 Chirality : 0.044 0.276 10748 Planarity : 0.005 0.055 12421 Dihedral : 6.292 115.299 10228 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.09 % Favored : 96.90 % Rotamer: Outliers : 3.07 % Allowed : 11.48 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.09), residues: 8868 helix: 2.19 (0.09), residues: 3495 sheet: 0.55 (0.11), residues: 2078 loop : -0.09 (0.11), residues: 3295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 570 HIS 0.011 0.001 HIS O 152 PHE 0.032 0.002 PHE 2 71 TYR 0.021 0.002 TYR T 171 ARG 0.009 0.001 ARG Q 14 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17736 Ramachandran restraints generated. 8868 Oldfield, 0 Emsley, 8868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17736 Ramachandran restraints generated. 8868 Oldfield, 0 Emsley, 8868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1074 residues out of total 7050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 858 time to evaluate : 6.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 13 MET cc_start: 0.7249 (ttm) cc_final: 0.6802 (tmm) REVERT: 0 114 GLN cc_start: 0.6027 (mp10) cc_final: 0.5460 (mp10) REVERT: 0 121 GLU cc_start: 0.7413 (tt0) cc_final: 0.7141 (tt0) REVERT: 0 143 TYR cc_start: 0.6408 (p90) cc_final: 0.6111 (p90) REVERT: 2 11 GLN cc_start: 0.4675 (mt0) cc_final: 0.3866 (tm-30) REVERT: 2 13 MET cc_start: 0.6134 (ttp) cc_final: 0.5879 (tmm) REVERT: 2 22 LYS cc_start: 0.6633 (ptpp) cc_final: 0.6393 (tptt) REVERT: 2 135 ARG cc_start: 0.8008 (tpp80) cc_final: 0.7109 (ttm-80) REVERT: 2 234 LEU cc_start: 0.6942 (OUTLIER) cc_final: 0.6535 (pt) REVERT: 4 45 ASN cc_start: 0.7982 (t0) cc_final: 0.7459 (t0) REVERT: 4 51 GLN cc_start: 0.6544 (mt0) cc_final: 0.5944 (mm-40) REVERT: 4 101 ASN cc_start: 0.6978 (t0) cc_final: 0.6764 (m-40) REVERT: 4 173 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7264 (mm-30) REVERT: 4 179 ASP cc_start: 0.7703 (m-30) cc_final: 0.7416 (m-30) REVERT: 6 11 GLN cc_start: 0.4462 (OUTLIER) cc_final: 0.4087 (mm-40) REVERT: 6 28 LYS cc_start: 0.7328 (mmtt) cc_final: 0.6914 (mmtt) REVERT: 6 44 GLU cc_start: 0.7864 (tt0) cc_final: 0.7221 (tm-30) REVERT: 6 97 ARG cc_start: 0.6676 (ttt-90) cc_final: 0.6353 (ttt-90) REVERT: 6 113 GLU cc_start: 0.7108 (mm-30) cc_final: 0.6537 (tt0) REVERT: 6 118 TYR cc_start: 0.8444 (m-10) cc_final: 0.8244 (m-80) REVERT: 6 168 LYS cc_start: 0.7216 (mttt) cc_final: 0.6905 (tttt) REVERT: 6 171 TYR cc_start: 0.6259 (t80) cc_final: 0.6053 (t80) REVERT: 6 234 LEU cc_start: 0.6267 (OUTLIER) cc_final: 0.5765 (pt) REVERT: 8 52 LYS cc_start: 0.7605 (OUTLIER) cc_final: 0.7349 (mtpt) REVERT: 8 80 GLN cc_start: 0.7650 (tp40) cc_final: 0.7415 (tp40) REVERT: 8 169 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6890 (tp30) REVERT: A 491 ASP cc_start: 0.7725 (OUTLIER) cc_final: 0.7436 (m-30) REVERT: B 520 GLN cc_start: 0.8423 (tt0) cc_final: 0.7999 (tt0) REVERT: B 545 GLN cc_start: 0.8608 (tp40) cc_final: 0.8099 (pm20) REVERT: C 281 TYR cc_start: 0.8179 (OUTLIER) cc_final: 0.7072 (t80) REVERT: C 297 CYS cc_start: 0.9052 (m) cc_final: 0.8676 (m) REVERT: C 508 MET cc_start: 0.8269 (mmt) cc_final: 0.7949 (mmp) REVERT: D 187 TRP cc_start: 0.7272 (m-10) cc_final: 0.6518 (m-90) REVERT: D 486 MET cc_start: 0.7355 (tmm) cc_final: 0.6955 (tmm) REVERT: E 352 ILE cc_start: 0.9191 (mt) cc_final: 0.8924 (mt) REVERT: F 137 LYS cc_start: 0.6494 (mmmt) cc_final: 0.6242 (mmmt) REVERT: F 168 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7947 (mt) REVERT: F 297 CYS cc_start: 0.8405 (m) cc_final: 0.8009 (m) REVERT: F 545 GLN cc_start: 0.7706 (tp-100) cc_final: 0.7470 (tp-100) REVERT: H 388 ARG cc_start: 0.7280 (tpt-90) cc_final: 0.6601 (ttp-110) REVERT: H 395 MET cc_start: 0.7370 (mmm) cc_final: 0.7118 (mmm) REVERT: I 73 ASN cc_start: 0.6691 (t0) cc_final: 0.6462 (t0) REVERT: I 111 PHE cc_start: 0.7050 (t80) cc_final: 0.6727 (t80) REVERT: I 168 LYS cc_start: 0.6558 (mtpp) cc_final: 0.6344 (mtpt) REVERT: I 233 LEU cc_start: 0.6861 (mm) cc_final: 0.6223 (tp) REVERT: J 325 MET cc_start: 0.8068 (mtm) cc_final: 0.7643 (ttm) REVERT: J 364 GLU cc_start: 0.7807 (tt0) cc_final: 0.7441 (pt0) REVERT: J 507 GLU cc_start: 0.7864 (tt0) cc_final: 0.7394 (tp30) REVERT: J 509 ARG cc_start: 0.6786 (tpt90) cc_final: 0.6331 (ttt180) REVERT: J 519 GLU cc_start: 0.8029 (tp30) cc_final: 0.7823 (tt0) REVERT: K 13 MET cc_start: 0.5903 (mmt) cc_final: 0.4604 (ttp) REVERT: K 26 ARG cc_start: 0.6536 (ttm110) cc_final: 0.6258 (ppt170) REVERT: K 67 LYS cc_start: 0.7649 (tttm) cc_final: 0.7190 (ttpt) REVERT: K 101 ASN cc_start: 0.6956 (t0) cc_final: 0.6449 (m-40) REVERT: K 112 THR cc_start: 0.7467 (m) cc_final: 0.7117 (p) REVERT: K 146 SER cc_start: 0.7330 (m) cc_final: 0.6867 (p) REVERT: K 150 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7054 (mm-30) REVERT: K 216 ASN cc_start: 0.7272 (t0) cc_final: 0.6422 (m-40) REVERT: L 325 MET cc_start: 0.8095 (mtm) cc_final: 0.7120 (ttp) REVERT: L 332 ARG cc_start: 0.7336 (mtt-85) cc_final: 0.6527 (mtt180) REVERT: M 307 LYS cc_start: 0.8182 (mtpt) cc_final: 0.7918 (mtmm) REVERT: M 325 MET cc_start: 0.8173 (mtm) cc_final: 0.7528 (ttt) REVERT: M 430 ASN cc_start: 0.7053 (t0) cc_final: 0.6725 (t0) REVERT: M 432 GLU cc_start: 0.6537 (tp30) cc_final: 0.6269 (mm-30) REVERT: N 325 MET cc_start: 0.8097 (mtm) cc_final: 0.7594 (ttp) REVERT: N 354 GLU cc_start: 0.6960 (mt-10) cc_final: 0.6576 (mm-30) REVERT: N 364 GLU cc_start: 0.8246 (tt0) cc_final: 0.7567 (pt0) REVERT: N 399 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7689 (tt) REVERT: N 432 GLU cc_start: 0.6702 (tp30) cc_final: 0.6314 (mm-30) REVERT: N 433 GLU cc_start: 0.8329 (mt-10) cc_final: 0.8044 (mt-10) REVERT: N 434 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7610 (pm20) REVERT: N 447 LYS cc_start: 0.7973 (mtmt) cc_final: 0.7494 (mtpp) REVERT: N 519 GLU cc_start: 0.7143 (mt-10) cc_final: 0.6902 (mm-30) REVERT: O 26 ARG cc_start: 0.7282 (ttm110) cc_final: 0.6733 (ppt170) REVERT: O 146 SER cc_start: 0.6942 (m) cc_final: 0.6694 (t) REVERT: O 169 GLU cc_start: 0.7481 (mm-30) cc_final: 0.7274 (mm-30) REVERT: O 174 ASN cc_start: 0.7529 (t0) cc_final: 0.7322 (t0) REVERT: O 226 THR cc_start: 0.6147 (t) cc_final: 0.5730 (m) REVERT: P 325 MET cc_start: 0.8003 (mtm) cc_final: 0.7185 (ttp) REVERT: P 388 ARG cc_start: 0.7422 (tpt-90) cc_final: 0.6745 (ttm110) REVERT: Q 24 ILE cc_start: 0.6458 (mt) cc_final: 0.6129 (mt) REVERT: Q 49 SER cc_start: 0.7327 (m) cc_final: 0.6792 (p) REVERT: Q 97 ARG cc_start: 0.6203 (ttp80) cc_final: 0.5907 (mtm110) REVERT: Q 113 GLU cc_start: 0.7577 (tp30) cc_final: 0.6968 (tt0) REVERT: Q 134 LYS cc_start: 0.7356 (ttpp) cc_final: 0.7007 (tttm) REVERT: Q 135 ARG cc_start: 0.7052 (ttm110) cc_final: 0.6848 (ttm110) REVERT: Q 146 SER cc_start: 0.7131 (m) cc_final: 0.6700 (p) REVERT: Q 156 MET cc_start: 0.6598 (mtm) cc_final: 0.6231 (mtm) REVERT: Q 228 SER cc_start: 0.6774 (p) cc_final: 0.6553 (p) REVERT: Q 234 LEU cc_start: 0.6456 (OUTLIER) cc_final: 0.6101 (tp) REVERT: R 322 GLN cc_start: 0.7903 (mt0) cc_final: 0.7647 (mt0) REVERT: R 325 MET cc_start: 0.7736 (mtm) cc_final: 0.6950 (ttp) REVERT: R 519 GLU cc_start: 0.7471 (mt-10) cc_final: 0.7010 (tp30) REVERT: S 512 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7374 (tp30) REVERT: S 519 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7474 (tm-30) REVERT: T 52 LYS cc_start: 0.7603 (mtpt) cc_final: 0.7118 (mtmm) REVERT: T 113 GLU cc_start: 0.7483 (tp30) cc_final: 0.7092 (tm-30) REVERT: T 121 GLU cc_start: 0.7135 (tt0) cc_final: 0.6355 (mm-30) REVERT: T 134 LYS cc_start: 0.7291 (ttpt) cc_final: 0.7069 (ttpt) REVERT: T 207 SER cc_start: 0.5778 (p) cc_final: 0.5571 (t) REVERT: T 216 ASN cc_start: 0.7625 (t0) cc_final: 0.7001 (m110) REVERT: U 314 MET cc_start: 0.8604 (ttm) cc_final: 0.8155 (ttm) REVERT: U 395 MET cc_start: 0.7747 (tpp) cc_final: 0.6923 (ttm) REVERT: U 509 ARG cc_start: 0.6787 (tpt170) cc_final: 0.6397 (ttp80) REVERT: V 325 MET cc_start: 0.7813 (mtm) cc_final: 0.7360 (mmt) REVERT: V 509 ARG cc_start: 0.6602 (OUTLIER) cc_final: 0.5962 (ttt180) REVERT: V 519 GLU cc_start: 0.7678 (tt0) cc_final: 0.7267 (mt-10) REVERT: W 345 ILE cc_start: 0.7920 (OUTLIER) cc_final: 0.7673 (mm) REVERT: W 364 GLU cc_start: 0.7600 (tt0) cc_final: 0.7056 (pt0) REVERT: W 388 ARG cc_start: 0.7053 (ttt180) cc_final: 0.6368 (ttm110) REVERT: W 416 SER cc_start: 0.7031 (p) cc_final: 0.6639 (t) REVERT: W 522 SER cc_start: 0.6132 (t) cc_final: 0.5731 (m) REVERT: X 26 ARG cc_start: 0.7475 (ptm-80) cc_final: 0.7151 (mtm110) REVERT: X 52 LYS cc_start: 0.7555 (mtpt) cc_final: 0.7102 (mtmm) REVERT: X 80 GLN cc_start: 0.7823 (tp40) cc_final: 0.7602 (tp-100) REVERT: X 111 PHE cc_start: 0.6373 (t80) cc_final: 0.6155 (t80) REVERT: X 119 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7736 (mp0) REVERT: X 130 TYR cc_start: 0.7709 (t80) cc_final: 0.6341 (t80) REVERT: X 179 ASP cc_start: 0.6509 (m-30) cc_final: 0.5770 (t0) REVERT: X 216 ASN cc_start: 0.7494 (t0) cc_final: 0.6701 (t0) REVERT: Y 325 MET cc_start: 0.8052 (mtm) cc_final: 0.7150 (ttt) REVERT: Y 399 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7442 (tp) REVERT: Z 113 GLU cc_start: 0.7155 (mm-30) cc_final: 0.6572 (tm-30) REVERT: Z 150 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7730 (mm-30) REVERT: Z 152 HIS cc_start: 0.7268 (m-70) cc_final: 0.6917 (m-70) REVERT: Z 216 ASN cc_start: 0.8552 (t0) cc_final: 0.7978 (m-40) REVERT: a 325 MET cc_start: 0.7749 (mtm) cc_final: 0.6911 (ttm) REVERT: a 401 LEU cc_start: 0.7563 (mt) cc_final: 0.7229 (mp) REVERT: b 339 ASP cc_start: 0.8177 (t0) cc_final: 0.7819 (m-30) REVERT: d 11 GLN cc_start: 0.6431 (mt0) cc_final: 0.6016 (mt0) REVERT: d 13 MET cc_start: 0.5151 (mtp) cc_final: 0.4289 (mmm) REVERT: d 67 LYS cc_start: 0.7007 (tttt) cc_final: 0.6665 (tttm) REVERT: d 101 ASN cc_start: 0.7587 (t0) cc_final: 0.7256 (m-40) REVERT: d 118 TYR cc_start: 0.7872 (m-10) cc_final: 0.7625 (m-10) REVERT: d 149 ASP cc_start: 0.8184 (m-30) cc_final: 0.7972 (m-30) REVERT: d 189 ARG cc_start: 0.5871 (ttm-80) cc_final: 0.5342 (mtm-85) REVERT: d 234 LEU cc_start: 0.6718 (OUTLIER) cc_final: 0.6315 (pt) REVERT: f 52 LYS cc_start: 0.6840 (OUTLIER) cc_final: 0.6346 (mtpt) REVERT: f 69 ASN cc_start: 0.7032 (p0) cc_final: 0.6323 (m-40) REVERT: f 73 ASN cc_start: 0.7334 (t0) cc_final: 0.6925 (m-40) REVERT: f 101 ASN cc_start: 0.7097 (t0) cc_final: 0.6755 (m-40) REVERT: f 112 THR cc_start: 0.8024 (OUTLIER) cc_final: 0.7806 (p) REVERT: f 149 ASP cc_start: 0.7580 (t0) cc_final: 0.7314 (p0) outliers start: 216 outliers final: 128 residues processed: 1018 average time/residue: 0.6569 time to fit residues: 1133.3002 Evaluate side-chains 918 residues out of total 7050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 772 time to evaluate : 6.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 51 GLN Chi-restraints excluded: chain 0 residue 70 GLU Chi-restraints excluded: chain 0 residue 147 ILE Chi-restraints excluded: chain 0 residue 225 ILE Chi-restraints excluded: chain 0 residue 226 THR Chi-restraints excluded: chain 0 residue 233 LEU Chi-restraints excluded: chain 2 residue 147 ILE Chi-restraints excluded: chain 2 residue 170 SER Chi-restraints excluded: chain 2 residue 179 ASP Chi-restraints excluded: chain 2 residue 226 THR Chi-restraints excluded: chain 2 residue 228 SER Chi-restraints excluded: chain 2 residue 234 LEU Chi-restraints excluded: chain 4 residue 147 ILE Chi-restraints excluded: chain 4 residue 173 GLU Chi-restraints excluded: chain 4 residue 219 ARG Chi-restraints excluded: chain 4 residue 234 LEU Chi-restraints excluded: chain 6 residue 11 GLN Chi-restraints excluded: chain 6 residue 99 LEU Chi-restraints excluded: chain 6 residue 110 ILE Chi-restraints excluded: chain 6 residue 147 ILE Chi-restraints excluded: chain 6 residue 234 LEU Chi-restraints excluded: chain 8 residue 52 LYS Chi-restraints excluded: chain 8 residue 147 ILE Chi-restraints excluded: chain 8 residue 169 GLU Chi-restraints excluded: chain 8 residue 226 THR Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 430 ARG Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain D residue 244 GLU Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain D residue 560 ASP Chi-restraints excluded: chain E residue 129 ASN Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 354 GLN Chi-restraints excluded: chain E residue 408 ASN Chi-restraints excluded: chain E residue 551 ILE Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain E residue 581 ILE Chi-restraints excluded: chain E residue 584 ILE Chi-restraints excluded: chain E residue 588 VAL Chi-restraints excluded: chain E residue 604 ASN Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 378 ARG Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain H residue 345 ILE Chi-restraints excluded: chain H residue 396 GLN Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain J residue 345 ILE Chi-restraints excluded: chain J residue 424 ASP Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 69 ASN Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain K residue 156 MET Chi-restraints excluded: chain K residue 179 ASP Chi-restraints excluded: chain L residue 363 LEU Chi-restraints excluded: chain L residue 399 LEU Chi-restraints excluded: chain L residue 409 ILE Chi-restraints excluded: chain M residue 354 GLU Chi-restraints excluded: chain M residue 363 LEU Chi-restraints excluded: chain N residue 345 ILE Chi-restraints excluded: chain N residue 399 LEU Chi-restraints excluded: chain O residue 31 VAL Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain O residue 133 THR Chi-restraints excluded: chain O residue 147 ILE Chi-restraints excluded: chain O residue 176 SER Chi-restraints excluded: chain P residue 399 LEU Chi-restraints excluded: chain P residue 409 ILE Chi-restraints excluded: chain P residue 444 LEU Chi-restraints excluded: chain Q residue 147 ILE Chi-restraints excluded: chain Q residue 210 VAL Chi-restraints excluded: chain Q residue 234 LEU Chi-restraints excluded: chain R residue 396 GLN Chi-restraints excluded: chain R residue 399 LEU Chi-restraints excluded: chain S residue 386 MET Chi-restraints excluded: chain S residue 409 ILE Chi-restraints excluded: chain S residue 512 GLU Chi-restraints excluded: chain T residue 112 THR Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain T residue 147 ILE Chi-restraints excluded: chain T residue 154 VAL Chi-restraints excluded: chain T residue 178 THR Chi-restraints excluded: chain U residue 313 VAL Chi-restraints excluded: chain U residue 434 GLU Chi-restraints excluded: chain V residue 399 LEU Chi-restraints excluded: chain V residue 412 SER Chi-restraints excluded: chain V residue 444 LEU Chi-restraints excluded: chain V residue 504 ASP Chi-restraints excluded: chain V residue 509 ARG Chi-restraints excluded: chain W residue 345 ILE Chi-restraints excluded: chain W residue 512 GLU Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 110 ILE Chi-restraints excluded: chain X residue 112 THR Chi-restraints excluded: chain X residue 133 THR Chi-restraints excluded: chain X residue 146 SER Chi-restraints excluded: chain X residue 210 VAL Chi-restraints excluded: chain Y residue 399 LEU Chi-restraints excluded: chain Y residue 409 ILE Chi-restraints excluded: chain Y residue 444 LEU Chi-restraints excluded: chain Y residue 503 VAL Chi-restraints excluded: chain Z residue 99 LEU Chi-restraints excluded: chain Z residue 146 SER Chi-restraints excluded: chain Z residue 147 ILE Chi-restraints excluded: chain Z residue 178 THR Chi-restraints excluded: chain a residue 341 THR Chi-restraints excluded: chain a residue 409 ILE Chi-restraints excluded: chain d residue 47 SER Chi-restraints excluded: chain d residue 109 THR Chi-restraints excluded: chain d residue 160 THR Chi-restraints excluded: chain d residue 179 ASP Chi-restraints excluded: chain d residue 234 LEU Chi-restraints excluded: chain f residue 52 LYS Chi-restraints excluded: chain f residue 112 THR Chi-restraints excluded: chain f residue 147 ILE Chi-restraints excluded: chain f residue 228 SER Chi-restraints excluded: chain f residue 233 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 886 random chunks: chunk 796 optimal weight: 5.9990 chunk 606 optimal weight: 0.4980 chunk 418 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 384 optimal weight: 9.9990 chunk 541 optimal weight: 3.9990 chunk 808 optimal weight: 0.9980 chunk 856 optimal weight: 1.9990 chunk 422 optimal weight: 10.0000 chunk 766 optimal weight: 1.9990 chunk 230 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 11 GLN 2 69 ASN 2 114 GLN 8 73 ASN ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 339 ASN ** D 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 ASN F 348 HIS ** F 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 5 GLN O 152 HIS ** P 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 73 ASN T 80 GLN U 322 GLN V 322 GLN Z 69 ASN b 322 GLN d 98 GLN f 80 GLN f 165 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 69864 Z= 0.203 Angle : 0.515 8.724 94566 Z= 0.269 Chirality : 0.043 0.284 10748 Planarity : 0.004 0.049 12421 Dihedral : 5.993 107.727 10211 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.98 % Allowed : 12.51 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.09), residues: 8868 helix: 2.40 (0.09), residues: 3497 sheet: 0.70 (0.12), residues: 2018 loop : -0.07 (0.11), residues: 3353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 187 HIS 0.006 0.001 HIS S 365 PHE 0.031 0.002 PHE 6 71 TYR 0.015 0.001 TYR M 359 ARG 0.010 0.000 ARG D 543 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17736 Ramachandran restraints generated. 