Starting phenix.real_space_refine on Sat Feb 24 20:54:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d6w_27224/02_2024/8d6w_27224.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d6w_27224/02_2024/8d6w_27224.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d6w_27224/02_2024/8d6w_27224.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d6w_27224/02_2024/8d6w_27224.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d6w_27224/02_2024/8d6w_27224.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d6w_27224/02_2024/8d6w_27224.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 112 5.16 5 C 29077 2.51 5 N 8225 2.21 5 O 8966 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 10": "OE1" <-> "OE2" Residue "C GLU 126": "OE1" <-> "OE2" Residue "C GLU 132": "OE1" <-> "OE2" Residue "C GLU 161": "OE1" <-> "OE2" Residue "D GLU 18": "OE1" <-> "OE2" Residue "E GLU 15": "OE1" <-> "OE2" Residue "E GLU 137": "OE1" <-> "OE2" Residue "E TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 144": "OD1" <-> "OD2" Residue "F GLU 18": "OE1" <-> "OE2" Residue "F PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 70": "OE1" <-> "OE2" Residue "G PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 121": "OE1" <-> "OE2" Residue "G GLU 209": "OE1" <-> "OE2" Residue "H PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 137": "OE1" <-> "OE2" Residue "J GLU 161": "OE1" <-> "OE2" Residue "J GLU 173": "OE1" <-> "OE2" Residue "K GLU 161": "OE1" <-> "OE2" Residue "L GLU 44": "OE1" <-> "OE2" Residue "L PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 173": "OE1" <-> "OE2" Residue "M GLU 10": "OE1" <-> "OE2" Residue "M GLU 137": "OE1" <-> "OE2" Residue "M GLU 161": "OE1" <-> "OE2" Residue "N PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 70": "OE1" <-> "OE2" Residue "N GLU 173": "OE1" <-> "OE2" Residue "P TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 364": "OE1" <-> "OE2" Residue "P GLU 432": "OE1" <-> "OE2" Residue "P GLU 433": "OE1" <-> "OE2" Residue "P GLU 434": "OE1" <-> "OE2" Residue "P GLU 512": "OE1" <-> "OE2" Residue "P GLU 519": "OE1" <-> "OE2" Residue "Q GLU 469": "OE1" <-> "OE2" Residue "R GLU 519": "OE1" <-> "OE2" Residue "S GLU 519": "OE1" <-> "OE2" Residue "U GLU 354": "OE1" <-> "OE2" Residue "V GLU 362": "OE1" <-> "OE2" Residue "V GLU 434": "OE1" <-> "OE2" Residue "V GLU 507": "OE1" <-> "OE2" Residue "V GLU 519": "OE1" <-> "OE2" Residue "W GLU 364": "OE1" <-> "OE2" Residue "W GLU 432": "OE1" <-> "OE2" Residue "W GLU 433": "OE1" <-> "OE2" Residue "W GLU 434": "OE1" <-> "OE2" Residue "W GLU 507": "OE1" <-> "OE2" Residue "Y GLU 354": "OE1" <-> "OE2" Residue "Y TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 364": "OE1" <-> "OE2" Residue "Z GLU 512": "OE1" <-> "OE2" Residue "a GLU 364": "OE1" <-> "OE2" Residue "a GLU 367": "OE1" <-> "OE2" Residue "a GLU 512": "OE1" <-> "OE2" Residue "b GLU 364": "OE1" <-> "OE2" Residue "b GLU 434": "OE1" <-> "OE2" Residue "b GLU 507": "OE1" <-> "OE2" Residue "c ASP 424": "OD1" <-> "OD2" Residue "c GLU 512": "OE1" <-> "OE2" Residue "O GLU 18": "OE1" <-> "OE2" Residue "O PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 46380 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" 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: "C" 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: "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: "E" 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: "G" 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: "H" 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: "I" 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: "J" 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: "K" 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: "L" 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: "M" 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: "N" 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: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "Q" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "R" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "S" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "T" 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: "U" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "V" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "W" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "X" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "Y" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "Z" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "a" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "b" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "c" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "d" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Link