8868 Oldfield, 0 Emsley, 8868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17736 Ramachandran restraints generated. 8868 Oldfield, 0 Emsley, 8868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1016 residues out of total 7050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 806 time to evaluate : 6.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 13 MET cc_start: 0.7264 (ttm) cc_final: 0.6581 (tmm) REVERT: 2 11 GLN cc_start: 0.4563 (mt0) cc_final: 0.3605 (tm-30) REVERT: 2 13 MET cc_start: 0.6023 (ttp) cc_final: 0.5673 (tmm) REVERT: 2 22 LYS cc_start: 0.6548 (ptpp) cc_final: 0.6292 (tptt) REVERT: 2 135 ARG cc_start: 0.8018 (tpp80) cc_final: 0.7242 (ttm-80) REVERT: 2 170 SER cc_start: 0.7079 (OUTLIER) cc_final: 0.6874 (t) REVERT: 2 234 LEU cc_start: 0.7036 (OUTLIER) cc_final: 0.6645 (pt) REVERT: 4 45 ASN cc_start: 0.7878 (t0) cc_final: 0.7405 (t0) REVERT: 4 51 GLN cc_start: 0.6632 (mt0) cc_final: 0.5924 (mm-40) REVERT: 4 156 MET cc_start: 0.7400 (mtm) cc_final: 0.6990 (mtp) REVERT: 4 179 ASP cc_start: 0.7776 (m-30) cc_final: 0.7521 (m-30) REVERT: 4 214 ASP cc_start: 0.6710 (t0) cc_final: 0.6463 (t0) REVERT: 6 11 GLN cc_start: 0.4100 (OUTLIER) cc_final: 0.3876 (mm-40) REVERT: 6 28 LYS cc_start: 0.7414 (mmtt) cc_final: 0.6899 (mmtt) REVERT: 6 44 GLU cc_start: 0.7497 (tt0) cc_final: 0.6961 (tm-30) REVERT: 6 113 GLU cc_start: 0.7039 (mm-30) cc_final: 0.6569 (tt0) REVERT: 6 168 LYS cc_start: 0.7356 (mttt) cc_final: 0.7036 (tttt) REVERT: 6 234 LEU cc_start: 0.5957 (OUTLIER) cc_final: 0.5487 (pt) REVERT: 8 52 LYS cc_start: 0.7630 (OUTLIER) cc_final: 0.7299 (mtpp) REVERT: 8 80 GLN cc_start: 0.7591 (tp40) cc_final: 0.7380 (tp40) REVERT: 8 169 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6819 (tp30) REVERT: B 352 ILE cc_start: 0.8880 (OUTLIER) cc_final: 0.8669 (mp) REVERT: B 520 GLN cc_start: 0.8448 (tt0) cc_final: 0.8076 (tt0) REVERT: B 545 GLN cc_start: 0.8619 (tp40) cc_final: 0.8087 (pm20) REVERT: C 281 TYR cc_start: 0.8149 (OUTLIER) cc_final: 0.7018 (t80) REVERT: C 297 CYS cc_start: 0.9009 (m) cc_final: 0.8632 (m) REVERT: C 508 MET cc_start: 0.8180 (mmt) cc_final: 0.7966 (mmp) REVERT: D 187 TRP cc_start: 0.7337 (m-10) cc_final: 0.6907 (m-10) REVERT: D 486 MET cc_start: 0.7462 (tmm) cc_final: 0.6992 (tmm) REVERT: E 352 ILE cc_start: 0.9184 (mt) cc_final: 0.8968 (mt) REVERT: E 395 GLN cc_start: 0.8600 (tp40) cc_final: 0.7855 (tp40) REVERT: F 137 LYS cc_start: 0.6490 (mmmt) cc_final: 0.6271 (mmmt) REVERT: F 168 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7844 (mt) REVERT: F 297 CYS cc_start: 0.8339 (m) cc_final: 0.7935 (m) REVERT: H 388 ARG cc_start: 0.7295 (tpt-90) cc_final: 0.6588 (ttp-110) REVERT: I 73 ASN cc_start: 0.6591 (t0) cc_final: 0.6329 (t0) REVERT: I 105 GLN cc_start: 0.7167 (tt0) cc_final: 0.6681 (tm-30) REVERT: I 111 PHE cc_start: 0.7531 (t80) cc_final: 0.7281 (t80) REVERT: I 168 LYS cc_start: 0.6773 (mtpp) cc_final: 0.6569 (mtpt) REVERT: I 233 LEU cc_start: 0.6835 (mm) cc_final: 0.6344 (tp) REVERT: J 325 MET cc_start: 0.8038 (mtm) cc_final: 0.7566 (ttm) REVERT: J 364 GLU cc_start: 0.7483 (tt0) cc_final: 0.7061 (pt0) REVERT: J 509 ARG cc_start: 0.6793 (tpt90) cc_final: 0.6373 (ttt180) REVERT: K 13 MET cc_start: 0.5933 (mmt) cc_final: 0.4589 (ttp) REVERT: K 26 ARG cc_start: 0.6686 (ttm110) cc_final: 0.6382 (ppt170) REVERT: K 101 ASN cc_start: 0.6849 (t0) cc_final: 0.6457 (m-40) REVERT: K 112 THR cc_start: 0.7449 (m) cc_final: 0.7100 (p) REVERT: K 146 SER cc_start: 0.7359 (m) cc_final: 0.6905 (p) REVERT: K 150 GLU cc_start: 0.7395 (mm-30) cc_final: 0.6872 (mm-30) REVERT: K 216 ASN cc_start: 0.7319 (t0) cc_final: 0.6483 (m-40) REVERT: L 325 MET cc_start: 0.8089 (mtm) cc_final: 0.7171 (ttp) REVERT: L 332 ARG cc_start: 0.7331 (mtt-85) cc_final: 0.6530 (mtt180) REVERT: M 307 LYS cc_start: 0.8040 (mtpt) cc_final: 0.7718 (mtmm) REVERT: M 325 MET cc_start: 0.8167 (mtm) cc_final: 0.7544 (ttm) REVERT: M 430 ASN cc_start: 0.7231 (t0) cc_final: 0.6783 (t0) REVERT: N 325 MET cc_start: 0.8078 (mtm) cc_final: 0.7564 (ttp) REVERT: N 354 GLU cc_start: 0.7038 (mt-10) cc_final: 0.6653 (mm-30) REVERT: N 364 GLU cc_start: 0.8317 (tt0) cc_final: 0.7592 (pt0) REVERT: N 399 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7635 (tt) REVERT: N 432 GLU cc_start: 0.6738 (tp30) cc_final: 0.6400 (mm-30) REVERT: N 433 GLU cc_start: 0.8326 (mt-10) cc_final: 0.8003 (mt-10) REVERT: N 434 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7745 (pm20) REVERT: N 447 LYS cc_start: 0.7903 (mtmt) cc_final: 0.7423 (mtpp) REVERT: N 519 GLU cc_start: 0.7238 (mt-10) cc_final: 0.6926 (mm-30) REVERT: O 26 ARG cc_start: 0.7211 (ttm110) cc_final: 0.6715 (ppt170) REVERT: O 146 SER cc_start: 0.6930 (m) cc_final: 0.6646 (t) REVERT: O 151 PRO cc_start: 0.7942 (Cg_endo) cc_final: 0.7723 (Cg_exo) REVERT: O 152 HIS cc_start: 0.7006 (m-70) cc_final: 0.6593 (m-70) REVERT: O 226 THR cc_start: 0.6077 (t) cc_final: 0.5637 (m) REVERT: P 325 MET cc_start: 0.7720 (mtm) cc_final: 0.6943 (ttp) REVERT: P 345 ILE cc_start: 0.8030 (OUTLIER) cc_final: 0.7701 (mm) REVERT: P 388 ARG cc_start: 0.7385 (tpt-90) cc_final: 0.6648 (ttm110) REVERT: Q 44 GLU cc_start: 0.6881 (OUTLIER) cc_final: 0.6502 (pm20) REVERT: Q 49 SER cc_start: 0.7336 (m) cc_final: 0.6847 (p) REVERT: Q 97 ARG cc_start: 0.6187 (ttp80) cc_final: 0.5875 (mtm110) REVERT: Q 113 GLU cc_start: 0.7521 (tp30) cc_final: 0.7125 (tm-30) REVERT: Q 134 LYS cc_start: 0.7129 (ttpp) cc_final: 0.6799 (tttm) REVERT: Q 146 SER cc_start: 0.7106 (m) cc_final: 0.6761 (p) REVERT: Q 156 MET cc_start: 0.6590 (mtm) cc_final: 0.6239 (mtm) REVERT: Q 234 LEU cc_start: 0.6486 (OUTLIER) cc_final: 0.6134 (tp) REVERT: R 322 GLN cc_start: 0.7896 (mt0) cc_final: 0.7685 (mt0) REVERT: R 325 MET cc_start: 0.7738 (mtm) cc_final: 0.6980 (ttp) REVERT: R 519 GLU cc_start: 0.7462 (mt-10) cc_final: 0.7033 (tp30) REVERT: S 461 ASP cc_start: 0.7232 (OUTLIER) cc_final: 0.7019 (t70) REVERT: S 512 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7326 (tp30) REVERT: S 519 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7457 (tm-30) REVERT: T 52 LYS cc_start: 0.7588 (mtpt) cc_final: 0.7279 (mtmm) REVERT: T 113 GLU cc_start: 0.7508 (tp30) cc_final: 0.7196 (tm-30) REVERT: T 121 GLU cc_start: 0.7089 (tt0) cc_final: 0.6372 (mm-30) REVERT: T 134 LYS cc_start: 0.7244 (ttpt) cc_final: 0.6838 (ttpt) REVERT: T 207 SER cc_start: 0.5819 (p) cc_final: 0.5555 (t) REVERT: T 214 ASP cc_start: 0.6514 (t0) cc_final: 0.6282 (t0) REVERT: T 216 ASN cc_start: 0.7660 (t0) cc_final: 0.6989 (m110) REVERT: U 314 MET cc_start: 0.8601 (ttm) cc_final: 0.8184 (ttm) REVERT: U 433 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7677 (mm-30) REVERT: U 509 ARG cc_start: 0.6925 (tpt170) cc_final: 0.6493 (ttp80) REVERT: V 325 MET cc_start: 0.8038 (mtm) cc_final: 0.7574 (mmt) REVERT: V 509 ARG cc_start: 0.6701 (OUTLIER) cc_final: 0.6009 (ttt180) REVERT: V 519 GLU cc_start: 0.7617 (tt0) cc_final: 0.7229 (mt-10) REVERT: W 345 ILE cc_start: 0.7842 (OUTLIER) cc_final: 0.7633 (mm) REVERT: W 364 GLU cc_start: 0.7604 (tt0) cc_final: 0.7039 (pt0) REVERT: W 388 ARG cc_start: 0.7041 (ttt180) cc_final: 0.6311 (ttm110) REVERT: W 416 SER cc_start: 0.7063 (p) cc_final: 0.6720 (t) REVERT: W 522 SER cc_start: 0.6210 (t) cc_final: 0.5785 (m) REVERT: X 26 ARG cc_start: 0.7540 (ptm-80) cc_final: 0.7297 (mtm110) REVERT: X 51 GLN cc_start: 0.7600 (OUTLIER) cc_final: 0.7020 (mm-40) REVERT: X 52 LYS cc_start: 0.7706 (mtpt) cc_final: 0.7270 (mtmm) REVERT: X 80 GLN cc_start: 0.7726 (tp40) cc_final: 0.7422 (tp40) REVERT: X 119 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7760 (mp0) REVERT: X 130 TYR cc_start: 0.7736 (t80) cc_final: 0.6375 (t80) REVERT: X 179 ASP cc_start: 0.6591 (m-30) cc_final: 0.5838 (t0) REVERT: X 216 ASN cc_start: 0.7476 (t0) cc_final: 0.6704 (t0) REVERT: Y 325 MET cc_start: 0.7932 (mtm) cc_final: 0.7226 (ttm) REVERT: Y 399 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7451 (tp) REVERT: Z 28 LYS cc_start: 0.7118 (mmtm) cc_final: 0.6855 (tppt) REVERT: Z 113 GLU cc_start: 0.7222 (mm-30) cc_final: 0.6678 (tm-30) REVERT: Z 150 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7755 (mm-30) REVERT: Z 216 ASN cc_start: 0.8586 (t0) cc_final: 0.7987 (m-40) REVERT: a 325 MET cc_start: 0.7748 (mtm) cc_final: 0.6900 (ttm) REVERT: a 401 LEU cc_start: 0.7533 (mt) cc_final: 0.7106 (mp) REVERT: b 339 ASP cc_start: 0.8243 (t0) cc_final: 0.7902 (m-30) REVERT: b 396 GLN cc_start: 0.7234 (tp40) cc_final: 0.6972 (mm110) REVERT: d 13 MET cc_start: 0.5029 (mtp) cc_final: 0.4354 (mmm) REVERT: d 67 LYS cc_start: 0.7180 (tttt) cc_final: 0.6867 (tttm) REVERT: d 101 ASN cc_start: 0.7569 (t0) cc_final: 0.7286 (m-40) REVERT: d 189 ARG cc_start: 0.6075 (ttm-80) cc_final: 0.5558 (mtm-85) REVERT: d 234 LEU cc_start: 0.6801 (OUTLIER) cc_final: 0.6360 (pt) REVERT: f 73 ASN cc_start: 0.7282 (t0) cc_final: 0.6881 (m-40) REVERT: f 101 ASN cc_start: 0.7146 (t0) cc_final: 0.6769 (m-40) REVERT: f 112 THR cc_start: 0.8057 (OUTLIER) cc_final: 0.7854 (p) REVERT: f 149 ASP cc_start: 0.7649 (t0) cc_final: 0.7368 (p0) outliers start: 210 outliers final: 132 residues processed: 960 average time/residue: 0.6646 time to fit residues: 1083.5543 Evaluate side-chains 894 residues out of total 7050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 741 time to evaluate : 6.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 70 GLU Chi-restraints excluded: chain 0 residue 147 ILE Chi-restraints excluded: chain 0 residue 188 LEU Chi-restraints excluded: chain 0 residue 225 ILE Chi-restraints excluded: chain 0 residue 226 THR Chi-restraints excluded: chain 0 residue 233 LEU Chi-restraints excluded: chain 2 residue 69 ASN Chi-restraints excluded: chain 2 residue 147 ILE Chi-restraints excluded: chain 2 residue 170 SER Chi-restraints excluded: chain 2 residue 179 ASP Chi-restraints excluded: chain 2 residue 226 THR Chi-restraints excluded: chain 2 residue 228 SER Chi-restraints excluded: chain 2 residue 234 LEU Chi-restraints excluded: chain 4 residue 52 LYS Chi-restraints excluded: chain 4 residue 73 ASN Chi-restraints excluded: chain 4 residue 147 ILE Chi-restraints excluded: chain 4 residue 216 ASN Chi-restraints excluded: chain 4 residue 219 ARG Chi-restraints excluded: chain 6 residue 11 GLN Chi-restraints excluded: chain 6 residue 99 LEU Chi-restraints excluded: chain 6 residue 112 THR Chi-restraints excluded: chain 6 residue 147 ILE Chi-restraints excluded: chain 6 residue 149 ASP Chi-restraints excluded: chain 6 residue 234 LEU Chi-restraints excluded: chain 8 residue 52 LYS Chi-restraints excluded: chain 8 residue 147 ILE Chi-restraints excluded: chain 8 residue 169 GLU Chi-restraints excluded: chain 8 residue 226 THR Chi-restraints excluded: chain 8 residue 233 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 430 ARG Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 348 HIS Chi-restraints excluded: chain B residue 352 ILE Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 518 MET Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain D residue 244 GLU Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain D residue 518 MET Chi-restraints excluded: chain D residue 560 ASP Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 228 TYR Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 354 GLN Chi-restraints excluded: chain E residue 408 ASN Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain E residue 581 ILE Chi-restraints excluded: chain E residue 584 ILE Chi-restraints excluded: chain E residue 588 VAL Chi-restraints excluded: chain E residue 604 ASN Chi-restraints excluded: chain E residue 605 LEU Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 378 ARG Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 459 VAL Chi-restraints excluded: chain H residue 396 GLN Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain J residue 345 ILE Chi-restraints excluded: chain J residue 424 ASP Chi-restraints excluded: chain K residue 69 ASN Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain K residue 156 MET Chi-restraints excluded: chain L residue 399 LEU Chi-restraints excluded: chain L residue 409 ILE Chi-restraints excluded: chain M residue 354 GLU Chi-restraints excluded: chain M residue 363 LEU Chi-restraints excluded: chain N residue 358 LEU Chi-restraints excluded: chain N residue 399 LEU Chi-restraints excluded: chain N residue 444 LEU Chi-restraints excluded: chain O residue 29 SER Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain O residue 133 THR Chi-restraints excluded: chain P residue 345 ILE Chi-restraints excluded: chain P residue 396 GLN Chi-restraints excluded: chain P residue 399 LEU Chi-restraints excluded: chain P residue 409 ILE Chi-restraints excluded: chain P residue 444 LEU Chi-restraints excluded: chain Q residue 44 GLU Chi-restraints excluded: chain Q residue 147 ILE Chi-restraints excluded: chain Q residue 210 VAL Chi-restraints excluded: chain Q residue 234 LEU Chi-restraints excluded: chain R residue 396 GLN Chi-restraints excluded: chain R residue 399 LEU Chi-restraints excluded: chain S residue 348 THR Chi-restraints excluded: chain S residue 386 MET Chi-restraints excluded: chain S residue 409 ILE Chi-restraints excluded: chain S residue 461 ASP Chi-restraints excluded: chain S residue 512 GLU Chi-restraints excluded: chain T residue 112 THR Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain T residue 149 ASP Chi-restraints excluded: chain T residue 154 VAL Chi-restraints excluded: chain T residue 225 ILE Chi-restraints excluded: chain U residue 313 VAL Chi-restraints excluded: chain U residue 520 SER Chi-restraints excluded: chain V residue 412 SER Chi-restraints excluded: chain V residue 444 LEU Chi-restraints excluded: chain V residue 504 ASP Chi-restraints excluded: chain V residue 509 ARG Chi-restraints excluded: chain W residue 345 ILE Chi-restraints excluded: chain W residue 396 GLN Chi-restraints excluded: chain W residue 486 LEU Chi-restraints excluded: chain W residue 512 GLU Chi-restraints excluded: chain X residue 51 GLN Chi-restraints excluded: chain X residue 110 ILE Chi-restraints excluded: chain X residue 112 THR Chi-restraints excluded: chain Y residue 399 LEU Chi-restraints excluded: chain Y residue 409 ILE Chi-restraints excluded: chain Y residue 444 LEU Chi-restraints excluded: chain Y residue 503 VAL Chi-restraints excluded: chain Z residue 146 SER Chi-restraints excluded: chain Z residue 147 ILE Chi-restraints excluded: chain Z residue 178 THR Chi-restraints excluded: chain d residue 47 SER Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain d residue 160 THR Chi-restraints excluded: chain d residue 234 LEU Chi-restraints excluded: chain f residue 24 ILE Chi-restraints excluded: chain f residue 49 SER Chi-restraints excluded: chain f residue 99 LEU Chi-restraints excluded: chain f residue 112 THR Chi-restraints excluded: chain f residue 147 ILE Chi-restraints excluded: chain f residue 228 SER Chi-restraints excluded: chain f residue 233 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 886 random chunks: chunk 713 optimal weight: 0.9990 chunk 486 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 637 optimal weight: 2.9990 chunk 353 optimal weight: 3.9990 chunk 730 optimal weight: 5.9990 chunk 591 optimal weight: 0.9980 chunk 1 optimal weight: 7.9990 chunk 437 optimal weight: 6.9990 chunk 768 optimal weight: 8.9990 chunk 216 optimal weight: 0.0870 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 69 ASN 2 114 GLN ** 6 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN ** D 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 437 GLN O 174 ASN ** P 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 322 GLN Y 396 GLN b 322 GLN d 80 GLN f 80 GLN f 165 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 69864 Z= 0.194 Angle : 0.503 9.351 94566 Z= 0.263 Chirality : 0.042 0.308 10748 Planarity : 0.004 0.050 12421 Dihedral : 5.902 108.423 10205 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.23 % Allowed : 13.02 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.09), residues: 8868 helix: 2.52 (0.09), residues: 3499 sheet: 0.71 (0.12), residues: 2025 loop : -0.04 (0.11), residues: 3344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 187 HIS 0.006 0.001 HIS S 365 PHE 0.032 0.002 PHE 2 71 TYR 0.015 0.001 TYR 6 118 ARG 0.006 0.000 ARG I 21 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17736 Ramachandran restraints generated. 8868 Oldfield, 0 Emsley, 8868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17736 Ramachandran restraints generated. 