IDs: {'TRANS': 3} Chain: "e" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Link IDs: {'TRANS': 3} Chain: "f" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Link IDs: {'TRANS': 3} Chain: "g" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Link IDs: {'TRANS': 3} Chain: "h" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Link IDs: {'TRANS': 3} Chain: "i" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Link IDs: {'TRANS': 3} Chain: "j" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Link IDs: {'TRANS': 3} 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 Time building chain proxies: 24.50, per 1000 atoms: 0.53 Number of scatterers: 46380 At special positions: 0 Unit cell: (134.964, 133.308, 170.568, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 112 16.00 O 8966 8.00 N 8225 7.00 C 29077 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 17.82 Conformation dependent library (CDL) restraints added in 8.5 seconds 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11158 Finding SS restraints... Secondary structure from input PDB file: 203 helices and 70 sheets defined 46.5% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.38 Creating SS restraints... Processing helix chain 'A' and resid 8 through 26 Processing helix chain 'A' and resid 67 through 89 Processing helix chain 'A' and resid 90 through 94 removed outlier: 3.517A pdb=" N VAL A 94 " --> pdb=" O ARG A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 114 removed outlier: 3.557A pdb=" N LEU A 99 " --> pdb=" O THR A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 171 removed outlier: 4.438A pdb=" N ILE A 163 " --> pdb=" O THR A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 190 removed outlier: 3.688A pdb=" N ALA A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 234 removed outlier: 3.595A pdb=" N LEU A 230 " --> pdb=" O THR A 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 26 Processing helix chain 'C' and resid 67 through 89 Processing helix chain 'C' and resid 90 through 94 Processing helix chain 'C' and resid 95 through 113 removed outlier: 3.572A pdb=" N LEU C 99 " --> pdb=" O THR C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 170 removed outlier: 4.511A pdb=" N ILE C 163 " --> pdb=" O THR C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 190 Processing helix chain 'C' and resid 227 through 234 Processing helix chain 'D' and resid 9 through 26 Processing helix chain 'D' and resid 67 through 89 Processing helix chain 'D' and resid 90 through 94 Processing helix chain 'D' and resid 95 through 113 Processing helix chain 'D' and resid 159 through 171 removed outlier: 4.331A pdb=" N ILE D 163 " --> pdb=" O THR D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 190 removed outlier: 3.535A pdb=" N ALA D 190 " --> pdb=" O ALA D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 234 Processing helix chain 'E' and resid 9 through 26 Processing helix chain 'E' and resid 67 through 89 Processing helix chain 'E' and resid 90 through 94 Processing helix chain 'E' and resid 95 through 114 Processing helix chain 'E' and resid 159 through 171 removed outlier: 4.392A pdb=" N ILE E 163 " --> pdb=" O THR E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 190 Processing helix chain 'E' and resid 227 through 234 Processing helix chain 'F' and resid 9 through 26 Processing helix chain 'F' and resid 67 through 89 Processing helix chain 'F' and resid 90 through 94 removed outlier: 3.507A pdb=" N VAL F 94 " --> pdb=" O ARG F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 114 removed outlier: 3.546A pdb=" N LEU F 99 " --> pdb=" O THR F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 171 removed outlier: 4.297A pdb=" N ILE F 163 " --> pdb=" O THR F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 190 Processing helix chain 'F' and resid 227 through 234 removed outlier: 3.699A pdb=" N GLN F 231 " --> pdb=" O GLY F 227 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 26 Processing helix chain 'G' and resid 67 through 89 Processing helix chain 'G' and resid 90 through 94 Processing helix chain 'G' and resid 95 through 114 removed outlier: 3.519A pdb=" N LEU G 99 " --> pdb=" O THR G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 171 removed outlier: 4.493A pdb=" N ILE G 163 " --> pdb=" O THR G 159 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 190 removed outlier: 3.533A pdb=" N ALA G 190 " --> pdb=" O ALA G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 234 removed outlier: 3.585A pdb=" N GLN G 231 " --> pdb=" O GLY G 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 27 Processing helix chain 'H' and resid 67 through 89 Processing helix chain 'H' and resid 90 through 94 Processing helix chain 'H' and resid 95 through 114 removed outlier: 3.545A pdb=" N LEU H 99 " --> pdb=" O THR H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 159 through 171 removed outlier: 3.783A pdb=" N ILE H 163 " --> pdb=" O THR H 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 190 removed outlier: 3.942A pdb=" N ALA H 190 " --> pdb=" O ALA H 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 234 Processing helix chain 'I' and resid 9 through 26 Processing helix chain 'I' and resid 67 through 89 removed outlier: 3.539A pdb=" N PHE I 71 " --> pdb=" O LYS I 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 90 through 94 removed outlier: 3.690A pdb=" N VAL I 94 " --> pdb=" O ARG I 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 95 through 114 Processing helix chain 'I' and resid 159 through 171 removed outlier: 3.839A pdb=" N ILE I 163 " --> pdb=" O THR I 159 " (cutoff:3.500A) Processing helix chain 'I' and resid 176 through 190 removed outlier: 3.859A pdb=" N ALA I 190 " --> pdb=" O ALA I 186 " (cutoff:3.500A) Processing helix chain 'I' and resid 227 through 234 Processing helix chain 'J' and resid 9 through 26 Processing helix chain 'J' and resid 67 through 89 Processing helix chain 'J' and resid 90 through 94 Processing helix chain 'J' and resid 95 through 114 removed outlier: 3.539A pdb=" N LEU J 99 " --> pdb=" O THR J 95 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 171 removed outlier: 4.270A pdb=" N ILE J 163 " --> pdb=" O THR J 159 " (cutoff:3.500A) Processing helix chain 'J' and resid 176 through 190 Processing helix chain 'J' and resid 227 through 234 Processing helix chain 'K' and resid 9 through 26 Processing helix chain 'K' and resid 67 through 89 Processing helix chain 'K' and resid 90 through 94 Processing helix chain 'K' and resid 95 through 114 removed outlier: 3.678A pdb=" N LEU K 99 " --> pdb=" O THR K 95 " (cutoff:3.500A) Processing helix chain 'K' and resid 159 through 171 removed outlier: 4.492A pdb=" N ILE K 163 " --> pdb=" O THR K 159 " (cutoff:3.500A) Processing helix chain 'K' and resid 176 through 190 Processing helix chain 'K' and resid 226 through 234 removed outlier: 3.528A pdb=" N LEU K 230 " --> pdb=" O THR K 226 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 26 Processing helix chain 'L' and resid 67 through 89 Processing helix chain 'L' and resid 90 through 94 Processing helix chain 'L' and resid 95 through 114 removed outlier: 3.506A pdb=" N LEU L 99 " --> pdb=" O THR L 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 160 through 171 Processing helix chain 'L' and resid 176 through 190 Processing helix chain 'L' and resid 227 through 234 Processing helix chain 'M' and resid 9 through 26 Processing helix chain 'M' and resid 67 through 89 Processing helix chain 'M' and resid 90 through 94 Processing helix chain 'M' and resid 95 through 114 removed outlier: 3.579A pdb=" N LEU M 99 " --> pdb=" O THR M 95 " (cutoff:3.500A) Processing helix chain 'M' and resid 159 through 171 removed outlier: 4.473A pdb=" N ILE M 163 " --> pdb=" O THR M 159 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 190 Processing helix chain 'M' and resid 226 through 234 Processing helix chain 'N' and resid 9 through 26 Processing helix chain 'N' and resid 67 through 89 Processing helix chain 'N' and resid 95 through 114 removed outlier: 3.547A pdb=" N LEU N 99 " --> pdb=" O THR N 95 " (cutoff:3.500A) Processing helix chain 'N' and resid 159 through 171 removed outlier: 4.391A pdb=" N ILE N 163 " --> pdb=" O THR N 159 " (cutoff:3.500A) Processing helix chain 'N' and resid 176 through 190 Processing helix chain 'N' and resid 227 through 234 Processing helix chain 'P' and resid 348 through 371 Processing helix chain 'P' and resid 375 through 395 removed outlier: 4.799A pdb=" N ALA P 392 " --> pdb=" O ARG P 388 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ALA P 393 " --> pdb=" O GLY P 389 " (cutoff:3.500A) Processing helix chain 'P' and resid 413 through 416 Processing helix chain 'P' and resid 442 through 454 removed outlier: 3.776A pdb=" N LYS P 452 " --> pdb=" O SER P 448 " (cutoff:3.500A) Processing helix chain 'P' and resid 455 through 457 No H-bonds generated for 'chain 'P' and resid 455 through 457' Processing helix chain 'P' and resid 459 through 478 Processing helix chain 'P' and resid 506 through 522 removed outlier: 3.545A pdb=" N ILE P 510 " --> pdb=" O PRO P 506 " (cutoff:3.500A) Processing helix chain 'Q' and resid 348 through 371 Processing helix chain 'Q' and resid 375 through 389 Processing helix chain 'Q' and resid 390 