8868 Oldfield, 0 Emsley, 8868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 997 residues out of total 7050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 770 time to evaluate : 6.087 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 13 MET cc_start: 0.7294 (ttm) cc_final: 0.6643 (tmm) REVERT: 0 156 MET cc_start: 0.7939 (mtm) cc_final: 0.7496 (mtm) REVERT: 2 11 GLN cc_start: 0.4731 (mt0) cc_final: 0.3648 (tm-30) REVERT: 2 13 MET cc_start: 0.6039 (ttp) cc_final: 0.5685 (tmm) REVERT: 2 22 LYS cc_start: 0.6712 (ptpp) cc_final: 0.6466 (tptt) REVERT: 2 135 ARG cc_start: 0.8039 (tpp80) cc_final: 0.7267 (ttm-80) REVERT: 2 234 LEU cc_start: 0.7135 (OUTLIER) cc_final: 0.6719 (pt) REVERT: 4 45 ASN cc_start: 0.7875 (t0) cc_final: 0.7380 (t0) REVERT: 4 149 ASP cc_start: 0.8106 (t0) cc_final: 0.7804 (m-30) REVERT: 4 156 MET cc_start: 0.7356 (mtm) cc_final: 0.7134 (mtm) REVERT: 4 168 LYS cc_start: 0.6825 (OUTLIER) cc_final: 0.6014 (mttm) REVERT: 4 179 ASP cc_start: 0.8047 (m-30) cc_final: 0.7816 (m-30) REVERT: 4 214 ASP cc_start: 0.6766 (t0) cc_final: 0.6486 (t0) REVERT: 6 11 GLN cc_start: 0.4086 (OUTLIER) cc_final: 0.3743 (mm-40) REVERT: 6 28 LYS cc_start: 0.7692 (mmtt) cc_final: 0.7322 (mmtt) REVERT: 6 44 GLU cc_start: 0.7514 (tt0) cc_final: 0.6956 (tm-30) REVERT: 6 113 GLU cc_start: 0.7024 (mm-30) cc_final: 0.6507 (tt0) REVERT: 6 168 LYS cc_start: 0.7186 (mttt) cc_final: 0.6945 (tttt) REVERT: 6 234 LEU cc_start: 0.5846 (OUTLIER) cc_final: 0.5388 (pt) REVERT: 8 52 LYS cc_start: 0.7661 (OUTLIER) cc_final: 0.7328 (mtpp) REVERT: 8 169 GLU cc_start: 0.7097 (OUTLIER) cc_final: 0.6809 (tp30) REVERT: 8 174 ASN cc_start: 0.8004 (m110) cc_final: 0.7771 (m110) REVERT: A 491 ASP cc_start: 0.7744 (OUTLIER) cc_final: 0.7461 (m-30) REVERT: B 354 GLN cc_start: 0.7447 (mt0) cc_final: 0.7239 (mt0) REVERT: B 520 GLN cc_start: 0.8441 (tt0) cc_final: 0.8062 (tt0) REVERT: B 545 GLN cc_start: 0.8628 (tp40) cc_final: 0.8136 (pm20) REVERT: C 297 CYS cc_start: 0.9070 (m) cc_final: 0.8708 (m) REVERT: C 508 MET cc_start: 0.8251 (mmt) cc_final: 0.8021 (mmp) REVERT: D 187 TRP cc_start: 0.7323 (m-10) cc_final: 0.6952 (m-10) REVERT: D 486 MET cc_start: 0.7494 (tmm) cc_final: 0.7066 (tmm) REVERT: E 145 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8209 (pm20) REVERT: F 168 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7837 (mt) REVERT: F 297 CYS cc_start: 0.8374 (m) cc_final: 0.7954 (m) REVERT: F 545 GLN cc_start: 0.7687 (tp-100) cc_final: 0.7458 (tp-100) REVERT: H 388 ARG cc_start: 0.7265 (tpt-90) cc_final: 0.6568 (ttp-110) REVERT: I 73 ASN cc_start: 0.6572 (t0) cc_final: 0.6351 (t0) REVERT: I 105 GLN cc_start: 0.7154 (tt0) cc_final: 0.6658 (tm-30) REVERT: J 325 MET cc_start: 0.8077 (mtm) cc_final: 0.7637 (ttm) REVERT: J 364 GLU cc_start: 0.7227 (tt0) cc_final: 0.6778 (pt0) REVERT: J 509 ARG cc_start: 0.6780 (tpt90) cc_final: 0.6378 (ttt180) REVERT: K 13 MET cc_start: 0.5961 (mmt) cc_final: 0.4607 (ttp) REVERT: K 26 ARG cc_start: 0.6728 (ttm110) cc_final: 0.6502 (ppt170) REVERT: K 67 LYS cc_start: 0.7694 (OUTLIER) cc_final: 0.7390 (tptp) REVERT: K 101 ASN cc_start: 0.6780 (t0) cc_final: 0.6428 (m-40) REVERT: K 112 THR cc_start: 0.7395 (m) cc_final: 0.7090 (p) REVERT: K 146 SER cc_start: 0.7391 (m) cc_final: 0.6951 (p) REVERT: K 150 GLU cc_start: 0.7264 (mm-30) cc_final: 0.6725 (mm-30) REVERT: K 189 ARG cc_start: 0.5625 (ttp-170) cc_final: 0.5113 (tpt-90) REVERT: K 216 ASN cc_start: 0.7322 (t0) cc_final: 0.6481 (m-40) REVERT: L 325 MET cc_start: 0.8122 (mtm) cc_final: 0.7263 (ttp) REVERT: L 332 ARG cc_start: 0.7189 (mtt-85) cc_final: 0.6490 (mtt180) REVERT: M 307 LYS cc_start: 0.8009 (mtpt) cc_final: 0.7695 (mtmm) REVERT: M 325 MET cc_start: 0.8160 (mtm) cc_final: 0.7545 (ttm) REVERT: M 338 ASP cc_start: 0.8042 (p0) cc_final: 0.7546 (p0) REVERT: M 424 ASP cc_start: 0.6920 (p0) cc_final: 0.6544 (p0) REVERT: N 325 MET cc_start: 0.8084 (mtm) cc_final: 0.7561 (ttp) REVERT: N 354 GLU cc_start: 0.7037 (mt-10) cc_final: 0.6692 (mm-30) REVERT: N 364 GLU cc_start: 0.8329 (tt0) cc_final: 0.7588 (pt0) REVERT: N 399 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7616 (tt) REVERT: N 433 GLU cc_start: 0.8312 (mt-10) cc_final: 0.8066 (mt-10) REVERT: N 434 GLU cc_start: 0.8329 (mt-10) cc_final: 0.8083 (mm-30) REVERT: N 447 LYS cc_start: 0.8003 (mtmt) cc_final: 0.7500 (mtpp) REVERT: O 26 ARG cc_start: 0.7243 (OUTLIER) cc_final: 0.6708 (ppt170) REVERT: O 113 GLU cc_start: 0.7506 (tt0) cc_final: 0.7266 (tm-30) REVERT: O 146 SER cc_start: 0.6963 (m) cc_final: 0.6676 (t) REVERT: O 151 PRO cc_start: 0.8000 (Cg_endo) cc_final: 0.7729 (Cg_exo) REVERT: O 152 HIS cc_start: 0.7048 (m-70) cc_final: 0.6515 (m-70) REVERT: P 325 MET cc_start: 0.7745 (mtm) cc_final: 0.6986 (ttp) REVERT: P 345 ILE cc_start: 0.8050 (OUTLIER) cc_final: 0.7721 (mm) REVERT: P 388 ARG cc_start: 0.7502 (tpt-90) cc_final: 0.6742 (ttm110) REVERT: P 432 GLU cc_start: 0.6967 (OUTLIER) cc_final: 0.6118 (mp0) REVERT: Q 49 SER cc_start: 0.7214 (m) cc_final: 0.6793 (p) REVERT: Q 70 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.6709 (mm-30) REVERT: Q 97 ARG cc_start: 0.6258 (ttp80) cc_final: 0.5846 (mtm110) REVERT: Q 113 GLU cc_start: 0.7686 (tp30) cc_final: 0.7217 (tm-30) REVERT: Q 134 LYS cc_start: 0.7102 (ttpp) cc_final: 0.6754 (tttm) REVERT: Q 146 SER cc_start: 0.7004 (m) cc_final: 0.6652 (p) REVERT: Q 156 MET cc_start: 0.6719 (mtm) cc_final: 0.6328 (mtm) REVERT: R 325 MET cc_start: 0.7726 (mtm) cc_final: 0.7067 (ttp) REVERT: R 519 GLU cc_start: 0.7428 (mt-10) cc_final: 0.7010 (tp30) REVERT: S 512 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7367 (tp30) REVERT: S 519 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7445 (tm-30) REVERT: T 52 LYS cc_start: 0.7586 (mtpt) cc_final: 0.7255 (mtmm) REVERT: T 113 GLU cc_start: 0.7497 (tp30) cc_final: 0.7194 (tm-30) REVERT: T 121 GLU cc_start: 0.7019 (tt0) cc_final: 0.6254 (mm-30) REVERT: T 134 LYS cc_start: 0.7244 (ttpt) cc_final: 0.7005 (ttpt) REVERT: T 207 SER cc_start: 0.5764 (p) cc_final: 0.5431 (t) REVERT: T 214 ASP cc_start: 0.6422 (t0) cc_final: 0.6135 (t0) REVERT: T 216 ASN cc_start: 0.7720 (t0) cc_final: 0.7126 (m110) REVERT: U 314 MET cc_start: 0.8592 (ttm) cc_final: 0.8209 (ttm) REVERT: U 401 LEU cc_start: 0.7830 (mt) cc_final: 0.7564 (mt) REVERT: U 509 ARG cc_start: 0.6915 (tpt170) cc_final: 0.6486 (ttp80) REVERT: V 325 MET cc_start: 0.8147 (mtm) cc_final: 0.7521 (mmt) REVERT: V 509 ARG cc_start: 0.6712 (OUTLIER) cc_final: 0.6023 (ttt180) REVERT: V 519 GLU cc_start: 0.7636 (tt0) cc_final: 0.7267 (mt-10) REVERT: W 345 ILE cc_start: 0.7847 (OUTLIER) cc_final: 0.7644 (mm) REVERT: W 364 GLU cc_start: 0.7583 (tt0) cc_final: 0.7005 (pt0) REVERT: W 388 ARG cc_start: 0.7013 (ttt180) cc_final: 0.6298 (ttm110) REVERT: W 416 SER cc_start: 0.7106 (p) cc_final: 0.6775 (t) REVERT: W 522 SER cc_start: 0.6216 (t) cc_final: 0.5784 (m) REVERT: X 26 ARG cc_start: 0.7540 (ptm-80) cc_final: 0.7330 (mtm110) REVERT: X 33 LEU cc_start: 0.7172 (OUTLIER) cc_final: 0.6932 (pp) REVERT: X 52 LYS cc_start: 0.7754 (mtpt) cc_final: 0.7436 (mtmm) REVERT: X 80 GLN cc_start: 0.7708 (tp40) cc_final: 0.7408 (tp40) REVERT: X 130 TYR cc_start: 0.7727 (t80) cc_final: 0.6329 (t80) REVERT: X 179 ASP cc_start: 0.6575 (m-30) cc_final: 0.5958 (t0) REVERT: X 216 ASN cc_start: 0.7456 (t0) cc_final: 0.6732 (t0) REVERT: Y 325 MET cc_start: 0.8016 (mtm) cc_final: 0.7328 (ttm) REVERT: Y 395 MET cc_start: 0.6612 (mmm) cc_final: 0.6261 (mmm) REVERT: Y 399 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7459 (tp) REVERT: Y 509 ARG cc_start: 0.7482 (tpt90) cc_final: 0.6781 (ttp80) REVERT: Y 519 GLU cc_start: 0.7795 (tt0) cc_final: 0.7100 (tp30) REVERT: Z 70 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.6929 (mm-30) REVERT: Z 113 GLU cc_start: 0.7268 (mm-30) cc_final: 0.6708 (tm-30) REVERT: Z 143 TYR cc_start: 0.5834 (p90) cc_final: 0.4953 (p90) REVERT: Z 150 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7724 (mm-30) REVERT: Z 216 ASN cc_start: 0.8494 (t0) cc_final: 0.7973 (m-40) REVERT: a 325 MET cc_start: 0.7586 (mtm) cc_final: 0.6819 (ttm) REVERT: b 339 ASP cc_start: 0.8373 (t0) cc_final: 0.8044 (m-30) REVERT: b 396 GLN cc_start: 0.7024 (tp40) cc_final: 0.6746 (mm110) REVERT: d 13 MET cc_start: 0.4956 (mtp) cc_final: 0.4238 (mmm) REVERT: d 51 GLN cc_start: 0.7256 (mt0) cc_final: 0.6997 (mt0) REVERT: d 67 LYS cc_start: 0.7091 (tttt) cc_final: 0.6782 (tttm) REVERT: d 101 ASN cc_start: 0.7570 (t0) cc_final: 0.7307 (m-40) REVERT: d 189 ARG cc_start: 0.5966 (ttm-80) cc_final: 0.5474 (mtm-85) REVERT: d 234 LEU cc_start: 0.6816 (OUTLIER) cc_final: 0.6347 (pt) REVERT: f 52 LYS cc_start: 0.6723 (OUTLIER) cc_final: 0.6235 (mtpt) REVERT: f 73 ASN cc_start: 0.7041 (t0) cc_final: 0.6650 (m-40) REVERT: f 101 ASN cc_start: 0.7195 (t0) cc_final: 0.6808 (m-40) REVERT: f 112 THR cc_start: 0.8123 (OUTLIER) cc_final: 0.7915 (p) REVERT: f 149 ASP cc_start: 0.7642 (t0) cc_final: 0.7370 (p0) outliers start: 227 outliers final: 151 residues processed: 932 average time/residue: 0.6567 time to fit residues: 1036.9149 Evaluate side-chains 907 residues out of total 7050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 732 time to evaluate : 6.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 51 GLN Chi-restraints excluded: chain 0 residue 70 GLU Chi-restraints excluded: chain 0 residue 147 ILE Chi-restraints excluded: chain 0 residue 188 LEU Chi-restraints excluded: chain 0 residue 225 ILE Chi-restraints excluded: chain 0 residue 226 THR Chi-restraints excluded: chain 0 residue 233 LEU Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 147 ILE Chi-restraints excluded: chain 2 residue 179 ASP Chi-restraints excluded: chain 2 residue 226 THR Chi-restraints excluded: chain 2 residue 228 SER Chi-restraints excluded: chain 2 residue 234 LEU Chi-restraints excluded: chain 4 residue 30 VAL Chi-restraints excluded: chain 4 residue 52 LYS Chi-restraints excluded: chain 4 residue 73 ASN Chi-restraints excluded: chain 4 residue 102 VAL Chi-restraints excluded: chain 4 residue 147 ILE Chi-restraints excluded: chain 4 residue 168 LYS Chi-restraints excluded: chain 4 residue 216 ASN Chi-restraints excluded: chain 4 residue 219 ARG Chi-restraints excluded: chain 6 residue 11 GLN Chi-restraints excluded: chain 6 residue 99 LEU Chi-restraints excluded: chain 6 residue 112 THR Chi-restraints excluded: chain 6 residue 147 ILE Chi-restraints excluded: chain 6 residue 149 ASP Chi-restraints excluded: chain 6 residue 234 LEU Chi-restraints excluded: chain 8 residue 52 LYS Chi-restraints excluded: chain 8 residue 99 LEU Chi-restraints excluded: chain 8 residue 147 ILE Chi-restraints excluded: chain 8 residue 169 GLU Chi-restraints excluded: chain 8 residue 233 LEU Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 297 CYS Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 430 ARG Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 348 HIS Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 518 MET Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain D residue 139 GLN Chi-restraints excluded: chain D residue 244 GLU Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain D residue 560 ASP Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 228 TYR Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 354 GLN Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 408 ASN Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain E residue 581 ILE Chi-restraints excluded: chain E residue 584 ILE Chi-restraints excluded: chain E residue 588 VAL Chi-restraints excluded: chain E residue 604 ASN Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 223 ASP Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 459 VAL Chi-restraints excluded: chain H residue 396 GLN Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain I residue 174 ASN Chi-restraints excluded: chain J residue 345 ILE Chi-restraints excluded: chain J residue 424 ASP Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 67 LYS Chi-restraints excluded: chain K residue 69 ASN Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain K residue 156 MET Chi-restraints excluded: chain L residue 409 ILE Chi-restraints excluded: chain M residue 354 GLU Chi-restraints excluded: chain M residue 363 LEU Chi-restraints excluded: chain N residue 358 LEU Chi-restraints excluded: chain N residue 399 LEU Chi-restraints excluded: chain N residue 412 SER Chi-restraints excluded: chain N residue 444 LEU Chi-restraints excluded: chain N residue 450 MET Chi-restraints excluded: chain O residue 26 ARG Chi-restraints excluded: chain O residue 29 SER Chi-restraints excluded: chain O residue 31 VAL Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain O residue 133 THR Chi-restraints excluded: chain O residue 147 ILE Chi-restraints excluded: chain O residue 159 THR Chi-restraints excluded: chain O residue 176 SER Chi-restraints excluded: chain P residue 345 ILE Chi-restraints excluded: chain P residue 399 LEU Chi-restraints excluded: chain P residue 409 ILE Chi-restraints excluded: chain P residue 432 GLU Chi-restraints excluded: chain P residue 444 LEU Chi-restraints excluded: chain Q residue 70 GLU Chi-restraints excluded: chain Q residue 147 ILE Chi-restraints excluded: chain Q residue 228 SER Chi-restraints excluded: chain R residue 396 GLN Chi-restraints excluded: chain R residue 399 LEU Chi-restraints excluded: chain R residue 401 LEU Chi-restraints excluded: chain S residue 348 THR Chi-restraints excluded: chain S residue 409 ILE Chi-restraints excluded: chain S residue 512 GLU Chi-restraints excluded: chain T residue 49 SER Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain T residue 110 ILE Chi-restraints excluded: chain T residue 112 THR Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain T residue 147 ILE Chi-restraints excluded: chain T residue 149 ASP Chi-restraints excluded: chain T residue 154 VAL Chi-restraints excluded: chain T residue 178 THR Chi-restraints excluded: chain T residue 225 ILE Chi-restraints excluded: chain U residue 313 VAL Chi-restraints excluded: chain U residue 338 ASP Chi-restraints excluded: chain U residue 520 SER Chi-restraints excluded: chain V residue 399 LEU Chi-restraints excluded: chain V residue 504 ASP Chi-restraints excluded: chain V residue 509 ARG Chi-restraints excluded: chain W residue 331 VAL Chi-restraints excluded: chain W residue 345 ILE Chi-restraints excluded: chain W residue 363 LEU Chi-restraints excluded: chain W residue 396 GLN Chi-restraints excluded: chain W residue 486 LEU Chi-restraints excluded: chain W residue 512 GLU Chi-restraints excluded: chain X residue 8 SER Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain X residue 110 ILE Chi-restraints excluded: chain X residue 112 THR Chi-restraints excluded: chain Y residue 399 LEU Chi-restraints excluded: chain Y residue 409 ILE Chi-restraints excluded: chain Y residue 444 LEU Chi-restraints excluded: chain Y residue 503 VAL Chi-restraints excluded: chain Z residue 70 GLU Chi-restraints excluded: chain Z residue 99 LEU Chi-restraints excluded: chain Z residue 146 SER Chi-restraints excluded: chain Z residue 147 ILE Chi-restraints excluded: chain Z residue 178 THR Chi-restraints excluded: chain d residue 47 SER Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain d residue 109 THR Chi-restraints excluded: chain d residue 160 THR Chi-restraints excluded: chain d residue 179 ASP Chi-restraints excluded: chain d residue 234 LEU Chi-restraints excluded: chain f residue 49 SER Chi-restraints excluded: chain f residue 52 LYS Chi-restraints excluded: chain f residue 99 LEU Chi-restraints excluded: chain f residue 112 THR Chi-restraints excluded: chain f residue 147 ILE Chi-restraints excluded: chain f residue 228 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 886 random chunks: chunk 288 optimal weight: 6.9990 chunk 771 optimal weight: 0.7980 chunk 169 optimal weight: 0.5980 chunk 502 optimal weight: 0.9990 chunk 211 optimal weight: 7.9990 chunk 857 optimal weight: 6.9990 chunk 711 optimal weight: 3.9990 chunk 396 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 283 optimal weight: 10.0000 chunk 450 optimal weight: 7.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 69 ASN 2 114 GLN ** 6 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 HIS ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 GLN ** D 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 566 ASN ** F 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 152 HIS O 174 ASN ** P 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 165 ASN Q 174 ASN U 322 GLN X 11 GLN Z 129 HIS b 322 GLN f 80 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 69864 Z= 0.200 Angle : 0.505 10.452 94566 Z= 0.263 Chirality : 0.042 0.260 10748 Planarity : 0.004 0.046 12421 Dihedral : 5.798 107.639 10196 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.18 % Allowed : 13.40 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.09), residues: 8868 helix: 2.54 (0.09), residues: 3500 sheet: 0.72 (0.12), residues: 2048 loop : -0.03 (0.11), residues: 3320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 187 HIS 0.008 0.001 HIS I 152 PHE 0.030 0.002 PHE Z 111 TYR 0.014 0.001 TYR 6 118 ARG 0.005 0.000 ARG 0 135 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17736 Ramachandran restraints generated. 8868 Oldfield, 0 Emsley, 8868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17736 Ramachandran restraints generated. 8868 Oldfield, 0 Emsley, 8868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 984 residues out of total 7050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 760 time to evaluate : 6.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 13 MET cc_start: 0.7295 (ttm) cc_final: 0.6651 (tmm) REVERT: 0 156 MET cc_start: 0.8000 (mtm) cc_final: 0.7711 (mtm) REVERT: 2 11 GLN cc_start: 0.4730 (mt0) cc_final: 0.3626 (tm-30) REVERT: 2 69 ASN cc_start: 0.8504 (OUTLIER) cc_final: 0.7826 (m-40) REVERT: 2 110 ILE cc_start: 0.8070 (mt) cc_final: 0.7740 (tp) REVERT: 2 135 ARG cc_start: 0.8071 (tpp80) cc_final: 0.7316 (ttm-80) REVERT: 2 234 LEU cc_start: 0.7249 (OUTLIER) cc_final: 0.6861 (pt) REVERT: 4 45 ASN cc_start: 0.7778 (t0) cc_final: 0.7428 (t0) REVERT: 4 51 GLN cc_start: 0.6636 (mt0) cc_final: 0.6285 (mt0) REVERT: 4 67 LYS cc_start: 0.7622 (ttmt) cc_final: 0.7351 (ttmm) REVERT: 4 149 ASP cc_start: 0.8131 (t0) cc_final: 0.7825 (m-30) REVERT: 4 168 LYS cc_start: 0.6938 (OUTLIER) cc_final: 0.6147 (mttm) REVERT: 4 179 ASP cc_start: 0.7905 (m-30) cc_final: 0.7662 (m-30) REVERT: 4 214 ASP cc_start: 0.6772 (t0) cc_final: 0.6493 (t0) REVERT: 6 11 GLN cc_start: 0.4164 (OUTLIER) cc_final: 0.3891 (mm-40) REVERT: 6 28 LYS cc_start: 0.7669 (mmtt) cc_final: 0.7301 (mmtt) REVERT: 6 44 GLU cc_start: 0.7517 (tt0) cc_final: 0.6948 (tm-30) REVERT: 6 113 GLU cc_start: 0.7057 (mm-30) cc_final: 0.6592 (tt0) REVERT: 6 168 LYS cc_start: 0.7299 (mttt) cc_final: 0.7004 (tttt) REVERT: 6 234 LEU cc_start: 0.5845 (OUTLIER) cc_final: 0.5392 (pt) REVERT: 8 52 LYS cc_start: 0.7628 (OUTLIER) cc_final: 0.7342 (mtpp) REVERT: 8 113 GLU cc_start: 0.7434 (mm-30) cc_final: 0.7103 (mp0) REVERT: 8 169 GLU cc_start: 0.7094 (OUTLIER) cc_final: 0.6820 (tp30) REVERT: 8 174 ASN cc_start: 0.8015 (m110) cc_final: 0.7785 (m110) REVERT: B 520 GLN cc_start: 0.8446 (tt0) cc_final: 0.7937 (tp40) REVERT: B 545 GLN cc_start: 0.8634 (tp40) cc_final: 0.8140 (pm20) REVERT: C 297 CYS cc_start: 0.9057 (m) cc_final: 0.8692 (m) REVERT: C 336 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8176 (mp0) REVERT: C 508 MET cc_start: 0.8240 (mmt) cc_final: 0.7944 (mmp) REVERT: D 124 LEU cc_start: 0.7937 (mp) cc_final: 0.6996 (mt) REVERT: D 187 TRP cc_start: 0.7430 (m-10) cc_final: 0.7106 (m-10) REVERT: D 262 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7365 (mm-30) REVERT: D 486 MET cc_start: 0.7490 (tmm) cc_final: 0.7062 (tmm) REVERT: E 122 MET cc_start: 0.7766 (mtm) cc_final: 0.7537 (mtm) REVERT: E 145 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8201 (pm20) REVERT: F 168 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7834 (mt) REVERT: F 297 CYS cc_start: 0.8366 (m) cc_final: 0.7940 (m) REVERT: F 382 THR cc_start: 0.7692 (OUTLIER) cc_final: 0.7382 (p) REVERT: F 545 GLN cc_start: 0.7757 (tp-100) cc_final: 0.7529 (tp-100) REVERT: H 388 ARG cc_start: 0.7281 (tpt-90) cc_final: 0.6571 (ttp-110) REVERT: I 73 ASN cc_start: 0.6551 (t0) cc_final: 0.6342 (t0) REVERT: I 111 PHE cc_start: 0.7575 (t80) cc_final: 0.7224 (t80) REVERT: J 325 MET cc_start: 0.8056 (mtm) cc_final: 0.7611 (ttm) REVERT: J 364 GLU cc_start: 0.7222 (tt0) cc_final: 0.6906 (mt-10) REVERT: J 509 ARG cc_start: 0.6782 (tpt90) cc_final: 0.6380 (ttt180) REVERT: K 13 MET cc_start: 0.6115 (mmt) cc_final: 0.4604 (ttp) REVERT: K 26 ARG cc_start: 0.6833 (ttm110) cc_final: 0.6478 (ppt170) REVERT: K 67 LYS cc_start: 0.7696 (OUTLIER) cc_final: 0.7378 (tptp) REVERT: K 101 ASN cc_start: 0.6762 (t0) cc_final: 0.6544 (m-40) REVERT: K 112 THR cc_start: 0.6938 (m) cc_final: 0.6684 (p) REVERT: K 146 SER cc_start: 0.7310 (m) cc_final: 0.6852 (p) REVERT: K 150 GLU cc_start: 0.7161 (mm-30) cc_final: 0.6648 (mm-30) REVERT: K 216 ASN cc_start: 0.7324 (t0) cc_final: 0.6486 (m-40) REVERT: L 325 MET cc_start: 0.8094 (mtm) cc_final: 0.7239 (ttp) REVERT: L 332 ARG cc_start: 0.7071 (mtt-85) cc_final: 0.6508 (mtt180) REVERT: M 307 LYS cc_start: 0.7990 (mtpt) cc_final: 0.7684 (mtmm) REVERT: M 325 MET cc_start: 0.8241 (mtm) cc_final: 0.7682 (ttm) REVERT: M 338 ASP cc_start: 0.8019 (p0) cc_final: 0.7568 (p0) REVERT: M 424 ASP cc_start: 0.6887 (p0) cc_final: 0.6484 (p0) REVERT: N 325 MET cc_start: 0.8070 (mtm) cc_final: 0.7275 (ttt) REVERT: N 364 GLU cc_start: 0.8335 (tt0) cc_final: 0.7582 (pt0) REVERT: N 399 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7685 (tt) REVERT: N 433 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8180 (mt-10) REVERT: N 434 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8057 (mm-30) REVERT: N 447 LYS cc_start: 0.8014 (mtmt) cc_final: 0.7492 (mtpp) REVERT: O 26 ARG cc_start: 0.7285 (OUTLIER) cc_final: 0.6696 (ppt170) REVERT: O 113 GLU cc_start: 0.7504 (tt0) cc_final: 0.7303 (tm-30) REVERT: O 146 SER cc_start: 0.6903 (m) cc_final: 0.6535 (t) REVERT: O 151 PRO cc_start: 0.7900 (Cg_endo) cc_final: 0.7608 (Cg_exo) REVERT: O 152 HIS cc_start: 0.7145 (m-70) cc_final: 0.6508 (m-70) REVERT: P 325 MET cc_start: 0.7727 (mtm) cc_final: 0.6973 (ttp) REVERT: P 345 ILE cc_start: 0.8085 (OUTLIER) cc_final: 0.7708 (mm) REVERT: P 388 ARG cc_start: 0.7558 (tpt-90) cc_final: 0.6747 (ttm110) REVERT: P 432 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.6242 (mp0) REVERT: Q 49 SER cc_start: 0.7201 (m) cc_final: 0.6958 (p) REVERT: Q 70 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.6702 (mm-30) REVERT: Q 97 ARG cc_start: 0.6296 (ttp80) cc_final: 0.5928 (mtm110) REVERT: Q 113 GLU cc_start: 0.7639 (tp30) cc_final: 0.7125 (tm-30) REVERT: Q 134 LYS cc_start: 0.7075 (ttpp) cc_final: 0.6742 (tttm) REVERT: Q 146 SER cc_start: 0.7017 (m) cc_final: 0.6657 (p) REVERT: Q 156 MET cc_start: 0.6585 (mtm) cc_final: 0.6214 (mtm) REVERT: R 325 MET cc_start: 0.7762 (mtm) cc_final: 0.6976 (ttp) REVERT: R 519 GLU cc_start: 0.7311 (mt-10) cc_final: 0.7006 (tp30) REVERT: S 512 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7366 (tp30) REVERT: S 519 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7423 (tm-30) REVERT: T 52 LYS cc_start: 0.7653 (mtpt) cc_final: 0.7313 (mtmm) REVERT: T 113 GLU cc_start: 0.7538 (tp30) cc_final: 0.7208 (tm-30) REVERT: T 121 GLU cc_start: 0.6985 (tt0) cc_final: 0.6239 (mm-30) REVERT: T 134 LYS cc_start: 0.7297 (ttpt) cc_final: 0.6911 (ttpt) REVERT: T 207 SER cc_start: 0.5798 (p) cc_final: 0.5458 (t) REVERT: T 214 ASP cc_start: 0.6419 (t0) cc_final: 0.6116 (t0) REVERT: T 216 ASN cc_start: 0.7713 (t0) cc_final: 0.7133 (m110) REVERT: U 314 MET cc_start: 0.8581 (ttm) cc_final: 0.8212 (ttm) REVERT: U 401 LEU cc_start: 0.7755 (mt) cc_final: 0.7359 (mt) REVERT: U 509 ARG cc_start: 0.6909 (tpt170) cc_final: 0.6482 (ttp80) REVERT: V 325 MET cc_start: 0.8203 (mtm) cc_final: 0.7578 (mmt) REVERT: V 401 LEU cc_start: 0.7638 (tp) cc_final: 0.7264 (mt) REVERT: V 509 ARG cc_start: 0.6679 (OUTLIER) cc_final: 0.6003 (ttt180) REVERT: V 519 GLU cc_start: 0.7661 (tt0) cc_final: 0.7266 (mt-10) REVERT: W 364 GLU cc_start: 0.7586 (tt0) cc_final: 0.6980 (pt0) REVERT: W 388 ARG cc_start: 0.7120 (ttt180) cc_final: 0.6387 (ttm110) REVERT: W 522 SER cc_start: 0.6291 (t) cc_final: 0.5735 (m) REVERT: X 26 ARG cc_start: 0.7550 (ptm-80) cc_final: 0.7348 (mtm110) REVERT: X 52 LYS cc_start: 0.7778 (mtpt) cc_final: 0.7430 (mtmm) REVERT: X 80 GLN cc_start: 0.7699 (tp40) cc_final: 0.7408 (tp40) REVERT: X 130 TYR cc_start: 0.7689 (t80) cc_final: 0.6294 (t80) REVERT: X 156 MET cc_start: 0.4915 (mtm) cc_final: 0.4574 (mtm) REVERT: X 179 ASP cc_start: 0.6584 (m-30) cc_final: 0.5965 (t0) REVERT: X 216 ASN cc_start: 0.7513 (t0) cc_final: 0.6814 (t0) REVERT: Y 325 MET cc_start: 0.7968 (mtm) cc_final: 0.7291 (ttm) REVERT: Y 395 MET cc_start: 0.6848 (mmm) cc_final: 0.6513 (mmm) REVERT: Y 399 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7381 (tp) REVERT: Y 509 ARG cc_start: 0.7509 (tpt90) cc_final: 0.6772 (ttp80) REVERT: Z 70 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.6943 (mm-30) REVERT: Z 111 PHE cc_start: 0.6943 (t80) cc_final: 0.6627 (t80) REVERT: Z 113 GLU cc_start: 0.7302 (mm-30) cc_final: 0.6807 (tm-30) REVERT: Z 150 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7725 (mm-30) REVERT: Z 216 ASN cc_start: 0.8495 (t0) cc_final: 0.7964 (m-40) REVERT: a 325 MET cc_start: 0.7569 (mtm) cc_final: 0.6870 (ttm) REVERT: b 339 ASP cc_start: 0.8368 (t0) cc_final: 0.8042 (m-30) REVERT: b 396 GLN cc_start: 0.7261 (tp40) cc_final: 0.7004 (mm110) REVERT: d 13 MET cc_start: 0.4869 (mtp) cc_final: 0.4264 (mmm) REVERT: d 51 GLN cc_start: 0.7284 (mt0) cc_final: 0.6992 (mt0) REVERT: d 67 LYS cc_start: 0.7097 (tttt) cc_final: 0.6770 (tttm) REVERT: d 101 ASN cc_start: 0.7552 (t0) cc_final: 0.7293 (m-40) REVERT: d 189 ARG cc_start: 0.5965 (ttm-80) cc_final: 0.5521 (mtm-85) REVERT: d 234 LEU cc_start: 0.7069 (OUTLIER) cc_final: 0.6638 (pt) REVERT: f 44 GLU cc_start: 0.7245 (tt0) cc_final: 0.7027 (pt0) REVERT: f 73 ASN cc_start: 0.7031 (OUTLIER) cc_final: 0.6787 (t0) REVERT: f 101 ASN cc_start: 0.7230 (t0) cc_final: 0.6920 (m-40) REVERT: f 112 THR cc_start: 0.8137 (OUTLIER) cc_final: 0.7915 (p) REVERT: f 149 ASP cc_start: 0.7755 (t0) cc_final: 0.7450 (p0) outliers start: 224 outliers final: 161 residues processed: 917 average time/residue: 0.6705 time to fit residues: 1039.6562 Evaluate side-chains 912 residues out of total 7050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 727 time to evaluate : 6.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 11 GLN Chi-restraints excluded: chain 0 residue 51 GLN Chi-restraints excluded: chain 0 residue 70 GLU Chi-restraints excluded: chain 0 residue 147 ILE Chi-restraints excluded: chain 0 residue 149 ASP Chi-restraints excluded: chain 0 residue 188 LEU Chi-restraints excluded: chain 0 residue 225 ILE Chi-restraints excluded: chain 0 residue 233 LEU Chi-restraints excluded: chain 2 residue 69 ASN Chi-restraints excluded: chain 2 residue 147 ILE Chi-restraints excluded: chain 2 residue 179 ASP Chi-restraints excluded: chain 2 residue 226 THR Chi-restraints excluded: chain 2 residue 228 SER Chi-restraints excluded: chain 2 residue 234 LEU Chi-restraints excluded: chain 4 residue 52 LYS Chi-restraints excluded: chain 4 residue 73 ASN Chi-restraints excluded: chain 4 residue 147 ILE Chi-restraints excluded: chain 4 residue 168 LYS Chi-restraints excluded: chain 4 residue 216 ASN Chi-restraints excluded: chain 4 residue 219 ARG Chi-restraints excluded: chain 6 residue 11 GLN Chi-restraints excluded: chain 6 residue 99 LEU Chi-restraints excluded: chain 6 residue 147 ILE Chi-restraints excluded: chain 6 residue 149 ASP Chi-restraints excluded: chain 6 residue 179 ASP Chi-restraints excluded: chain 6 residue 234 LEU Chi-restraints excluded: chain 8 residue 52 LYS Chi-restraints excluded: chain 8 residue 99 LEU Chi-restraints excluded: chain 8 residue 169 GLU Chi-restraints excluded: chain 8 residue 233 LEU Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 430 ARG Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 225 LYS Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 336 GLU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 518 MET Chi-restraints excluded: chain D residue 244 GLU Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain D residue 518 MET Chi-restraints excluded: chain D residue 560 ASP Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 228 TYR Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 354 GLN Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 408 ASN Chi-restraints excluded: chain E residue 454 THR Chi-restraints excluded: chain E residue 566 ASN Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain E residue 581 ILE Chi-restraints excluded: chain E residue 584 ILE Chi-restraints excluded: chain E residue 588 VAL Chi-restraints excluded: chain E residue 604 ASN Chi-restraints excluded: chain E residue 605 LEU Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 223 ASP Chi-restraints excluded: chain F residue 378 ARG Chi-restraints excluded: chain F residue 382 THR Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 459 VAL Chi-restraints excluded: chain H residue 396 GLN Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain I residue 168 LYS Chi-restraints excluded: chain J residue 424 ASP Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 67 LYS Chi-restraints excluded: chain K residue 69 ASN Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 123 CYS Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain K residue 156 MET Chi-restraints excluded: chain L residue 409 ILE Chi-restraints excluded: chain M residue 354 GLU Chi-restraints excluded: chain M residue 363 LEU Chi-restraints excluded: chain N residue 345 ILE Chi-restraints excluded: chain N residue 358 LEU Chi-restraints excluded: chain N residue 361 VAL Chi-restraints excluded: chain N residue 399 LEU Chi-restraints excluded: chain N residue 412 SER Chi-restraints excluded: chain N residue 444 LEU Chi-restraints excluded: chain N residue 450 MET Chi-restraints excluded: chain N residue 461 ASP Chi-restraints excluded: chain O residue 26 ARG Chi-restraints excluded: chain O residue 29 SER Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain O residue 133 THR Chi-restraints excluded: chain O residue 147 ILE Chi-restraints excluded: chain O residue 159 THR Chi-restraints excluded: chain P residue 345 ILE Chi-restraints excluded: chain P residue 399 LEU Chi-restraints excluded: chain P residue 409 ILE Chi-restraints excluded: chain P residue 432 GLU Chi-restraints excluded: chain P residue 444 LEU Chi-restraints excluded: chain Q residue 70 GLU Chi-restraints excluded: chain Q residue 147 ILE Chi-restraints excluded: chain Q residue 207 SER Chi-restraints excluded: chain Q residue 228 SER Chi-restraints excluded: chain R residue 396 GLN Chi-restraints excluded: chain R residue 399 LEU Chi-restraints excluded: chain R residue 401 LEU Chi-restraints excluded: chain R residue 512 GLU Chi-restraints excluded: chain S residue 348 THR Chi-restraints excluded: chain S residue 409 ILE Chi-restraints excluded: chain S residue 512 GLU Chi-restraints excluded: chain T residue 49 SER Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain T residue 110 ILE Chi-restraints excluded: chain T residue 112 THR Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain T residue 147 ILE Chi-restraints excluded: chain T residue 149 ASP Chi-restraints excluded: chain T residue 154 VAL Chi-restraints excluded: chain T residue 178 THR Chi-restraints excluded: chain T residue 225 ILE Chi-restraints excluded: chain U residue 313 VAL Chi-restraints excluded: chain U residue 338 ASP Chi-restraints excluded: chain U residue 348 THR Chi-restraints excluded: chain U residue 520 SER Chi-restraints excluded: chain V residue 395 MET Chi-restraints excluded: chain V residue 412 SER Chi-restraints excluded: chain V residue 444 LEU Chi-restraints excluded: chain V residue 504 ASP Chi-restraints excluded: chain V residue 509 ARG Chi-restraints excluded: chain W residue 331 VAL Chi-restraints excluded: chain W residue 363 LEU Chi-restraints excluded: chain W residue 396 GLN Chi-restraints excluded: chain W residue 486 LEU Chi-restraints excluded: chain W residue 512 GLU Chi-restraints excluded: chain X residue 8 SER Chi-restraints excluded: chain X residue 110 ILE Chi-restraints excluded: chain X residue 112 THR Chi-restraints excluded: chain X residue 146 SER Chi-restraints excluded: chain Y residue 399 LEU Chi-restraints excluded: chain Y residue 441 SER Chi-restraints excluded: chain Y residue 444 LEU Chi-restraints excluded: chain Y residue 503 VAL Chi-restraints excluded: chain Z residue 30 VAL Chi-restraints excluded: chain Z residue 70 GLU Chi-restraints excluded: chain Z residue 99 LEU Chi-restraints excluded: chain Z residue 146 SER Chi-restraints excluded: chain Z residue 147 ILE Chi-restraints excluded: chain Z residue 178 THR Chi-restraints excluded: chain a residue 409 ILE Chi-restraints excluded: chain b residue 355 PHE Chi-restraints excluded: chain d residue 47 SER Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain d residue 109 THR Chi-restraints excluded: chain d residue 160 THR Chi-restraints excluded: chain d residue 179 ASP Chi-restraints excluded: chain d residue 234 LEU Chi-restraints excluded: chain f residue 49 SER Chi-restraints excluded: chain f residue 73 ASN Chi-restraints excluded: chain f residue 112 THR Chi-restraints excluded: chain f residue 147 ILE Chi-restraints excluded: chain f residue 228 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 886 random chunks: chunk 826 optimal weight: 5.9990 chunk 96 optimal weight: 0.4980 chunk 488 optimal weight: 0.9980 chunk 626 optimal weight: 2.9990 chunk 485 optimal weight: 0.5980 chunk 721 optimal weight: 3.9990 chunk 478 optimal weight: 2.9990 chunk 853 optimal weight: 3.9990 chunk 534 optimal weight: 2.9990 chunk 520 optimal weight: 0.6980 chunk 394 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 174 ASN ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 GLN ** D 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 101 ASN O 174 ASN ** P 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 165 ASN U 322 GLN b 322 GLN f 165 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.4113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 69864 Z= 0.140 Angle : 0.479 11.827 94566 Z= 0.248 Chirality : 0.041 0.251 10748 Planarity : 0.003 0.045 12421 Dihedral : 5.668 107.007 10192 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.76 % Allowed : 14.01 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.09), residues: 8868 helix: 2.68 (0.09), residues: 3500 sheet: 0.79 (0.12), residues: 2041 loop : 0.03 (0.11), residues: 3327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 187 HIS 0.004 0.001 HIS S 365 PHE 0.027 0.002 PHE 6 71 TYR 0.016 0.001 TYR 6 118 ARG 0.006 0.000 ARG 0 135 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17736 Ramachandran restraints generated. 