through 395 Processing helix chain 'Q' and resid 413 through 416 Processing helix chain 'Q' and resid 442 through 454 removed outlier: 3.588A pdb=" N LYS Q 452 " --> pdb=" O SER Q 448 " (cutoff:3.500A) Processing helix chain 'Q' and resid 455 through 457 No H-bonds generated for 'chain 'Q' and resid 455 through 457' Processing helix chain 'Q' and resid 459 through 478 Processing helix chain 'Q' and resid 506 through 522 removed outlier: 3.583A pdb=" N ILE Q 510 " --> pdb=" O PRO Q 506 " (cutoff:3.500A) Processing helix chain 'R' and resid 348 through 371 Processing helix chain 'R' and resid 375 through 395 removed outlier: 4.686A pdb=" N ALA R 392 " --> pdb=" O ARG R 388 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N ALA R 393 " --> pdb=" O GLY R 389 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET R 395 " --> pdb=" O LEU R 391 " (cutoff:3.500A) Processing helix chain 'R' and resid 413 through 416 Processing helix chain 'R' and resid 442 through 454 removed outlier: 3.620A pdb=" N LYS R 452 " --> pdb=" O SER R 448 " (cutoff:3.500A) Processing helix chain 'R' and resid 455 through 457 No H-bonds generated for 'chain 'R' and resid 455 through 457' Processing helix chain 'R' and resid 459 through 478 Processing helix chain 'R' and resid 506 through 522 removed outlier: 3.635A pdb=" N ILE R 510 " --> pdb=" O PRO R 506 " (cutoff:3.500A) Processing helix chain 'S' and resid 348 through 371 Processing helix chain 'S' and resid 375 through 389 Processing helix chain 'S' and resid 390 through 397 Processing helix chain 'S' and resid 413 through 416 Processing helix chain 'S' and resid 442 through 454 removed outlier: 3.724A pdb=" N LYS S 452 " --> pdb=" O SER S 448 " (cutoff:3.500A) Processing helix chain 'S' and resid 455 through 457 No H-bonds generated for 'chain 'S' and resid 455 through 457' Processing helix chain 'S' and resid 459 through 478 Processing helix chain 'S' and resid 506 through 522 removed outlier: 3.588A pdb=" N ILE S 510 " --> pdb=" O PRO S 506 " (cutoff:3.500A) Processing helix chain 'T' and resid 348 through 371 Processing helix chain 'T' and resid 375 through 389 Processing helix chain 'T' and resid 390 through 397 Processing helix chain 'T' and resid 413 through 416 Processing helix chain 'T' and resid 442 through 454 removed outlier: 3.654A pdb=" N LYS T 452 " --> pdb=" O SER T 448 " (cutoff:3.500A) Processing helix chain 'T' and resid 455 through 457 No H-bonds generated for 'chain 'T' and resid 455 through 457' Processing helix chain 'T' and resid 459 through 478 Processing helix chain 'T' and resid 506 through 522 removed outlier: 3.576A pdb=" N ILE T 510 " --> pdb=" O PRO T 506 " (cutoff:3.500A) Processing helix chain 'U' and resid 348 through 371 Processing helix chain 'U' and resid 375 through 389 Processing helix chain 'U' and resid 390 through 396 removed outlier: 3.895A pdb=" N GLN U 396 " --> pdb=" O ALA U 392 " (cutoff:3.500A) Processing helix chain 'U' and resid 413 through 416 Processing helix chain 'U' and resid 442 through 454 removed outlier: 3.928A pdb=" N LYS U 452 " --> pdb=" O SER U 448 " (cutoff:3.500A) Processing helix chain 'U' and resid 455 through 457 No H-bonds generated for 'chain 'U' and resid 455 through 457' Processing helix chain 'U' and resid 459 through 478 Processing helix chain 'U' and resid 506 through 522 removed outlier: 3.594A pdb=" N ILE U 510 " --> pdb=" O PRO U 506 " (cutoff:3.500A) Processing helix chain 'V' and resid 348 through 371 Processing helix chain 'V' and resid 375 through 390 Processing helix chain 'V' and resid 390 through 397 Processing helix chain 'V' and resid 442 through 454 removed outlier: 3.655A pdb=" N LYS V 452 " --> pdb=" O SER V 448 " (cutoff:3.500A) Processing helix chain 'V' and resid 455 through 457 No H-bonds generated for 'chain 'V' and resid 455 through 457' Processing helix chain 'V' and resid 459 through 478 Processing helix chain 'V' and resid 506 through 522 removed outlier: 3.656A pdb=" N ILE V 510 " --> pdb=" O PRO V 506 " (cutoff:3.500A) Processing helix chain 'W' and resid 348 through 371 Processing helix chain 'W' and resid 375 through 390 Processing helix chain 'W' and resid 390 through 395 Processing helix chain 'W' and resid 413 through 416 Processing helix chain 'W' and resid 442 through 454 removed outlier: 3.523A pdb=" N LYS W 452 " --> pdb=" O SER W 448 " (cutoff:3.500A) Processing helix chain 'W' and resid 455 through 457 No H-bonds generated for 'chain 'W' and resid 455 through 457' Processing helix chain 'W' and resid 459 through 478 Processing helix chain 'W' and resid 506 through 522 removed outlier: 3.655A pdb=" N ILE W 510 " --> pdb=" O PRO W 506 " (cutoff:3.500A) Processing