8868 Oldfield, 0 Emsley, 8868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17736 Ramachandran restraints generated. 8868 Oldfield, 0 Emsley, 8868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 951 residues out of total 7050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 757 time to evaluate : 6.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 13 MET cc_start: 0.7289 (ttm) cc_final: 0.6643 (tmm) REVERT: 0 156 MET cc_start: 0.8164 (mtm) cc_final: 0.7936 (mtm) REVERT: 2 11 GLN cc_start: 0.4700 (mt0) cc_final: 0.3607 (tm-30) REVERT: 2 110 ILE cc_start: 0.8059 (mt) cc_final: 0.7738 (tp) REVERT: 2 135 ARG cc_start: 0.8017 (tpp80) cc_final: 0.7254 (ttm-80) REVERT: 2 234 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.6844 (pt) REVERT: 4 45 ASN cc_start: 0.7763 (t0) cc_final: 0.7421 (t0) REVERT: 4 51 GLN cc_start: 0.6621 (mt0) cc_final: 0.6324 (mt0) REVERT: 4 67 LYS cc_start: 0.7622 (ttmt) cc_final: 0.7382 (ttmm) REVERT: 4 73 ASN cc_start: 0.7243 (OUTLIER) cc_final: 0.6912 (m-40) REVERT: 4 149 ASP cc_start: 0.8131 (t0) cc_final: 0.7832 (m-30) REVERT: 4 168 LYS cc_start: 0.6849 (OUTLIER) cc_final: 0.6019 (mttm) REVERT: 4 179 ASP cc_start: 0.7908 (m-30) cc_final: 0.7670 (m-30) REVERT: 4 214 ASP cc_start: 0.6799 (t0) cc_final: 0.6519 (t0) REVERT: 4 225 ILE cc_start: 0.8372 (mt) cc_final: 0.7909 (mm) REVERT: 6 11 GLN cc_start: 0.4036 (OUTLIER) cc_final: 0.3773 (mm-40) REVERT: 6 28 LYS cc_start: 0.7702 (mmtt) cc_final: 0.7320 (mmtt) REVERT: 6 44 GLU cc_start: 0.7756 (tt0) cc_final: 0.7136 (tm-30) REVERT: 6 113 GLU cc_start: 0.7042 (mm-30) cc_final: 0.6601 (tt0) REVERT: 6 168 LYS cc_start: 0.7304 (mttt) cc_final: 0.7044 (tttt) REVERT: 6 234 LEU cc_start: 0.5830 (OUTLIER) cc_final: 0.5571 (pp) REVERT: 8 52 LYS cc_start: 0.7655 (OUTLIER) cc_final: 0.7409 (mtpp) REVERT: 8 73 ASN cc_start: 0.7652 (m110) cc_final: 0.7390 (m110) REVERT: 8 113 GLU cc_start: 0.7492 (mm-30) cc_final: 0.7137 (mp0) REVERT: 8 174 ASN cc_start: 0.8111 (m110) cc_final: 0.7855 (m110) REVERT: A 491 ASP cc_start: 0.7788 (OUTLIER) cc_final: 0.7508 (m-30) REVERT: B 520 GLN cc_start: 0.8422 (tt0) cc_final: 0.8023 (tt0) REVERT: B 545 GLN cc_start: 0.8615 (tp40) cc_final: 0.8124 (pm20) REVERT: C 297 CYS cc_start: 0.9034 (m) cc_final: 0.8648 (m) REVERT: C 336 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8190 (mp0) REVERT: C 508 MET cc_start: 0.8204 (mmt) cc_final: 0.7935 (mmp) REVERT: D 124 LEU cc_start: 0.7719 (mp) cc_final: 0.6827 (mt) REVERT: D 187 TRP cc_start: 0.7411 (m-10) cc_final: 0.7055 (m-10) REVERT: D 262 GLU cc_start: 0.7453 (mm-30) cc_final: 0.7231 (mm-30) REVERT: D 486 MET cc_start: 0.7491 (tmm) cc_final: 0.7074 (tmm) REVERT: E 122 MET cc_start: 0.7779 (mtm) cc_final: 0.7536 (mtm) REVERT: E 145 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.8123 (pm20) REVERT: E 486 MET cc_start: 0.6508 (ttm) cc_final: 0.6249 (mtm) REVERT: F 168 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7808 (mt) REVERT: F 297 CYS cc_start: 0.8332 (m) cc_final: 0.7965 (m) REVERT: F 382 THR cc_start: 0.7666 (OUTLIER) cc_final: 0.7388 (p) REVERT: F 545 GLN cc_start: 0.7794 (tp-100) cc_final: 0.7574 (tp-100) REVERT: H 388 ARG cc_start: 0.7148 (tpt-90) cc_final: 0.6564 (ttp-110) REVERT: I 101 ASN cc_start: 0.6993 (t0) cc_final: 0.6634 (m-40) REVERT: J 325 MET cc_start: 0.8053 (mtm) cc_final: 0.7625 (ttm) REVERT: J 364 GLU cc_start: 0.7171 (tt0) cc_final: 0.6832 (mt-10) REVERT: J 509 ARG cc_start: 0.6725 (tpt90) cc_final: 0.6371 (ttt180) REVERT: K 13 MET cc_start: 0.6158 (mmt) cc_final: 0.4624 (ttp) REVERT: K 26 ARG cc_start: 0.6884 (ttm110) cc_final: 0.6312 (ttp80) REVERT: K 67 LYS cc_start: 0.7711 (OUTLIER) cc_final: 0.7390 (tptp) REVERT: K 112 THR cc_start: 0.6977 (m) cc_final: 0.6722 (p) REVERT: K 146 SER cc_start: 0.7227 (m) cc_final: 0.6762 (p) REVERT: K 150 GLU cc_start: 0.7102 (mm-30) cc_final: 0.6502 (mm-30) REVERT: K 216 ASN cc_start: 0.7334 (t0) cc_final: 0.6495 (m-40) REVERT: L 325 MET cc_start: 0.8089 (mtm) cc_final: 0.7187 (ttp) REVERT: L 332 ARG cc_start: 0.7036 (mtt-85) cc_final: 0.6527 (mtt180) REVERT: M 307 LYS cc_start: 0.7962 (mtpt) cc_final: 0.7660 (mtmm) REVERT: M 325 MET cc_start: 0.8157 (mtm) cc_final: 0.7561 (ttm) REVERT: M 338 ASP cc_start: 0.7978 (p0) cc_final: 0.7538 (p0) REVERT: M 424 ASP cc_start: 0.6878 (p0) cc_final: 0.6461 (p0) REVERT: N 325 MET cc_start: 0.8084 (mtm) cc_final: 0.7313 (ttt) REVERT: N 364 GLU cc_start: 0.8308 (tt0) cc_final: 0.7532 (pt0) REVERT: N 399 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7696 (tt) REVERT: N 447 LYS cc_start: 0.7996 (mtmt) cc_final: 0.7481 (mtpp) REVERT: O 26 ARG cc_start: 0.7258 (OUTLIER) cc_final: 0.6593 (ppt170) REVERT: O 121 GLU cc_start: 0.7300 (tt0) cc_final: 0.6939 (tp30) REVERT: O 135 ARG cc_start: 0.6574 (mtp85) cc_final: 0.6336 (mtm-85) REVERT: O 146 SER cc_start: 0.6871 (m) cc_final: 0.6506 (t) REVERT: O 152 HIS cc_start: 0.7190 (m-70) cc_final: 0.6536 (m-70) REVERT: P 325 MET cc_start: 0.7690 (mtm) cc_final: 0.6939 (ttp) REVERT: P 345 ILE cc_start: 0.8037 (OUTLIER) cc_final: 0.7702 (mm) REVERT: P 432 GLU cc_start: 0.7082 (OUTLIER) cc_final: 0.6264 (mp0) REVERT: Q 70 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.6506 (mm-30) REVERT: Q 97 ARG cc_start: 0.6282 (ttp80) cc_final: 0.5920 (mtm110) REVERT: Q 113 GLU cc_start: 0.7620 (tp30) cc_final: 0.7090 (tm-30) REVERT: Q 134 LYS cc_start: 0.7074 (ttpp) cc_final: 0.6670 (tttm) REVERT: Q 146 SER cc_start: 0.7035 (m) cc_final: 0.6692 (p) REVERT: Q 156 MET cc_start: 0.6609 (mtm) cc_final: 0.6252 (mtm) REVERT: R 325 MET cc_start: 0.7799 (mtm) cc_final: 0.7066 (ttp) REVERT: R 519 GLU cc_start: 0.7363 (mt-10) cc_final: 0.7055 (tp30) REVERT: S 512 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7356 (tp30) REVERT: S 519 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7481 (tm-30) REVERT: T 52 LYS cc_start: 0.7651 (mtpt) cc_final: 0.7313 (mtmm) REVERT: T 113 GLU cc_start: 0.7569 (tp30) cc_final: 0.7220 (tm-30) REVERT: T 121 GLU cc_start: 0.6872 (tt0) cc_final: 0.6191 (mm-30) REVERT: T 134 LYS cc_start: 0.7293 (ttpt) cc_final: 0.6911 (ttpt) REVERT: T 207 SER cc_start: 0.5815 (p) cc_final: 0.5469 (t) REVERT: T 214 ASP cc_start: 0.6368 (t0) cc_final: 0.6070 (t0) REVERT: T 216 ASN cc_start: 0.7708 (t0) cc_final: 0.7128 (m110) REVERT: U 314 MET cc_start: 0.8590 (ttm) cc_final: 0.8219 (ttm) REVERT: U 401 LEU cc_start: 0.7772 (mt) cc_final: 0.7389 (mt) REVERT: U 509 ARG cc_start: 0.6860 (tpt170) cc_final: 0.6476 (ttp80) REVERT: V 325 MET cc_start: 0.8206 (mtm) cc_final: 0.7587 (mmt) REVERT: V 509 ARG cc_start: 0.6653 (OUTLIER) cc_final: 0.6014 (ttt180) REVERT: V 519 GLU cc_start: 0.7647 (tt0) cc_final: 0.7150 (mm-30) REVERT: W 364 GLU cc_start: 0.7568 (tt0) cc_final: 0.6970 (pt0) REVERT: W 388 ARG cc_start: 0.7127 (ttt180) cc_final: 0.6350 (ttm110) REVERT: W 522 SER cc_start: 0.6224 (t) cc_final: 0.5810 (m) REVERT: X 26 ARG cc_start: 0.7548 (ptm-80) cc_final: 0.7343 (mtm110) REVERT: X 52 LYS cc_start: 0.7781 (mtpt) cc_final: 0.7437 (mtmm) REVERT: X 80 GLN cc_start: 0.7638 (tp40) cc_final: 0.7354 (tp40) REVERT: X 130 TYR cc_start: 0.7743 (t80) cc_final: 0.6374 (t80) REVERT: X 156 MET cc_start: 0.4907 (mtm) cc_final: 0.4575 (mtm) REVERT: X 179 ASP cc_start: 0.6587 (m-30) cc_final: 0.5968 (t0) REVERT: X 216 ASN cc_start: 0.7420 (t0) cc_final: 0.6801 (t0) REVERT: Y 325 MET cc_start: 0.8053 (mtm) cc_final: 0.7402 (ttm) REVERT: Y 395 MET cc_start: 0.6644 (mmm) cc_final: 0.6253 (mmm) REVERT: Y 399 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7408 (tp) REVERT: Y 509 ARG cc_start: 0.7491 (tpt90) cc_final: 0.6748 (ttp80) REVERT: Z 70 GLU cc_start: 0.7111 (OUTLIER) cc_final: 0.6867 (mm-30) REVERT: Z 113 GLU cc_start: 0.7307 (mm-30) cc_final: 0.6862 (tm-30) REVERT: Z 143 TYR cc_start: 0.5730 (p90) cc_final: 0.5085 (p90) REVERT: Z 150 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7608 (mm-30) REVERT: Z 216 ASN cc_start: 0.8481 (t0) cc_final: 0.7940 (m-40) REVERT: a 325 MET cc_start: 0.7760 (mtm) cc_final: 0.7097 (ttm) REVERT: b 339 ASP cc_start: 0.8385 (t0) cc_final: 0.8056 (m-30) REVERT: b 396 GLN cc_start: 0.7047 (tp40) cc_final: 0.6757 (mm110) REVERT: d 13 MET cc_start: 0.4840 (mtp) cc_final: 0.4230 (mmm) REVERT: d 51 GLN cc_start: 0.7317 (mt0) cc_final: 0.7022 (mt0) REVERT: d 67 LYS cc_start: 0.7156 (tttt) cc_final: 0.6821 (tttm) REVERT: d 101 ASN cc_start: 0.7585 (t0) cc_final: 0.7336 (m-40) REVERT: d 189 ARG cc_start: 0.5843 (ttm-80) cc_final: 0.5329 (mtm-85) REVERT: d 234 LEU cc_start: 0.7004 (OUTLIER) cc_final: 0.6563 (pt) REVERT: f 44 GLU cc_start: 0.7222 (tt0) cc_final: 0.6994 (pt0) REVERT: f 52 LYS cc_start: 0.6685 (OUTLIER) cc_final: 0.6246 (mtpt) REVERT: f 101 ASN cc_start: 0.7450 (t0) cc_final: 0.7119 (m-40) REVERT: f 112 THR cc_start: 0.8223 (OUTLIER) cc_final: 0.7994 (p) REVERT: f 149 ASP cc_start: 0.7805 (t0) cc_final: 0.7480 (p0) outliers start: 194 outliers final: 133 residues processed: 896 average time/residue: 0.6700 time to fit residues: 1013.4223 Evaluate side-chains 877 residues out of total 7050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 720 time to evaluate : 6.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 11 GLN Chi-restraints excluded: chain 0 residue 51 GLN Chi-restraints excluded: chain 0 residue 70 GLU Chi-restraints excluded: chain 0 residue 147 ILE Chi-restraints excluded: chain 0 residue 188 LEU Chi-restraints excluded: chain 0 residue 233 LEU Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 147 ILE Chi-restraints excluded: chain 2 residue 234 LEU Chi-restraints excluded: chain 4 residue 30 VAL Chi-restraints excluded: chain 4 residue 73 ASN Chi-restraints excluded: chain 4 residue 147 ILE Chi-restraints excluded: chain 4 residue 168 LYS Chi-restraints excluded: chain 4 residue 216 ASN Chi-restraints excluded: chain 4 residue 219 ARG Chi-restraints excluded: chain 6 residue 11 GLN Chi-restraints excluded: chain 6 residue 147 ILE Chi-restraints excluded: chain 6 residue 149 ASP Chi-restraints excluded: chain 6 residue 234 LEU Chi-restraints excluded: chain 8 residue 52 LYS Chi-restraints excluded: chain 8 residue 99 LEU Chi-restraints excluded: chain 8 residue 233 LEU Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 297 CYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 430 ARG Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 336 GLU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 518 MET Chi-restraints excluded: chain D residue 244 GLU Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 518 MET Chi-restraints excluded: chain D residue 560 ASP Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 228 TYR Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 354 GLN Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 408 ASN Chi-restraints excluded: chain E residue 454 THR Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain E residue 581 ILE Chi-restraints excluded: chain E residue 584 ILE Chi-restraints excluded: chain E residue 588 VAL Chi-restraints excluded: chain E residue 604 ASN Chi-restraints excluded: chain E residue 605 LEU Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 223 ASP Chi-restraints excluded: chain F residue 382 THR Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 459 VAL Chi-restraints excluded: chain H residue 396 GLN Chi-restraints excluded: chain H residue 434 GLU Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain J residue 424 ASP Chi-restraints excluded: chain J residue 432 GLU Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 67 LYS Chi-restraints excluded: chain K residue 69 ASN Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain K residue 156 MET Chi-restraints excluded: chain M residue 345 ILE Chi-restraints excluded: chain M residue 354 GLU Chi-restraints excluded: chain N residue 345 ILE Chi-restraints excluded: chain N residue 358 LEU Chi-restraints excluded: chain N residue 399 LEU Chi-restraints excluded: chain N residue 412 SER Chi-restraints excluded: chain N residue 444 LEU Chi-restraints excluded: chain O residue 26 ARG Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain O residue 133 THR Chi-restraints excluded: chain O residue 147 ILE Chi-restraints excluded: chain P residue 345 ILE Chi-restraints excluded: chain P residue 399 LEU Chi-restraints excluded: chain P residue 409 ILE Chi-restraints excluded: chain P residue 432 GLU Chi-restraints excluded: chain Q residue 70 GLU Chi-restraints excluded: chain Q residue 147 ILE Chi-restraints excluded: chain Q residue 207 SER Chi-restraints excluded: chain Q residue 234 LEU Chi-restraints excluded: chain R residue 396 GLN Chi-restraints excluded: chain R residue 399 LEU Chi-restraints excluded: chain R residue 401 LEU Chi-restraints excluded: chain S residue 348 THR Chi-restraints excluded: chain S residue 512 GLU Chi-restraints excluded: chain T residue 49 SER Chi-restraints excluded: chain T residue 110 ILE Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain T residue 147 ILE Chi-restraints excluded: chain T residue 149 ASP Chi-restraints excluded: chain T residue 154 VAL Chi-restraints excluded: chain T residue 178 THR Chi-restraints excluded: chain U residue 313 VAL Chi-restraints excluded: chain U residue 338 ASP Chi-restraints excluded: chain U residue 520 SER Chi-restraints excluded: chain V residue 395 MET Chi-restraints excluded: chain V residue 399 LEU Chi-restraints excluded: chain V residue 412 SER Chi-restraints excluded: chain V residue 444 LEU Chi-restraints excluded: chain V residue 504 ASP Chi-restraints excluded: chain V residue 509 ARG Chi-restraints excluded: chain W residue 363 LEU Chi-restraints excluded: chain W residue 416 SER Chi-restraints excluded: chain W residue 486 LEU Chi-restraints excluded: chain W residue 512 GLU Chi-restraints excluded: chain X residue 8 SER Chi-restraints excluded: chain X residue 110 ILE Chi-restraints excluded: chain X residue 146 SER Chi-restraints excluded: chain Y residue 399 LEU Chi-restraints excluded: chain Y residue 441 SER Chi-restraints excluded: chain Y residue 444 LEU Chi-restraints excluded: chain Y residue 503 VAL Chi-restraints excluded: chain Z residue 30 VAL Chi-restraints excluded: chain Z residue 70 GLU Chi-restraints excluded: chain Z residue 99 LEU Chi-restraints excluded: chain Z residue 146 SER Chi-restraints excluded: chain Z residue 147 ILE Chi-restraints excluded: chain Z residue 178 THR Chi-restraints excluded: chain b residue 355 PHE Chi-restraints excluded: chain d residue 47 SER Chi-restraints excluded: chain d residue 160 THR Chi-restraints excluded: chain d residue 179 ASP Chi-restraints excluded: chain d residue 234 LEU Chi-restraints excluded: chain f residue 49 SER Chi-restraints excluded: chain f residue 52 LYS Chi-restraints excluded: chain f residue 99 LEU Chi-restraints excluded: chain f residue 112 THR Chi-restraints excluded: chain f residue 147 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 886 random chunks: chunk 528 optimal weight: 7.9990 chunk 341 optimal weight: 0.3980 chunk 510 optimal weight: 3.9990 chunk 257 optimal weight: 9.9990 chunk 167 optimal weight: 7.9990 chunk 165 optimal weight: 7.9990 chunk 542 optimal weight: 0.9980 chunk 581 optimal weight: 2.9990 chunk 422 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 chunk 671 optimal weight: 0.0970 overall best weight: 1.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 174 ASN ** 6 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 GLN ** D 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 566 ASN ** F 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 129 HIS ** P 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 165 ASN U 322 GLN b 322 GLN f 80 GLN f 165 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 69864 Z= 0.222 Angle : 0.520 12.910 94566 Z= 0.270 Chirality : 0.043 0.252 10748 Planarity : 0.004 0.061 12421 Dihedral : 5.709 107.429 10188 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.81 % Allowed : 14.34 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.09), residues: 8868 helix: 2.58 (0.09), residues: 3502 sheet: 0.77 (0.12), residues: 2038 loop : -0.01 (0.11), residues: 3328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 187 HIS 0.005 0.001 HIS a 365 PHE 0.031 0.002 PHE 6 71 TYR 0.017 0.001 TYR I 143 ARG 0.008 0.000 ARG K 21 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17736 Ramachandran restraints generated. 