helix chain 'X' and resid 348 through 371 Processing helix chain 'X' and resid 375 through 395 removed outlier: 4.666A pdb=" N ALA X 392 " --> pdb=" O ARG X 388 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ALA X 393 " --> pdb=" O GLY X 389 " (cutoff:3.500A) Processing helix chain 'X' and resid 413 through 416 Processing helix chain 'X' and resid 442 through 454 removed outlier: 3.815A pdb=" N LYS X 452 " --> pdb=" O SER X 448 " (cutoff:3.500A) Processing helix chain 'X' and resid 459 through 478 Processing helix chain 'X' and resid 506 through 522 removed outlier: 3.655A pdb=" N ILE X 510 " --> pdb=" O PRO X 506 " (cutoff:3.500A) Processing helix chain 'Y' and resid 348 through 371 Processing helix chain 'Y' and resid 375 through 390 Processing helix chain 'Y' and resid 390 through 397 Processing helix chain 'Y' and resid 413 through 416 Processing helix chain 'Y' and resid 442 through 454 removed outlier: 3.902A pdb=" N LYS Y 452 " --> pdb=" O SER Y 448 " (cutoff:3.500A) Processing helix chain 'Y' and resid 455 through 457 No H-bonds generated for 'chain 'Y' and resid 455 through 457' Processing helix chain 'Y' and resid 459 through 478 Processing helix chain 'Y' and resid 506 through 521 removed outlier: 3.558A pdb=" N ILE Y 510 " --> pdb=" O PRO Y 506 " (cutoff:3.500A) Processing helix chain 'Z' and resid 348 through 371 Processing helix chain 'Z' and resid 375 through 389 Processing helix chain 'Z' and resid 390 through 397 Processing helix chain 'Z' and resid 413 through 416 Processing helix chain 'Z' and resid 442 through 454 removed outlier: 3.685A pdb=" N LYS Z 452 " --> pdb=" O SER Z 448 " (cutoff:3.500A) Processing helix chain 'Z' and resid 455 through 457 No H-bonds generated for 'chain 'Z' and resid 455 through 457' Processing helix chain 'Z' and resid 459 through 478 Processing helix chain 'Z' and resid 506 through 522 removed outlier: 3.657A pdb=" N ILE Z 510 " --> pdb=" O PRO Z 506 " (cutoff:3.500A) Processing helix chain 'a' and resid 348 through 371 Processing helix chain 'a' and resid 375 through 389 Processing helix chain 'a' and resid 390 through 396 Processing helix chain 'a' and resid 413 through 416 Processing helix chain 'a' and resid 442 through 454 removed outlier: 3.671A pdb=" N LYS a 452 " --> pdb=" O SER a 448 " (cutoff:3.500A) Processing helix chain 'a' and resid 455 through 457 No H-bonds generated for 'chain 'a' and resid 455 through 457' Processing helix chain 'a' and resid 459 through 478 Processing helix chain 'a' and resid 506 through 522 removed outlier: 3.545A pdb=" N ILE a 510 " --> pdb=" O PRO a 506 " (cutoff:3.500A) Processing helix chain 'b' and resid 348 through 371 Processing helix chain 'b' and resid 375 through 389 Processing helix chain 'b' and resid 390 through 396 Processing helix chain 'b' and resid 442 through 454 removed outlier: 3.720A pdb=" N LYS b 452 " --> pdb=" O SER b 448 " (cutoff:3.500A) Processing helix chain 'b' and resid 455 through 457 No H-bonds generated for 'chain 'b' and resid 455 through 457' Processing helix chain 'b' and resid 459 through 478 Processing helix chain 'b' and resid 506 through 522 removed outlier: 3.578A pdb=" N ILE b 510 " --> pdb=" O PRO b 506 " (cutoff:3.500A) Processing helix chain 'c' and resid 348 through 371 Processing helix chain 'c' and resid 375 through 390 Processing helix chain 'c' and resid 390 through 396 Processing helix chain 'c' and resid 413 through 416 Processing helix chain 'c' and resid 442 through 454 removed outlier: 3.693A pdb=" N LYS c 452 " --> pdb=" O SER c 448 " (cutoff:3.500A) Processing helix chain 'c' and resid 455 through 457 No H-bonds generated for 'chain 'c' and resid 455 through 457' Processing helix chain 'c' and resid 459 through 478 Processing helix chain 'c' and resid 506 through 522 removed outlier: 3.625A pdb=" N ILE c 510 " --> pdb=" O PRO c 506 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 26 removed outlier: 3.508A pdb=" N ARG O 26 " --> pdb=" O LYS O 22 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 89 Processing helix chain 'O' and resid 90 through 94 removed outlier: 3.590A pdb=" N VAL O 94 " --> pdb=" O ARG O 91 " (cutoff:3.500A) Processing helix chain 'O' and resid 95 through 114 removed outlier: 3.547A pdb=" N LEU O 99 " --> pdb=" O THR O 95 " (cutoff:3.500A) Processing helix chain 'O' and resid 159 through 171 removed outlier: 4.549A pdb=" N ILE O 163 " --> pdb=" O THR O 159 " (cutoff:3.500A) Processing helix chain 'O' and resid 176 through 190 Processing helix chain 'O' and resid 227 through 234 Processing sheet with id=AA1, first strand: chain 'A' and resid 153 through 156 Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 57 removed outlier: 6.487A pdb=" N VAL A 60 " --> pdb=" O LEU A 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 153 through 156 Processing sheet with id=AA4, first strand: chain 'C' and resid 53 through 57 removed outlier: 6.452A pdb=" N VAL C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU C 138 " --> pdb=" O GLU C 150 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 153 through 156 removed outlier: 4.465A pdb=" N VAL D 210 " --> pdb=" O ILE D 225 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 53 through 57 removed outlier: 6.464A pdb=" N VAL D 60 " --> pdb=" O LEU D 56 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU D 138 " --> pdb=" O GLU D 150 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 153 through 156 Processing sheet with id=AA8, first strand: chain 'E' and resid 53 through 57 removed outlier: 6.511A pdb=" N VAL E 60 " --> pdb=" O LEU E 56 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 153 through 156 removed outlier: 4.643A pdb=" N VAL F 210 " --> pdb=" O ILE F 225 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 53 through 57 removed outlier: 6.507A pdb=" N VAL F 60 " --> pdb=" O LEU F 56 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 153 through 156 Processing sheet with id=AB3, first strand: chain 'G' and resid 53 through 57 removed outlier: 6.453A pdb=" N VAL G 60 " --> pdb=" O LEU G 56 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU G 138 " --> pdb=" O GLU G 150 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 153 through 156 Processing sheet with id=AB5, first strand: chain 'H' and resid 53 through 57 removed outlier: 6.475A pdb=" N VAL H 60 " --> pdb=" O LEU H 56 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 153 through 156 Processing sheet with id=AB7, first strand: chain 'I' and resid 53 through 57 removed outlier: 6.406A pdb=" N VAL I 60 " --> pdb=" O LEU I 56 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU I 138 " --> pdb=" O GLU I 150 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 153 through 156 Processing sheet with id=AB9, first strand: chain 'J' and resid 53 through 57 removed outlier: 6.519A pdb=" N VAL J 60 " --> pdb=" O LEU J 56 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU J 138 " --> pdb=" O GLU J 150 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 153 through 156 removed outlier: 4.314A pdb=" N VAL K 210 " --> pdb=" O ILE K 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 53 through 57 removed outlier: 6.496A pdb=" N VAL K 60 " --> pdb=" O LEU K 56 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU K 138 " --> pdb=" O GLU K 150 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 153 through 156 removed outlier: 4.371A pdb=" N VAL L 210 " --> pdb=" O ILE L 225 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 53 through 57 removed outlier: 6.509A pdb=" N VAL L 60 " --> pdb=" O LEU L 56 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU L 138 " --> pdb=" O GLU L 150 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'M' and resid 153 through 156 removed outlier: 4.117A pdb=" N VAL M 210 " --> pdb=" O ILE M 225 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 53 through 57 removed outlier: 6.421A pdb=" N VAL M 60 " --> pdb=" O LEU M 56 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU M 138 " --> pdb=" O GLU M 150 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'N' and resid 153 through 156 removed outlier: 4.357A pdb=" N VAL N 210 " --> pdb=" O ILE N 225 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'N' and resid 53 through 57 removed outlier: 6.510A pdb=" N VAL N 60 " --> pdb=" O LEU N 56 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU N 138 " --> pdb=" O GLU N 150 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'P' and resid 436 through 440 Processing sheet with id=AD1, first strand: chain 'P' and resid 320 through 322 removed outlier: 6.415A pdb=" N SER P 320 " --> pdb=" O SER P 327 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'P' and resid 334 through 338 removed outlier: 6.585A pdb=" N THR P 341 " --> pdb=" O THR P 337 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE P 423 " --> pdb=" O PRO P 402 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'Q' and resid 436 through 440 Processing sheet with id=AD4, first strand: chain 'Q' and resid 320 through 322 removed outlier: 6.431A pdb=" N GLN Q 322 " --> pdb=" O ILE Q 326 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ILE Q 326 " --> pdb=" O GLN Q 322 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'Q' and resid 334 through 338 removed outlier: 6.561A pdb=" N THR Q 341 " --> pdb=" O THR Q 337 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE Q 423 " --> pdb=" O PRO Q 402 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ILE Q 420 " --> pdb=" O GLU Q 432 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'R' and resid 436 through 440 Processing sheet with id=AD7, first strand: chain 'R' and resid 320 through 322 removed outlier: 6.477A pdb=" N SER R 320 " --> pdb=" O SER R 327 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'R' and resid 334 through 338 removed outlier: 6.633A pdb=" N THR R 341 " --> pdb=" O THR R 337 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE R 423 " --> pdb=" O PRO R 402 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'S' and resid 436 through 440 Processing sheet with id=AE1, first strand: chain 'S' and resid 320 through 322 removed outlier: 6.306A pdb=" N SER S 320 " --> pdb=" O SER S 327 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N MET S 325 " --> pdb=" O GLN S 322 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'S' and resid 334 through 338 removed outlier: 6.539A pdb=" N THR S 341 " --> pdb=" O THR S 337 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE S 423 " --> pdb=" O PRO S 402 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ILE S 420 " --> pdb=" O GLU S 432 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'T' and resid 436 through 440 Processing sheet with id=AE4, first strand: chain 'T' and resid 320 through 322 removed outlier: 6.400A pdb=" N SER T 320 " --> pdb=" O SER T 327 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'T' and resid 334 through 338 removed outlier: 6.551A pdb=" N THR T 341 " --> pdb=" O THR T 337 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE T 423 " --> pdb=" O PRO T 402 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'U' and resid 436 through 440 Processing sheet with id=AE7, first strand: chain 'U' and resid 320 through 322 removed outlier: 6.448A pdb=" N SER U 320 " --> pdb=" O SER U 327 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'U' and resid 334 through 338 removed outlier: 6.596A pdb=" N THR U 341 " --> pdb=" O THR U 337 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE U 423 " --> pdb=" O PRO U 402 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'V' and resid 436 through 440 Processing sheet with id=AF1, first strand: chain 'V' and resid 320 through 322 removed outlier: 6.375A pdb=" N GLN V 322 " --> pdb=" O ILE V 326 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ILE V 326 " --> pdb=" O GLN V 322 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'V' and resid 334 through 338 removed outlier: 6.587A pdb=" N THR V 341 " --> pdb=" O THR V 337 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE V 423 " --> pdb=" O PRO V 402 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'W' and resid 436 through 440 Processing sheet with id=AF4, first strand: chain 'W' and resid 320 through 322 removed outlier: 6.377A pdb=" N SER W 320 " --> pdb=" O SER W 327 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET W 325 " --> pdb=" O GLN W 322 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'W' and resid 334 through 338 removed outlier: 6.470A pdb=" N THR W 341 " --> pdb=" O THR W 337 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE W 423 " --> pdb=" O PRO W 402 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'X' and resid 436 through 440 Processing sheet with id=AF7, first strand: chain 'X' and resid 320 through 322 removed outlier: 6.496A pdb=" N GLN X 322 " --> pdb=" O ILE X 326 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N ILE X 326 " --> pdb=" O GLN X 322 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'X' and resid 334 through 338 removed outlier: 6.504A pdb=" N THR X 341 " --> pdb=" O THR X 337 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE X 423 " --> pdb=" O PRO X 402 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Y' and resid 436 through 440 Processing sheet with id=AG1, first strand: chain 'Y' and resid 320 through 322 removed outlier: 6.485A pdb=" N SER Y 320 " --> pdb=" O SER Y 327 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'Y' and resid 334 through 338 removed outlier: 6.562A pdb=" N THR Y 341 " --> pdb=" O THR Y 337 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE Y 423 " --> pdb=" O PRO Y 402 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'Z' and resid 436 through 440 Processing sheet with id=AG4, first strand: chain 'Z' and resid 320 through 322 removed outlier: 6.463A pdb=" N GLN Z 322 " --> pdb=" O ILE Z 326 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N ILE Z 326 " --> pdb=" O GLN Z 322 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'Z' and resid 334 through 336 removed outlier: 3.790A