8868 Oldfield, 0 Emsley, 8868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17736 Ramachandran restraints generated. 8868 Oldfield, 0 Emsley, 8868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 939 residues out of total 7050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 741 time to evaluate : 6.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 13 MET cc_start: 0.7300 (ttm) cc_final: 0.6650 (tmm) REVERT: 2 11 GLN cc_start: 0.4701 (mt0) cc_final: 0.3602 (tm-30) REVERT: 2 110 ILE cc_start: 0.8086 (mt) cc_final: 0.7784 (tp) REVERT: 2 135 ARG cc_start: 0.8078 (tpp80) cc_final: 0.7341 (mtm110) REVERT: 2 234 LEU cc_start: 0.7248 (OUTLIER) cc_final: 0.6854 (pt) REVERT: 4 45 ASN cc_start: 0.7748 (t0) cc_final: 0.7446 (t0) REVERT: 4 51 GLN cc_start: 0.6628 (mt0) cc_final: 0.6295 (mt0) REVERT: 4 67 LYS cc_start: 0.7638 (ttmt) cc_final: 0.7364 (ttmm) REVERT: 4 149 ASP cc_start: 0.8118 (t0) cc_final: 0.7864 (m-30) REVERT: 4 168 LYS cc_start: 0.7061 (OUTLIER) cc_final: 0.6293 (mttm) REVERT: 4 179 ASP cc_start: 0.7584 (m-30) cc_final: 0.7337 (m-30) REVERT: 4 214 ASP cc_start: 0.6806 (t0) cc_final: 0.6513 (t0) REVERT: 6 11 GLN cc_start: 0.3450 (OUTLIER) cc_final: 0.3128 (mm-40) REVERT: 6 28 LYS cc_start: 0.7629 (mmtt) cc_final: 0.7314 (mmtt) REVERT: 6 44 GLU cc_start: 0.7549 (tt0) cc_final: 0.6976 (tm-30) REVERT: 6 113 GLU cc_start: 0.7095 (mm-30) cc_final: 0.6659 (tt0) REVERT: 6 168 LYS cc_start: 0.7208 (mttt) cc_final: 0.6921 (tttt) REVERT: 6 234 LEU cc_start: 0.5833 (OUTLIER) cc_final: 0.5414 (pt) REVERT: 8 52 LYS cc_start: 0.7629 (OUTLIER) cc_final: 0.7332 (mtpp) REVERT: 8 73 ASN cc_start: 0.7575 (m110) cc_final: 0.7234 (m110) REVERT: 8 113 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7348 (mp0) REVERT: 8 174 ASN cc_start: 0.8137 (m110) cc_final: 0.7893 (m110) REVERT: A 491 ASP cc_start: 0.7758 (OUTLIER) cc_final: 0.7489 (m-30) REVERT: B 478 MET cc_start: 0.7833 (mtp) cc_final: 0.7578 (mtt) REVERT: B 520 GLN cc_start: 0.8477 (tt0) cc_final: 0.7961 (tp40) REVERT: B 545 GLN cc_start: 0.8638 (tp40) cc_final: 0.8138 (pm20) REVERT: C 297 CYS cc_start: 0.9058 (m) cc_final: 0.8679 (m) REVERT: C 336 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8198 (mp0) REVERT: C 508 MET cc_start: 0.8216 (mmt) cc_final: 0.7942 (mmp) REVERT: D 124 LEU cc_start: 0.7688 (mp) cc_final: 0.6782 (mt) REVERT: D 187 TRP cc_start: 0.7495 (m-10) cc_final: 0.7139 (m-10) REVERT: D 486 MET cc_start: 0.7499 (tmm) cc_final: 0.7065 (tmm) REVERT: E 122 MET cc_start: 0.7767 (mtm) cc_final: 0.7523 (mtm) REVERT: E 145 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.8073 (pm20) REVERT: E 486 MET cc_start: 0.6533 (ttm) cc_final: 0.6275 (mtm) REVERT: F 168 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7848 (mt) REVERT: F 297 CYS cc_start: 0.8404 (m) cc_final: 0.8021 (m) REVERT: F 382 THR cc_start: 0.7713 (OUTLIER) cc_final: 0.7434 (p) REVERT: F 545 GLN cc_start: 0.7750 (tp-100) cc_final: 0.7504 (tp-100) REVERT: H 388 ARG cc_start: 0.7171 (tpt-90) cc_final: 0.6554 (ttp-110) REVERT: I 101 ASN cc_start: 0.6881 (t0) cc_final: 0.6547 (m-40) REVERT: J 325 MET cc_start: 0.8081 (mtm) cc_final: 0.7565 (ttm) REVERT: J 509 ARG cc_start: 0.6764 (tpt90) cc_final: 0.6370 (ttt180) REVERT: K 13 MET cc_start: 0.6257 (mmt) cc_final: 0.4665 (ttp) REVERT: K 21 ARG cc_start: 0.6581 (ttp-110) cc_final: 0.6279 (ptm-80) REVERT: K 26 ARG cc_start: 0.6901 (ttm110) cc_final: 0.6317 (ttp80) REVERT: K 67 LYS cc_start: 0.7736 (OUTLIER) cc_final: 0.7371 (tptp) REVERT: K 112 THR cc_start: 0.6922 (m) cc_final: 0.6642 (p) REVERT: K 146 SER cc_start: 0.7652 (m) cc_final: 0.7211 (p) REVERT: K 150 GLU cc_start: 0.7117 (mm-30) cc_final: 0.6543 (mm-30) REVERT: K 216 ASN cc_start: 0.7313 (t0) cc_final: 0.6533 (m-40) REVERT: L 325 MET cc_start: 0.8091 (mtm) cc_final: 0.7235 (ttp) REVERT: L 332 ARG cc_start: 0.7178 (mtt-85) cc_final: 0.6387 (mtt180) REVERT: M 307 LYS cc_start: 0.7945 (mtpt) cc_final: 0.7621 (mtmm) REVERT: M 325 MET cc_start: 0.8289 (mtm) cc_final: 0.7678 (ttm) REVERT: M 338 ASP cc_start: 0.8021 (p0) cc_final: 0.7521 (p0) REVERT: N 325 MET cc_start: 0.8038 (mtm) cc_final: 0.7434 (ttp) REVERT: N 354 GLU cc_start: 0.7277 (tt0) cc_final: 0.6841 (mm-30) REVERT: N 364 GLU cc_start: 0.8370 (tt0) cc_final: 0.7628 (pt0) REVERT: N 399 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7692 (tt) REVERT: N 447 LYS cc_start: 0.7996 (mtmt) cc_final: 0.7492 (mtpp) REVERT: O 26 ARG cc_start: 0.7393 (OUTLIER) cc_final: 0.6631 (ppt170) REVERT: O 121 GLU cc_start: 0.7292 (tt0) cc_final: 0.6911 (tp30) REVERT: O 135 ARG cc_start: 0.6537 (mtp85) cc_final: 0.6329 (mtm-85) REVERT: O 152 HIS cc_start: 0.6996 (m-70) cc_final: 0.6535 (m-70) REVERT: P 325 MET cc_start: 0.7730 (mtm) cc_final: 0.6974 (ttp) REVERT: P 345 ILE cc_start: 0.8049 (OUTLIER) cc_final: 0.7709 (mm) REVERT: P 432 GLU cc_start: 0.6986 (OUTLIER) cc_final: 0.6244 (mp0) REVERT: Q 70 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.6666 (mm-30) REVERT: Q 97 ARG cc_start: 0.6301 (ttp80) cc_final: 0.5939 (mtm110) REVERT: Q 113 GLU cc_start: 0.7692 (tp30) cc_final: 0.7200 (tm-30) REVERT: Q 134 LYS cc_start: 0.7067 (ttpp) cc_final: 0.6696 (tttm) REVERT: Q 146 SER cc_start: 0.7028 (m) cc_final: 0.6656 (p) REVERT: Q 156 MET cc_start: 0.6606 (mtm) cc_final: 0.6231 (mtm) REVERT: R 325 MET cc_start: 0.7757 (mtm) cc_final: 0.6982 (ttp) REVERT: R 519 GLU cc_start: 0.7460 (mt-10) cc_final: 0.7115 (tp30) REVERT: S 512 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7370 (tp30) REVERT: S 519 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7414 (tm-30) REVERT: T 52 LYS cc_start: 0.7741 (mtpt) cc_final: 0.7447 (mtmm) REVERT: T 113 GLU cc_start: 0.7539 (tp30) cc_final: 0.7218 (tm-30) REVERT: T 121 GLU cc_start: 0.6925 (tt0) cc_final: 0.6184 (mm-30) REVERT: T 134 LYS cc_start: 0.7279 (ttpt) cc_final: 0.6894 (ttpt) REVERT: T 214 ASP cc_start: 0.6359 (t0) cc_final: 0.6088 (t0) REVERT: T 216 ASN cc_start: 0.7724 (t0) cc_final: 0.7157 (m110) REVERT: U 314 MET cc_start: 0.8570 (ttm) cc_final: 0.8214 (ttm) REVERT: U 401 LEU cc_start: 0.7618 (mt) cc_final: 0.7173 (mt) REVERT: U 509 ARG cc_start: 0.6916 (tpt170) cc_final: 0.6481 (ttp80) REVERT: V 325 MET cc_start: 0.8181 (mtm) cc_final: 0.7567 (mmt) REVERT: V 401 LEU cc_start: 0.7519 (tp) cc_final: 0.7184 (mt) REVERT: V 509 ARG cc_start: 0.6685 (OUTLIER) cc_final: 0.5935 (ttt180) REVERT: V 519 GLU cc_start: 0.7647 (tt0) cc_final: 0.7282 (mt-10) REVERT: W 364 GLU cc_start: 0.7618 (tt0) cc_final: 0.6992 (pt0) REVERT: W 388 ARG cc_start: 0.7220 (ttt180) cc_final: 0.6475 (ttm110) REVERT: W 522 SER cc_start: 0.6295 (t) cc_final: 0.5719 (m) REVERT: X 52 LYS cc_start: 0.7871 (mtpt) cc_final: 0.7571 (mtmm) REVERT: X 80 GLN cc_start: 0.7665 (tp40) cc_final: 0.7373 (tp40) REVERT: X 130 TYR cc_start: 0.7688 (t80) cc_final: 0.6282 (t80) REVERT: X 156 MET cc_start: 0.4599 (mtm) cc_final: 0.4302 (mtm) REVERT: X 179 ASP cc_start: 0.6621 (m-30) cc_final: 0.6207 (t0) REVERT: X 216 ASN cc_start: 0.7486 (t0) cc_final: 0.6788 (t0) REVERT: Y 325 MET cc_start: 0.7930 (mtm) cc_final: 0.7257 (ttt) REVERT: Y 395 MET cc_start: 0.6938 (mmm) cc_final: 0.6577 (mmm) REVERT: Y 399 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7432 (tp) REVERT: Y 509 ARG cc_start: 0.7507 (tpt90) cc_final: 0.6752 (ttp80) REVERT: Z 70 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6943 (mm-30) REVERT: Z 113 GLU cc_start: 0.7110 (mm-30) cc_final: 0.6782 (tm-30) REVERT: Z 143 TYR cc_start: 0.5598 (p90) cc_final: 0.4933 (p90) REVERT: Z 150 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7435 (mm-30) REVERT: Z 152 HIS cc_start: 0.7333 (m-70) cc_final: 0.6814 (m-70) REVERT: Z 216 ASN cc_start: 0.8479 (t0) cc_final: 0.7933 (m-40) REVERT: a 325 MET cc_start: 0.7578 (mtm) cc_final: 0.6871 (ttm) REVERT: b 339 ASP cc_start: 0.8370 (t0) cc_final: 0.8045 (m-30) REVERT: b 396 GLN cc_start: 0.7317 (tp40) cc_final: 0.7009 (mm110) REVERT: d 13 MET cc_start: 0.4862 (mtp) cc_final: 0.4247 (mmm) REVERT: d 51 GLN cc_start: 0.7294 (mt0) cc_final: 0.6990 (mt0) REVERT: d 67 LYS cc_start: 0.7100 (tttt) cc_final: 0.6783 (tttm) REVERT: d 101 ASN cc_start: 0.7570 (t0) cc_final: 0.7307 (m-40) REVERT: d 189 ARG cc_start: 0.5866 (ttm-80) cc_final: 0.5397 (mtm-85) REVERT: d 234 LEU cc_start: 0.7168 (OUTLIER) cc_final: 0.6716 (pt) REVERT: f 52 LYS cc_start: 0.6716 (OUTLIER) cc_final: 0.6215 (mtpt) REVERT: f 101 ASN cc_start: 0.7478 (t0) cc_final: 0.7153 (m-40) REVERT: f 112 THR cc_start: 0.8129 (OUTLIER) cc_final: 0.7915 (p) REVERT: f 149 ASP cc_start: 0.7808 (t0) cc_final: 0.7486 (p0) outliers start: 198 outliers final: 156 residues processed: 878 average time/residue: 0.6633 time to fit residues: 983.8555 Evaluate side-chains 901 residues out of total 7050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 722 time to evaluate : 6.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 11 GLN Chi-restraints excluded: chain 0 residue 51 GLN Chi-restraints excluded: chain 0 residue 70 GLU Chi-restraints excluded: chain 0 residue 147 ILE Chi-restraints excluded: chain 0 residue 149 ASP Chi-restraints excluded: chain 0 residue 225 ILE Chi-restraints excluded: chain 0 residue 233 LEU Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 69 ASN Chi-restraints excluded: chain 2 residue 147 ILE Chi-restraints excluded: chain 2 residue 179 ASP Chi-restraints excluded: chain 2 residue 226 THR Chi-restraints excluded: chain 2 residue 234 LEU Chi-restraints excluded: chain 4 residue 30 VAL Chi-restraints excluded: chain 4 residue 73 ASN Chi-restraints excluded: chain 4 residue 102 VAL Chi-restraints excluded: chain 4 residue 147 ILE Chi-restraints excluded: chain 4 residue 168 LYS Chi-restraints excluded: chain 4 residue 216 ASN Chi-restraints excluded: chain 4 residue 219 ARG Chi-restraints excluded: chain 6 residue 11 GLN Chi-restraints excluded: chain 6 residue 147 ILE Chi-restraints excluded: chain 6 residue 149 ASP Chi-restraints excluded: chain 6 residue 234 LEU Chi-restraints excluded: chain 8 residue 52 LYS Chi-restraints excluded: chain 8 residue 99 LEU Chi-restraints excluded: chain 8 residue 233 LEU Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 297 CYS Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 430 ARG Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain A residue 521 ASN Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 348 HIS Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 225 LYS Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 336 GLU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 518 MET Chi-restraints excluded: chain D residue 244 GLU Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain D residue 518 MET Chi-restraints excluded: chain D residue 560 ASP Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 228 TYR Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 348 HIS Chi-restraints excluded: chain E residue 354 GLN Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 408 ASN Chi-restraints excluded: chain E residue 454 THR Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain E residue 581 ILE Chi-restraints excluded: chain E residue 584 ILE Chi-restraints excluded: chain E residue 588 VAL Chi-restraints excluded: chain E residue 604 ASN Chi-restraints excluded: chain E residue 605 LEU Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 223 ASP Chi-restraints excluded: chain F residue 378 ARG Chi-restraints excluded: chain F residue 382 THR Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 459 VAL Chi-restraints excluded: chain H residue 396 GLN Chi-restraints excluded: chain H residue 434 GLU Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain I residue 174 ASN Chi-restraints excluded: chain J residue 345 ILE Chi-restraints excluded: chain J residue 424 ASP Chi-restraints excluded: chain J residue 432 GLU Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 67 LYS Chi-restraints excluded: chain K residue 69 ASN Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 123 CYS Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain K residue 156 MET Chi-restraints excluded: chain M residue 345 ILE Chi-restraints excluded: chain M residue 354 GLU Chi-restraints excluded: chain M residue 363 LEU Chi-restraints excluded: chain N residue 345 ILE Chi-restraints excluded: chain N residue 358 LEU Chi-restraints excluded: chain N residue 361 VAL Chi-restraints excluded: chain N residue 399 LEU Chi-restraints excluded: chain N residue 412 SER Chi-restraints excluded: chain N residue 444 LEU Chi-restraints excluded: chain O residue 26 ARG Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain O residue 109 THR Chi-restraints excluded: chain O residue 133 THR Chi-restraints excluded: chain O residue 147 ILE Chi-restraints excluded: chain P residue 345 ILE Chi-restraints excluded: chain P residue 399 LEU Chi-restraints excluded: chain P residue 409 ILE Chi-restraints excluded: chain P residue 432 GLU Chi-restraints excluded: chain Q residue 70 GLU Chi-restraints excluded: chain Q residue 147 ILE Chi-restraints excluded: chain Q residue 207 SER Chi-restraints excluded: chain Q residue 228 SER Chi-restraints excluded: chain R residue 396 GLN Chi-restraints excluded: chain R residue 399 LEU Chi-restraints excluded: chain R residue 401 LEU Chi-restraints excluded: chain R residue 476 ASP Chi-restraints excluded: chain S residue 348 THR Chi-restraints excluded: chain S residue 512 GLU Chi-restraints excluded: chain T residue 49 SER Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain T residue 147 ILE Chi-restraints excluded: chain T residue 149 ASP Chi-restraints excluded: chain T residue 154 VAL Chi-restraints excluded: chain T residue 178 THR Chi-restraints excluded: chain U residue 313 VAL Chi-restraints excluded: chain U residue 338 ASP Chi-restraints excluded: chain U residue 348 THR Chi-restraints excluded: chain U residue 520 SER Chi-restraints excluded: chain V residue 395 MET Chi-restraints excluded: chain V residue 399 LEU Chi-restraints excluded: chain V residue 444 LEU Chi-restraints excluded: chain V residue 504 ASP Chi-restraints excluded: chain V residue 509 ARG Chi-restraints excluded: chain W residue 396 GLN Chi-restraints excluded: chain W residue 416 SER Chi-restraints excluded: chain W residue 486 LEU Chi-restraints excluded: chain W residue 512 GLU Chi-restraints excluded: chain X residue 8 SER Chi-restraints excluded: chain X residue 110 ILE Chi-restraints excluded: chain X residue 112 THR Chi-restraints excluded: chain X residue 146 SER Chi-restraints excluded: chain Y residue 399 LEU Chi-restraints excluded: chain Y residue 409 ILE Chi-restraints excluded: chain Y residue 444 LEU Chi-restraints excluded: chain Y residue 503 VAL Chi-restraints excluded: chain Z residue 30 VAL Chi-restraints excluded: chain Z residue 70 GLU Chi-restraints excluded: chain Z residue 99 LEU Chi-restraints excluded: chain Z residue 146 SER Chi-restraints excluded: chain Z residue 147 ILE Chi-restraints excluded: chain Z residue 178 THR Chi-restraints excluded: chain b residue 355 PHE Chi-restraints excluded: chain d residue 47 SER Chi-restraints excluded: chain d residue 160 THR Chi-restraints excluded: chain d residue 179 ASP Chi-restraints excluded: chain d residue 234 LEU Chi-restraints excluded: chain f residue 49 SER Chi-restraints excluded: chain f residue 52 LYS Chi-restraints excluded: chain f residue 99 LEU Chi-restraints excluded: chain f residue 112 THR Chi-restraints excluded: chain f residue 147 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 886 random chunks: chunk 776 optimal weight: 4.9990 chunk 818 optimal weight: 1.9990 chunk 746 optimal weight: 3.9990 chunk 795 optimal weight: 9.9990 chunk 817 optimal weight: 2.9990 chunk 478 optimal weight: 2.9990 chunk 346 optimal weight: 30.0000 chunk 624 optimal weight: 2.9990 chunk 244 optimal weight: 8.9990 chunk 719 optimal weight: 0.9990 chunk 752 optimal weight: 20.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 174 ASN 2 114 GLN 6 11 GLN 8 165 ASN ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 HIS ** D 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 566 ASN ** F 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 165 ASN T 165 ASN U 322 GLN Y 396 GLN Z 101 ASN b 322 GLN f 80 GLN f 165 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 69864 Z= 0.293 Angle : 0.569 13.039 94566 Z= 0.296 Chirality : 0.044 0.205 10748 Planarity : 0.004 0.054 12421 Dihedral : 5.904 109.532 10188 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.98 % Allowed : 14.37 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.09), residues: 8868 helix: 2.37 (0.09), residues: 3504 sheet: 0.72 (0.12), residues: 2006 loop : -0.13 (0.11), residues: 3358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 429 HIS 0.006 0.001 HIS b 365 PHE 0.033 0.003 PHE 6 71 TYR 0.017 0.002 TYR 6 118 ARG 0.010 0.001 ARG X 26 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17736 Ramachandran restraints generated. 8868 Oldfield, 0 Emsley, 8868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17736 Ramachandran restraints generated. 8868 Oldfield, 0 Emsley, 8868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 956 residues out of total 7050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 746 time to evaluate : 6.169 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 13 MET cc_start: 0.7152 (ttm) cc_final: 0.6453 (tmm) REVERT: 0 114 GLN cc_start: 0.5901 (mp10) cc_final: 0.5369 (mp10) REVERT: 0 156 MET cc_start: 0.7940 (mtm) cc_final: 0.7504 (mtm) REVERT: 2 11 GLN cc_start: 0.4587 (mt0) cc_final: 0.3425 (tm-30) REVERT: 2 44 GLU cc_start: 0.7683 (tt0) cc_final: 0.7417 (tm-30) REVERT: 2 69 ASN cc_start: 0.8434 (OUTLIER) cc_final: 0.7860 (m-40) REVERT: 2 110 ILE cc_start: 0.8165 (mt) cc_final: 0.7863 (tp) REVERT: 2 135 ARG cc_start: 0.8093 (tpp80) cc_final: 0.7447 (mtm110) REVERT: 2 234 LEU cc_start: 0.7362 (OUTLIER) cc_final: 0.7099 (pt) REVERT: 4 51 GLN cc_start: 0.6644 (mt0) cc_final: 0.6281 (mt0) REVERT: 4 67 LYS cc_start: 0.7831 (ttmt) cc_final: 0.7627 (ttmm) REVERT: 4 98 GLN cc_start: 0.7497 (mt0) cc_final: 0.7165 (mt0) REVERT: 4 149 ASP cc_start: 0.8102 (t0) cc_final: 0.7857 (m-30) REVERT: 4 168 LYS cc_start: 0.6977 (OUTLIER) cc_final: 0.6224 (mttm) REVERT: 6 11 GLN cc_start: 0.3479 (OUTLIER) cc_final: 0.3188 (mm110) REVERT: 6 44 GLU cc_start: 0.7574 (tt0) cc_final: 0.7091 (tp30) REVERT: 6 51 GLN cc_start: 0.6654 (mm-40) cc_final: 0.6179 (mm-40) REVERT: 6 113 GLU cc_start: 0.7079 (mm-30) cc_final: 0.6660 (tt0) REVERT: 6 135 ARG cc_start: 0.7612 (mmm160) cc_final: 0.7150 (mtp85) REVERT: 6 234 LEU cc_start: 0.5580 (OUTLIER) cc_final: 0.5138 (pt) REVERT: 8 52 LYS cc_start: 0.7609 (OUTLIER) cc_final: 0.7381 (mtpp) REVERT: 8 113 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7098 (tt0) REVERT: 8 174 ASN cc_start: 0.8127 (m110) cc_final: 0.7910 (m110) REVERT: 8 205 VAL cc_start: 0.7688 (m) cc_final: 0.7386 (p) REVERT: A 395 GLN cc_start: 0.7943 (pm20) cc_final: 0.7682 (pm20) REVERT: A 491 ASP cc_start: 0.7779 (OUTLIER) cc_final: 0.7495 (m-30) REVERT: B 520 GLN cc_start: 0.8528 (tt0) cc_final: 0.8095 (tp40) REVERT: B 545 GLN cc_start: 0.8671 (tp40) cc_final: 0.8145 (pm20) REVERT: C 297 CYS cc_start: 0.9033 (m) cc_final: 0.8663 (m) REVERT: C 508 MET cc_start: 0.8211 (mmt) cc_final: 0.7946 (mmp) REVERT: D 124 LEU cc_start: 0.7722 (mp) cc_final: 0.6789 (mt) REVERT: D 314 MET cc_start: 0.6880 (mpp) cc_final: 0.6628 (mpp) REVERT: D 486 MET cc_start: 0.7519 (tmm) cc_final: 0.7076 (tmm) REVERT: E 145 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8112 (pm20) REVERT: E 486 MET cc_start: 0.6620 (ttm) cc_final: 0.6285 (mtm) REVERT: F 297 CYS cc_start: 0.8501 (m) cc_final: 0.8113 (m) REVERT: F 382 THR cc_start: 0.7774 (OUTLIER) cc_final: 0.7452 (p) REVERT: F 390 THR cc_start: 0.8693 (m) cc_final: 0.8388 (m) REVERT: H 388 ARG cc_start: 0.7136 (tpt-90) cc_final: 0.6467 (ttp-110) REVERT: I 101 ASN cc_start: 0.6834 (t0) cc_final: 0.6631 (m-40) REVERT: J 325 MET cc_start: 0.8115 (mtm) cc_final: 0.7545 (ttm) REVERT: J 509 ARG cc_start: 0.6802 (tpt90) cc_final: 0.6364 (ttt-90) REVERT: K 13 MET cc_start: 0.6163 (mmt) cc_final: 0.4654 (ttp) REVERT: K 21 ARG cc_start: 0.6637 (ttp-110) cc_final: 0.6316 (ptm-80) REVERT: K 26 ARG cc_start: 0.6923 (ttm110) cc_final: 0.6374 (ppt170) REVERT: K 67 LYS cc_start: 0.7750 (OUTLIER) cc_final: 0.7403 (tptp) REVERT: K 112 THR cc_start: 0.6896 (m) cc_final: 0.6630 (p) REVERT: K 133 THR cc_start: 0.8288 (OUTLIER) cc_final: 0.7968 (p) REVERT: K 146 SER cc_start: 0.7611 (m) cc_final: 0.7261 (p) REVERT: K 150 GLU cc_start: 0.7177 (mm-30) cc_final: 0.6628 (mm-30) REVERT: K 216 ASN cc_start: 0.7210 (t0) cc_final: 0.6574 (m-40) REVERT: L 325 MET cc_start: 0.8094 (mtm) cc_final: 0.7226 (ttp) REVERT: L 332 ARG cc_start: 0.7335 (mtt-85) cc_final: 0.6447 (mtt180) REVERT: M 307 LYS cc_start: 0.7898 (mtpt) cc_final: 0.7482 (mtmm) REVERT: M 325 MET cc_start: 0.8373 (mtm) cc_final: 0.7697 (ttm) REVERT: M 338 ASP cc_start: 0.8064 (p0) cc_final: 0.7602 (p0) REVERT: N 325 MET cc_start: 0.8036 (mtm) cc_final: 0.7198 (ttt) REVERT: N 364 GLU cc_start: 0.8341 (tt0) cc_final: 0.7634 (pt0) REVERT: N 399 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7593 (tt) REVERT: N 447 LYS cc_start: 0.8034 (mtmt) cc_final: 0.7532 (mtpp) REVERT: O 26 ARG cc_start: 0.7388 (OUTLIER) cc_final: 0.6582 (ppt170) REVERT: O 121 GLU cc_start: 0.7363 (tt0) cc_final: 0.6976 (tp30) REVERT: O 152 HIS cc_start: 0.7045 (m-70) cc_final: 0.6594 (m-70) REVERT: O 214 ASP cc_start: 0.7211 (t0) cc_final: 0.6864 (t0) REVERT: P 325 MET cc_start: 0.7605 (mtm) cc_final: 0.6939 (ttp) REVERT: P 345 ILE cc_start: 0.8072 (OUTLIER) cc_final: 0.7750 (mm) REVERT: P 432 GLU cc_start: 0.6904 (OUTLIER) cc_final: 0.6240 (mp0) REVERT: Q 70 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.6744 (mm-30) REVERT: Q 97 ARG cc_start: 0.6360 (ttp80) cc_final: 0.6017 (mtm110) REVERT: Q 113 GLU cc_start: 0.7701 (tp30) cc_final: 0.7213 (tm-30) REVERT: Q 134 LYS cc_start: 0.7103 (ttpp) cc_final: 0.6745 (tttm) REVERT: Q 146 SER cc_start: 0.7036 (m) cc_final: 0.6636 (p) REVERT: Q 156 MET cc_start: 0.6572 (mtm) cc_final: 0.6199 (mtm) REVERT: R 325 MET cc_start: 0.7768 (mtm) cc_final: 0.7012 (ttp) REVERT: R 519 GLU cc_start: 0.7468 (mt-10) cc_final: 0.7102 (tp30) REVERT: S 512 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7381 (tp30) REVERT: S 519 GLU cc_start: 0.7712 (mt-10) cc_final: 0.7316 (tm-30) REVERT: T 14 ARG cc_start: 0.6296 (tpt90) cc_final: 0.5989 (ttm-80) REVERT: T 52 LYS cc_start: 0.7543 (mtpt) cc_final: 0.7187 (mtmm) REVERT: T 67 LYS cc_start: 0.7662 (tttt) cc_final: 0.7439 (tttt) REVERT: T 113 GLU cc_start: 0.7559 (tp30) cc_final: 0.7249 (tm-30) REVERT: T 121 GLU cc_start: 0.6830 (tt0) cc_final: 0.6043 (mm-30) REVERT: T 134 LYS cc_start: 0.7125 (ttpt) cc_final: 0.6852 (ttpt) REVERT: T 151 PRO cc_start: 0.8272 (Cg_endo) cc_final: 0.8056 (Cg_exo) REVERT: T 214 ASP cc_start: 0.6733 (t0) cc_final: 0.6490 (t0) REVERT: T 216 ASN cc_start: 0.7942 (t0) cc_final: 0.7206 (m110) REVERT: U 314 MET cc_start: 0.8552 (ttm) cc_final: 0.8216 (ttm) REVERT: U 401 LEU cc_start: 0.7677 (mt) cc_final: 0.7204 (mt) REVERT: U 509 ARG cc_start: 0.6870 (tpt170) cc_final: 0.6427 (ttp80) REVERT: V 325 MET cc_start: 0.8196 (mtm) cc_final: 0.7601 (mmt) REVERT: V 401 LEU cc_start: 0.7582 (tp) cc_final: 0.7183 (mt) REVERT: V 509 ARG cc_start: 0.7011 (OUTLIER) cc_final: 0.6123 (ttt180) REVERT: V 519 GLU cc_start: 0.7688 (tt0) cc_final: 0.7418 (mt-10) REVERT: W 364 GLU cc_start: 0.7640 (tt0) cc_final: 0.7044 (pt0) REVERT: W 388 ARG cc_start: 0.7240 (ttt180) cc_final: 0.6491 (ttm110) REVERT: W 522 SER cc_start: 0.6425 (t) cc_final: 0.6141 (p) REVERT: X 52 LYS cc_start: 0.7858 (mtpt) cc_final: 0.7549 (mtmm) REVERT: X 80 GLN cc_start: 0.7705 (tp40) cc_final: 0.7390 (tp40) REVERT: X 130 TYR cc_start: 0.7573 (t80) cc_final: 0.6224 (t80) REVERT: X 156 MET cc_start: 0.4886 (mtm) cc_final: 0.4649 (mtm) REVERT: X 179 ASP cc_start: 0.6663 (m-30) cc_final: 0.6060 (t0) REVERT: X 216 ASN cc_start: 0.7583 (t0) cc_final: 0.6936 (t0) REVERT: Y 325 MET cc_start: 0.8035 (mtm) cc_final: 0.7806 (mtp) REVERT: Y 395 MET cc_start: 0.6985 (mmm) cc_final: 0.6701 (mmm) REVERT: Y 399 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7732 (tp) REVERT: Y 509 ARG cc_start: 0.7517 (tpt90) cc_final: 0.6779 (ttp80) REVERT: Z 70 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.7069 (mm-30) REVERT: Z 113 GLU cc_start: 0.7325 (mm-30) cc_final: 0.6930 (tm-30) REVERT: Z 143 TYR cc_start: 0.5404 (p90) cc_final: 0.4985 (p90) REVERT: Z 150 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7397 (mm-30) REVERT: Z 152 HIS cc_start: 0.7198 (m-70) cc_final: 0.6674 (m-70) REVERT: Z 216 ASN cc_start: 0.8470 (t0) cc_final: 0.7934 (m-40) REVERT: a 325 MET cc_start: 0.7605 (mtm) cc_final: 0.6881 (ttm) REVERT: b 339 ASP cc_start: 0.8380 (t0) cc_final: 0.8052 (m-30) REVERT: d 51 GLN cc_start: 0.7105 (mt0) cc_final: 0.6801 (mt0) REVERT: d 67 LYS cc_start: 0.7159 (tttt) cc_final: 0.6840 (tttm) REVERT: d 101 ASN cc_start: 0.7660 (t0) cc_final: 0.7352 (m-40) REVERT: d 189 ARG cc_start: 0.5837 (ttm-80) cc_final: 0.5375 (mtm-85) REVERT: d 234 LEU cc_start: 0.7117 (OUTLIER) cc_final: 0.6651 (pt) REVERT: f 14 ARG cc_start: 0.5528 (ttp-110) cc_final: 0.5286 (ttm-80) REVERT: f 52 LYS cc_start: 0.6732 (OUTLIER) cc_final: 0.6156 (mtpt) REVERT: f 69 ASN cc_start: 0.6946 (p0) cc_final: 0.6336 (m-40) REVERT: f 101 ASN cc_start: 0.7317 (t0) cc_final: 0.6985 (m-40) REVERT: f 112 THR cc_start: 0.8076 (OUTLIER) cc_final: 0.7860 (p) REVERT: f 149 ASP cc_start: 0.7815 (t0) cc_final: 0.7487 (p0) outliers start: 210 outliers final: 165 residues processed: 895 average time/residue: 0.6705 time to fit residues: 1017.5994 Evaluate side-chains 909 residues out of total 7050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 721 time to evaluate : 6.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 51 GLN Chi-restraints excluded: chain 0 residue 70 GLU Chi-restraints excluded: chain 0 residue 147 ILE Chi-restraints excluded: chain 0 residue 149 ASP Chi-restraints excluded: chain 0 residue 225 ILE Chi-restraints excluded: chain 0 residue 233 LEU Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 69 ASN Chi-restraints excluded: chain 2 residue 147 ILE Chi-restraints excluded: chain 2 residue 179 ASP Chi-restraints excluded: chain 2 residue 226 THR Chi-restraints excluded: chain 2 residue 228 SER Chi-restraints excluded: chain 2 residue 234 LEU Chi-restraints excluded: chain 4 residue 30 VAL Chi-restraints excluded: chain 4 residue 73 ASN Chi-restraints excluded: chain 4 residue 102 VAL Chi-restraints excluded: chain 4 residue 147 ILE Chi-restraints excluded: chain 4 residue 168 LYS Chi-restraints excluded: chain 4 residue 216 ASN Chi-restraints excluded: chain 4 residue 219 ARG Chi-restraints excluded: chain 6 residue 11 GLN Chi-restraints excluded: chain 6 residue 99 LEU Chi-restraints excluded: chain 6 residue 114 GLN Chi-restraints excluded: chain 6 residue 147 ILE Chi-restraints excluded: chain 6 residue 149 ASP Chi-restraints excluded: chain 6 residue 179 ASP Chi-restraints excluded: chain 6 residue 234 LEU Chi-restraints excluded: chain 8 residue 19 LEU Chi-restraints excluded: chain 8 residue 52 LYS Chi-restraints excluded: chain 8 residue 99 LEU Chi-restraints excluded: chain 8 residue 233 LEU Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 430 ARG Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain A residue 521 ASN Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 348 HIS Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 225 LYS Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 518 MET Chi-restraints excluded: chain D residue 244 GLU Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain D residue 518 MET Chi-restraints excluded: chain D residue 560 ASP Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 228 TYR Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 354 GLN Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 408 ASN Chi-restraints excluded: chain E residue 454 THR Chi-restraints excluded: chain E residue 581 ILE Chi-restraints excluded: chain E residue 584 ILE Chi-restraints excluded: chain E residue 588 VAL Chi-restraints excluded: chain E residue 604 ASN Chi-restraints excluded: chain E residue 605 LEU Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 378 ARG Chi-restraints excluded: chain F residue 382 THR Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 459 VAL Chi-restraints excluded: chain F residue 500 TYR Chi-restraints excluded: chain H residue 386 MET Chi-restraints excluded: chain H residue 396 GLN Chi-restraints excluded: chain H residue 434 GLU Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain I residue 174 ASN Chi-restraints excluded: chain J residue 345 ILE Chi-restraints excluded: chain J residue 424 ASP Chi-restraints excluded: chain J residue 432 GLU Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 67 LYS Chi-restraints excluded: chain K residue 69 ASN Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 123 CYS Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain K residue 156 MET Chi-restraints excluded: chain M residue 345 ILE Chi-restraints excluded: chain M residue 354 GLU Chi-restraints excluded: chain M residue 363 LEU Chi-restraints excluded: chain N residue 345 ILE Chi-restraints excluded: chain N residue 358 LEU Chi-restraints excluded: chain N residue 361 VAL Chi-restraints excluded: chain N residue 399 LEU Chi-restraints excluded: chain N residue 412 SER Chi-restraints excluded: chain N residue 444 LEU Chi-restraints excluded: chain N residue 450 MET Chi-restraints excluded: chain N residue 461 ASP Chi-restraints excluded: chain O residue 26 ARG Chi-restraints excluded: chain O residue 29 SER Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain O residue 133 THR Chi-restraints excluded: chain O residue 147 ILE Chi-restraints excluded: chain P residue 345 ILE Chi-restraints excluded: chain P residue 399 LEU Chi-restraints excluded: chain P residue 409 ILE Chi-restraints excluded: chain P residue 432 GLU Chi-restraints excluded: chain Q residue 70 GLU Chi-restraints excluded: chain Q residue 147 ILE Chi-restraints excluded: chain Q residue 207 SER Chi-restraints excluded: chain Q residue 228 SER Chi-restraints excluded: chain Q residue 233 LEU Chi-restraints excluded: chain R residue 396 GLN Chi-restraints excluded: chain R residue 399 LEU Chi-restraints excluded: chain R residue 401 LEU Chi-restraints excluded: chain R residue 476 ASP Chi-restraints excluded: chain R residue 512 GLU Chi-restraints excluded: chain S residue 348 THR Chi-restraints excluded: chain S residue 512 GLU Chi-restraints excluded: chain T residue 49 SER Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain T residue 133 THR Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain T residue 147 ILE Chi-restraints excluded: chain T residue 149 ASP Chi-restraints excluded: chain T residue 154 VAL Chi-restraints excluded: chain T residue 178 THR Chi-restraints excluded: chain T residue 225 ILE Chi-restraints excluded: chain U residue 313 VAL Chi-restraints excluded: chain U residue 348 THR Chi-restraints excluded: chain U residue 520 SER Chi-restraints excluded: chain V residue 395 MET Chi-restraints excluded: chain V residue 444 LEU Chi-restraints excluded: chain V residue 504 ASP Chi-restraints excluded: chain V residue 509 ARG Chi-restraints excluded: chain W residue 396 GLN Chi-restraints excluded: chain W residue 416 SER Chi-restraints excluded: chain W residue 486 LEU Chi-restraints excluded: chain W residue 512 GLU Chi-restraints excluded: chain X residue 8 SER Chi-restraints excluded: chain X residue 110 ILE Chi-restraints excluded: chain X residue 112 THR Chi-restraints excluded: chain X residue 146 SER Chi-restraints excluded: chain Y residue 320 SER Chi-restraints excluded: chain Y residue 399 LEU Chi-restraints excluded: chain Y residue 409 ILE Chi-restraints excluded: chain Y residue 441 SER Chi-restraints excluded: chain Y residue 444 LEU Chi-restraints excluded: chain Y residue 503 VAL Chi-restraints excluded: chain Z residue 30 VAL Chi-restraints excluded: chain Z residue 70 GLU Chi-restraints excluded: chain Z residue 99 LEU Chi-restraints excluded: chain Z residue 106 THR Chi-restraints excluded: chain Z residue 146 SER Chi-restraints excluded: chain Z residue 147 ILE Chi-restraints excluded: chain Z residue 178 THR Chi-restraints excluded: chain b residue 355 PHE Chi-restraints excluded: chain d residue 47 SER Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain d residue 109 THR Chi-restraints excluded: chain d residue 160 THR Chi-restraints excluded: chain d residue 179 ASP Chi-restraints excluded: chain d residue 234 LEU Chi-restraints excluded: chain f residue 52 LYS Chi-restraints excluded: chain f residue 99 LEU Chi-restraints excluded: chain f residue 112 THR Chi-restraints excluded: chain f residue 147 ILE Chi-restraints excluded: chain f residue 228 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 886 random chunks: chunk 793 optimal weight: 0.9980 chunk 522 optimal weight: 0.8980 chunk 841 optimal weight: 0.9980 chunk 513 optimal weight: 0.3980 chunk 399 optimal weight: 0.9990 chunk 584 optimal weight: 0.0770 chunk 882 optimal weight: 5.9990 chunk 812 optimal weight: 0.9980 chunk 702 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 542 optimal weight: 0.9980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 174 ASN ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 545 GLN D 339 ASN ** D 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 566 ASN ** F 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 322 GLN X 98 GLN X 114 GLN Z 101 ASN b 322 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 69864 Z= 0.146 Angle : 0.492 12.682 94566 Z= 0.256 Chirality : 0.042 0.282 10748 Planarity : 0.003 0.044 12421 Dihedral : 5.663 107.815 10186 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.46 % Allowed : 14.94 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.09), residues: 8868 helix: 2.62 (0.09), residues: 3503 sheet: 0.80 (0.12), residues: 2028 loop : -0.03 (0.11), residues: 3337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 187 HIS 0.005 0.001 HIS S 365 PHE 0.028 0.002 PHE f 71 TYR 0.020 0.001 TYR 6 118 ARG 0.008 0.000 ARG X 26 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17736 Ramachandran restraints generated. 8868 Oldfield, 0 Emsley, 8868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17736 Ramachandran restraints generated. 8868 Oldfield, 0 Emsley, 8868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 929 residues out of total 7050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 756 time to evaluate : 6.204 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 13 MET cc_start: 0.7291 (ttm) cc_final: 0.6652 (tmm) REVERT: 0 114 GLN cc_start: 0.5880 (mp10) cc_final: 0.5315 (mp10) REVERT: 0 156 MET cc_start: 0.7914 (mtm) cc_final: 0.7482 (mtm) REVERT: 2 11 GLN cc_start: 0.4388 (mt0) cc_final: 0.3294 (tm-30) REVERT: 2 44 GLU cc_start: 0.7671 (tt0) cc_final: 0.7407 (tm-30) REVERT: 2 69 ASN cc_start: 0.8437 (OUTLIER) cc_final: 0.7929 (m-40) REVERT: 2 110 ILE cc_start: 0.8152 (mt) cc_final: 0.7854 (tp) REVERT: 2 135 ARG cc_start: 0.8052 (tpp80) cc_final: 0.7385 (mtm110) REVERT: 2 234 LEU cc_start: 0.7388 (OUTLIER) cc_final: 0.7087 (pt) REVERT: 4 73 ASN cc_start: 0.7232 (OUTLIER) cc_final: 0.6932 (m-40) REVERT: 4 98 GLN cc_start: 0.7462 (mt0) cc_final: 0.7120 (mt0) REVERT: 4 149 ASP cc_start: 0.8102 (t0) cc_final: 0.7802 (m-30) REVERT: 4 168 LYS cc_start: 0.6956 (OUTLIER) cc_final: 0.6203 (mttm) REVERT: 4 225 ILE cc_start: 0.8323 (mt) cc_final: 0.7889 (mm) REVERT: 6 11 GLN cc_start: 0.3555 (OUTLIER) cc_final: 0.3226 (mm110) REVERT: 6 44 GLU cc_start: 0.7789 (tt0) cc_final: 0.7180 (tm-30) REVERT: 6 51 GLN cc_start: 0.6756 (mm-40) cc_final: 0.6271 (mm-40) REVERT: 6 113 GLU cc_start: 0.7012 (mm-30) cc_final: 0.6564 (tt0) REVERT: 6 135 ARG cc_start: 0.7537 (mmm160) cc_final: 0.7092 (mtp85) REVERT: 6 234 LEU cc_start: 0.5735 (OUTLIER) cc_final: 0.5529 (pp) REVERT: 8 52 LYS cc_start: 0.7657 (OUTLIER) cc_final: 0.7404 (mtpp) REVERT: 8 73 ASN cc_start: 0.7611 (m110) cc_final: 0.7371 (m110) REVERT: 8 113 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7088 (tt0) REVERT: 8 156 MET cc_start: 0.7593 (mtp) cc_final: 0.7200 (mtt) REVERT: 8 174 ASN cc_start: 0.8139 (m110) cc_final: 0.7916 (m110) REVERT: 8 205 VAL cc_start: 0.7691 (m) cc_final: 0.7375 (p) REVERT: A 395 GLN cc_start: 0.7878 (pm20) cc_final: 0.7631 (pm20) REVERT: A 491 ASP cc_start: 0.7777 (OUTLIER) cc_final: 0.7489 (m-30) REVERT: B 520 GLN cc_start: 0.8501 (tt0) cc_final: 0.7980 (tp40) REVERT: B 545 GLN cc_start: 0.8655 (tp40) cc_final: 0.8190 (pm20) REVERT: C 297 CYS cc_start: 0.9080 (m) cc_final: 0.8685 (m) REVERT: C 508 MET cc_start: 0.8154 (mmt) cc_final: 0.7911 (mmp) REVERT: C 570 TRP cc_start: 0.5869 (m-90) cc_final: 0.4049 (t-100) REVERT: D 122 MET cc_start: 0.7278 (mmm) cc_final: 0.7030 (tpp) REVERT: D 124 LEU cc_start: 0.7665 (mp) cc_final: 0.6737 (mt) REVERT: D 486 MET cc_start: 0.7531 (tmm) cc_final: 0.7095 (tmm) REVERT: E 145 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7955 (pm20) REVERT: E 486 MET cc_start: 0.6589 (ttm) cc_final: 0.6358 (mtt) REVERT: F 297 CYS cc_start: 0.8368 (m) cc_final: 0.7995 (m) REVERT: F 382 THR cc_start: 0.7893 (OUTLIER) cc_final: 0.7598 (p) REVERT: H 388 ARG cc_start: 0.7144 (tpt-90) cc_final: 0.6564 (ttp-110) REVERT: I 101 ASN cc_start: 0.6877 (t0) cc_final: 0.6677 (m-40) REVERT: J 325 MET cc_start: 0.8091 (mtm) cc_final: 0.7524 (ttm) REVERT: J 509 ARG cc_start: 0.6714 (tpt90) cc_final: 0.6355 (ttt180) REVERT: K 13 MET cc_start: 0.6061 (mmt) cc_final: 0.4525 (ttp) REVERT: K 21 ARG cc_start: 0.6563 (ttp-110) cc_final: 0.6212 (ptm-80) REVERT: K 26 ARG cc_start: 0.6920 (ttm110) cc_final: 0.6372 (ppt170) REVERT: K 67 LYS cc_start: 0.7792 (OUTLIER) cc_final: 0.7450 (tptp) REVERT: K 112 THR cc_start: 0.6789 (m) cc_final: 0.6482 (p) REVERT: K 133 THR cc_start: 0.8247 (OUTLIER) cc_final: 0.7939 (p) REVERT: K 146 SER cc_start: 0.7634 (m) cc_final: 0.7279 (p) REVERT: K 150 GLU cc_start: 0.6933 (mm-30) cc_final: 0.6402 (mm-30) REVERT: K 216 ASN cc_start: 0.7227 (t0) cc_final: 0.6595 (m-40) REVERT: L 325 MET cc_start: 0.8100 (mtm) cc_final: 0.7259 (ttp) REVERT: L 332 ARG cc_start: 0.7227 (mtt-85) cc_final: 0.6446 (mtt180) REVERT: M 307 LYS cc_start: 0.7771 (mtpt) cc_final: 0.7365 (mtmm) REVERT: M 325 MET cc_start: 0.8371 (mtm) cc_final: 0.7750 (ttm) REVERT: M 338 ASP cc_start: 0.7963 (p0) cc_final: 0.7432 (p0) REVERT: N 325 MET cc_start: 0.8091 (mtm) cc_final: 0.7255 (ttt) REVERT: N 354 GLU cc_start: 0.7453 (tt0) cc_final: 0.6817 (mm-30) REVERT: N 364 GLU cc_start: 0.8270 (tt0) cc_final: 0.7544 (pt0) REVERT: N 399 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7701 (tt) REVERT: N 433 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8204 (mt-10) REVERT: N 447 LYS cc_start: 0.7934 (mtmt) cc_final: 0.7468 (mtpp) REVERT: O 26 ARG cc_start: 0.7285 (OUTLIER) cc_final: 0.6514 (ppt170) REVERT: O 121 GLU cc_start: 0.7311 (tt0) cc_final: 0.6951 (tp30) REVERT: O 152 HIS cc_start: 0.6984 (m-70) cc_final: 0.6517 (m-70) REVERT: P 325 MET cc_start: 0.7630 (mtm) cc_final: 0.6969 (ttp) REVERT: P 345 ILE cc_start: 0.8009 (OUTLIER) cc_final: 0.7672 (mm) REVERT: P 432 GLU cc_start: 0.6910 (OUTLIER) cc_final: 0.6193 (mp0) REVERT: Q 70 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.6634 (mm-30) REVERT: Q 97 ARG cc_start: 0.6319 (ttp80) cc_final: 0.5978 (mtm110) REVERT: Q 134 LYS cc_start: 0.7064 (ttpp) cc_final: 0.6649 (tttm) REVERT: Q 146 SER cc_start: 0.7061 (m) cc_final: 0.6669 (p) REVERT: Q 156 MET cc_start: 0.6596 (mtm) cc_final: 0.6208 (mtm) REVERT: R 325 MET cc_start: 0.7703 (mtm) cc_final: 0.6959 (ttp) REVERT: R 519 GLU cc_start: 0.7356 (mt-10) cc_final: 0.7055 (tp30) REVERT: S 512 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7355 (tp30) REVERT: S 519 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7366 (tm-30) REVERT: T 52 LYS cc_start: 0.7588 (mtpt) cc_final: 0.7277 (mtmm) REVERT: T 67 LYS cc_start: 0.7619 (tttt) cc_final: 0.7380 (tttt) REVERT: T 113 GLU cc_start: 0.7580 (tp30) cc_final: 0.7248 (tm-30) REVERT: T 121 GLU cc_start: 0.6828 (tt0) cc_final: 0.6112 (mm-30) REVERT: T 134 LYS cc_start: 0.7188 (ttpt) cc_final: 0.6779 (ttpt) REVERT: T 151 PRO cc_start: 0.8192 (Cg_endo) cc_final: 0.7925 (Cg_exo) REVERT: T 214 ASP cc_start: 0.6674 (t0) cc_final: 0.6413 (t0) REVERT: T 216 ASN cc_start: 0.7916 (t0) cc_final: 0.7139 (m110) REVERT: U 314 MET cc_start: 0.8585 (ttm) cc_final: 0.8221 (ttm) REVERT: U 401 LEU cc_start: 0.7795 (mt) cc_final: 0.7387 (mt) REVERT: U 509 ARG cc_start: 0.6859 (tpt170) cc_final: 0.6469 (ttp80) REVERT: V 325 MET cc_start: 0.8237 (mtm) cc_final: 0.7700 (mmt) REVERT: V 401 LEU cc_start: 0.7472 (tp) cc_final: 0.7117 (mt) REVERT: V 509 ARG cc_start: 0.6718 (OUTLIER) cc_final: 0.5949 (ttt180) REVERT: V 519 GLU cc_start: 0.7664 (tt0) cc_final: 0.7170 (mm-30) REVERT: W 364 GLU cc_start: 0.7563 (tt0) cc_final: 0.6904 (mt-10) REVERT: W 388 ARG cc_start: 0.7182 (ttt180) cc_final: 0.6936 (ttm-80) REVERT: W 522 SER cc_start: 0.6387 (t) cc_final: 0.5799 (m) REVERT: X 52 LYS cc_start: 0.7870 (mtpt) cc_final: 0.7560 (mtmm) REVERT: X 80 GLN cc_start: 0.7613 (tp40) cc_final: 0.7332 (tp40) REVERT: X 130 TYR cc_start: 0.7695 (t80) cc_final: 0.6333 (t80) REVERT: X 156 MET cc_start: 0.4835 (mtm) cc_final: 0.4584 (mtm) REVERT: X 179 ASP cc_start: 0.6633 (m-30) cc_final: 0.6212 (t0) REVERT: X 216 ASN cc_start: 0.7463 (t0) cc_final: 0.6843 (t0) REVERT: Y 325 MET cc_start: 0.8039 (mtm) cc_final: 0.7288 (ttt) REVERT: Y 395 MET cc_start: 0.6914 (mmm) cc_final: 0.6653 (mmm) REVERT: Y 399 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7435 (tp) REVERT: Y 509 ARG cc_start: 0.7484 (tpt90) cc_final: 0.6743 (ttp80) REVERT: Z 70 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.6850 (mm-30) REVERT: Z 143 TYR cc_start: 0.5433 (p90) cc_final: 0.5004 (p90) REVERT: Z 150 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7374 (mm-30) REVERT: Z 152 HIS cc_start: 0.7282 (m-70) cc_final: 0.6673 (m-70) REVERT: Z 216 ASN cc_start: 0.8451 (t0) cc_final: 0.7912 (m-40) REVERT: a 325 MET cc_start: 0.7785 (mtm) cc_final: 0.7111 (ttm) REVERT: b 339 ASP cc_start: 0.8388 (t0) cc_final: 0.8052 (m-30) REVERT: b 396 GLN cc_start: 0.7411 (tp40) cc_final: 0.7093 (mm110) REVERT: d 51 GLN cc_start: 0.7312 (mt0) cc_final: 0.7007 (mt0) REVERT: d 67 LYS cc_start: 0.7102 (tttt) cc_final: 0.6783 (tttm) REVERT: d 101 ASN cc_start: 0.7600 (t0) cc_final: 0.7323 (m-40) REVERT: d 179 ASP cc_start: 0.7834 (OUTLIER) cc_final: 0.7338 (t0) REVERT: d 189 ARG cc_start: 0.5886 (ttm-80) cc_final: 0.5498 (mtm-85) REVERT: f 14 ARG cc_start: 0.5567 (ttp-110) cc_final: 0.5316 (ttm-80) REVERT: f 52 LYS cc_start: 0.6638 (OUTLIER) cc_final: 0.6236 (mtpt) REVERT: f 101 ASN cc_start: 0.7348 (t0) cc_final: 0.7053 (m-40) REVERT: f 112 THR cc_start: 0.8163 (OUTLIER) cc_final: 0.7935 (p) REVERT: f 149 ASP cc_start: 0.7804 (t0) cc_final: 0.7489 (p0) REVERT: f 209 GLU cc_start: 0.7233 (tt0) cc_final: 0.6958 (mt-10) outliers start: 173 outliers final: 135 residues processed: 870 average time/residue: 0.6707 time to fit residues: 989.5196 Evaluate side-chains 887 residues out of total 7050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 728 time to evaluate : 6.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 51 GLN Chi-restraints excluded: chain 0 residue 70 GLU Chi-restraints excluded: chain 0 residue 149 ASP Chi-restraints excluded: chain 0 residue 233 LEU Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 69 ASN Chi-restraints excluded: chain 2 residue 147 ILE Chi-restraints excluded: chain 2 residue 179 ASP Chi-restraints excluded: chain 2 residue 226 THR Chi-restraints excluded: chain 2 residue 228 SER Chi-restraints excluded: chain 2 residue 234 LEU Chi-restraints excluded: chain 4 residue 30 VAL Chi-restraints excluded: chain 4 residue 73 ASN Chi-restraints excluded: chain 4 residue 147 ILE Chi-restraints excluded: chain 4 residue 168 LYS Chi-restraints excluded: chain 4 residue 216 ASN Chi-restraints excluded: chain 4 residue 219 ARG Chi-restraints excluded: chain 6 residue 11 GLN Chi-restraints excluded: chain 6 residue 147 ILE Chi-restraints excluded: chain 6 residue 149 ASP Chi-restraints excluded: chain 6 residue 234 LEU Chi-restraints excluded: chain 8 residue 52 LYS Chi-restraints excluded: chain 8 residue 99 LEU Chi-restraints excluded: chain 8 residue 233 LEU Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 430 ARG Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 348 HIS Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 518 MET Chi-restraints excluded: chain D residue 244 GLU Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 518 MET Chi-restraints excluded: chain D residue 560 ASP Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 228 TYR Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 354 GLN Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 408 ASN Chi-restraints excluded: chain E residue 454 THR Chi-restraints excluded: chain E residue 566 ASN Chi-restraints excluded: chain E residue 581 ILE Chi-restraints excluded: chain E residue 584 ILE Chi-restraints excluded: chain E residue 588 VAL Chi-restraints excluded: chain E residue 604 ASN Chi-restraints excluded: chain E residue 605 LEU Chi-restraints excluded: chain F residue 118 SER Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 223 ASP Chi-restraints excluded: chain F residue 382 THR Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 459 VAL Chi-restraints excluded: chain H residue 386 MET Chi-restraints excluded: chain H residue 396 GLN Chi-restraints excluded: chain H residue 434 GLU Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain I residue 174 ASN Chi-restraints excluded: chain J residue 424 ASP Chi-restraints excluded: chain J residue 432 GLU Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 67 LYS Chi-restraints excluded: chain K residue 69 ASN Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain K residue 156 MET Chi-restraints excluded: chain L residue 399 LEU Chi-restraints excluded: chain L residue 409 ILE Chi-restraints excluded: chain M residue 345 ILE Chi-restraints excluded: chain M residue 354 GLU Chi-restraints excluded: chain M residue 363 LEU Chi-restraints excluded: chain N residue 345 ILE Chi-restraints excluded: chain N residue 361 VAL Chi-restraints excluded: chain N residue 399 LEU Chi-restraints excluded: chain N residue 412 SER Chi-restraints excluded: chain O residue 26 ARG Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain O residue 133 THR Chi-restraints excluded: chain O residue 147 ILE Chi-restraints excluded: chain P residue 345 ILE Chi-restraints excluded: chain P residue 399 LEU Chi-restraints excluded: chain P residue 409 ILE Chi-restraints excluded: chain P residue 432 GLU Chi-restraints excluded: chain Q residue 70 GLU Chi-restraints excluded: chain Q residue 147 ILE Chi-restraints excluded: chain Q residue 207 SER Chi-restraints excluded: chain Q residue 228 SER Chi-restraints excluded: chain R residue 396 GLN Chi-restraints excluded: chain R residue 399 LEU Chi-restraints excluded: chain R residue 401 LEU Chi-restraints excluded: chain R residue 476 ASP Chi-restraints excluded: chain S residue 348 THR Chi-restraints excluded: chain S residue 512 GLU Chi-restraints excluded: chain T residue 49 SER Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain T residue 147 ILE Chi-restraints excluded: chain T residue 149 ASP Chi-restraints excluded: chain T residue 178 THR Chi-restraints excluded: chain U residue 313 VAL Chi-restraints excluded: chain U residue 520 SER Chi-restraints excluded: chain V residue 395 MET Chi-restraints excluded: chain V residue 444 LEU Chi-restraints excluded: chain V residue 504 ASP Chi-restraints excluded: chain V residue 509 ARG Chi-restraints excluded: chain W residue 416 SER Chi-restraints excluded: chain W residue 486 LEU Chi-restraints excluded: chain W residue 512 GLU Chi-restraints excluded: chain X residue 8 SER Chi-restraints excluded: chain X residue 110 ILE Chi-restraints excluded: chain X residue 112 THR Chi-restraints excluded: chain X residue 146 SER Chi-restraints excluded: chain Y residue 399 LEU Chi-restraints excluded: chain Y residue 441 SER Chi-restraints excluded: chain Y residue 444 LEU Chi-restraints excluded: chain Y residue 503 VAL Chi-restraints excluded: chain Z residue 30 VAL Chi-restraints excluded: chain Z residue 70 GLU Chi-restraints excluded: chain Z residue 99 LEU Chi-restraints excluded: chain Z residue 146 SER Chi-restraints excluded: chain Z residue 147 ILE Chi-restraints excluded: chain Z residue 178 THR Chi-restraints excluded: chain b residue 355 PHE Chi-restraints excluded: chain d residue 47 SER Chi-restraints excluded: chain d residue 109 THR Chi-restraints excluded: chain d residue 179 ASP Chi-restraints excluded: chain d residue 234 LEU Chi-restraints excluded: chain f residue 52 LYS Chi-restraints excluded: chain f residue 99 LEU Chi-restraints excluded: chain f residue 112 THR Chi-restraints excluded: chain f residue 147 ILE Chi-restraints excluded: chain f residue 228 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 886 random chunks: chunk 430 optimal weight: 1.9990 chunk 558 optimal weight: 10.0000 chunk 748 optimal weight: 7.9990 chunk 215 optimal weight: 8.9990 chunk 648 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 195 optimal weight: 0.9990 chunk 704 optimal weight: 0.9980 chunk 294 optimal weight: 0.6980 chunk 722 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 174 ASN ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 566 ASN ** F 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 348 HIS ** F 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 322 GLN Z 101 ASN b 322 GLN f 80 GLN ** f 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.120972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.095540 restraints weight = 108260.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.093901 restraints weight = 257303.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.094016 restraints weight = 265133.978| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.4482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.453 69864 Z= 0.211 Angle : 0.550 59.148 94566 Z= 0.299 Chirality : 0.042 0.664 10748 Planarity : 0.003 0.064 12421 Dihedral : 5.668 107.806 10186 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.47 % Allowed : 15.02 % Favored : 82.50 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.09), residues: 8868 helix: 2.62 (0.09), residues: 3504 sheet: 0.80 (0.12), residues: 2028 loop : -0.03 (0.11), residues: 3336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 187 HIS 0.005 0.001 HIS S 365 PHE 0.029 0.002 PHE C 377 TYR 0.015 0.001 TYR 6 118 ARG 0.006 0.000 ARG X 26 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16586.06 seconds wall clock time: 291 minutes 25.35 seconds (17485.35 seconds total)