pdb=" N PHE Z 423 " --> pdb=" O PRO Z 402 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'a' and resid 436 through 440 Processing sheet with id=AG7, first strand: chain 'a' and resid 320 through 322 removed outlier: 6.302A pdb=" N SER a 320 " --> pdb=" O SER a 327 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N MET a 325 " --> pdb=" O GLN a 322 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'a' and resid 334 through 338 removed outlier: 6.463A pdb=" N THR a 341 " --> pdb=" O THR a 337 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE a 423 " --> pdb=" O PRO a 402 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'b' and resid 436 through 440 Processing sheet with id=AH1, first strand: chain 'b' and resid 320 through 322 removed outlier: 6.397A pdb=" N SER b 320 " --> pdb=" O SER b 327 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'b' and resid 334 through 338 removed outlier: 6.532A pdb=" N THR b 341 " --> pdb=" O THR b 337 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE b 423 " --> pdb=" O PRO b 402 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'c' and resid 436 through 440 Processing sheet with id=AH4, first strand: chain 'c' and resid 320 through 322 removed outlier: 6.456A pdb=" N SER c 320 " --> pdb=" O SER c 327 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'c' and resid 334 through 338 removed outlier: 6.583A pdb=" N THR c 341 " --> pdb=" O THR c 337 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE c 423 " --> pdb=" O PRO c 402 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'O' and resid 153 through 156 removed outlier: 4.233A pdb=" N VAL O 210 " --> pdb=" O ILE O 225 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'O' and resid 53 through 57 removed outlier: 6.484A pdb=" N VAL O 60 " --> pdb=" O LEU O 56 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU O 138 " --> pdb=" O GLU O 150 " (cutoff:3.500A) 3042 hydrogen bonds defined for protein. 8718 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 20.51 Time building geometry restraints manager: 19.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 15718 1.34 - 1.46: 7775 1.46 - 1.58: 23362 1.58 - 1.70: 1 1.70 - 1.82: 210 Bond restraints: 47066 Sorted by residual: bond pdb=" N VAL Y 439 " pdb=" CA VAL Y 439 " ideal model delta sigma weight residual 1.456 1.495 -0.040 1.15e-02 7.56e+03 1.18e+01 bond pdb=" N VAL D 30 " pdb=" CA VAL D 30 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.14e-02 7.69e+03 1.06e+01 bond pdb=" N ILE R 420 " pdb=" CA ILE R 420 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.17e-02 7.31e+03 9.80e+00 bond pdb=" N VAL H 155 " pdb=" CA VAL H 155 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.20e-02 6.94e+03 9.76e+00 bond pdb=" N ILE c 431 " pdb=" CA ILE c 431 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.10e-02 8.26e+03 9.58e+00 ... (remaining 47061 not shown) Histogram of bond angle deviations from ideal: 96.61 - 104.08: 519 104.08 - 111.56: 20855 111.56 - 119.03: 16625 119.03 - 126.50: 25410 126.50 - 133.98: 295 Bond angle restraints: 63704 Sorted by residual: angle pdb=" O TYR D 89 " pdb=" C TYR D 89 " pdb=" N ASP D 90 " ideal model delta sigma weight residual 120.83 124.17 -3.34 7.40e-01 1.83e+00 2.03e+01 angle pdb=" CA PRO D 151 " pdb=" N PRO D 151 " pdb=" CD PRO D 151 " ideal model delta sigma weight residual 112.00 105.90 6.10 1.40e+00 5.10e-01 1.90e+01 angle pdb=" CA GLY H 157 " pdb=" C GLY H 157 " pdb=" O GLY H 157 " ideal model delta sigma weight residual 122.39 118.48 3.91 9.30e-01 1.16e+00 1.76e+01 angle pdb=" CA GLY b 418 " pdb=" C GLY b 418 " pdb=" O GLY b 418 " ideal model delta sigma weight residual 121.41 117.99 3.42 8.80e-01 1.29e+00 1.51e+01 angle pdb=" C GLN E 11 " pdb=" N ALA E 12 " pdb=" CA ALA E 12 " ideal model delta sigma weight residual 120.28 125.82 -5.54 1.44e+00 4.82e-01 1.48e+01 ... (remaining 63699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 25314 17.99 - 35.97: 2275 35.97 - 53.96: 595 53.96 - 71.95: 104 71.95 - 89.93: 47 Dihedral angle restraints: 28335 sinusoidal: 10807 harmonic: 17528 Sorted by residual: dihedral pdb=" CA VAL A 212 " pdb=" C VAL A 212 " pdb=" N LEU A 213 " pdb=" CA LEU A 213 " ideal model delta harmonic sigma weight residual 180.00 155.51 24.49 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA VAL O 212 " pdb=" C VAL O 212 " pdb=" N LEU O 213 " pdb=" CA LEU O 213 " ideal model delta harmonic sigma weight residual 180.00 156.10 23.90 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA VAL J 212 " pdb=" C VAL J 212 " pdb=" N LEU J 213 " pdb=" CA LEU J 213 " ideal model delta harmonic sigma weight residual 180.00 156.18 23.82 0 5.00e+00 4.00e-02 2.27e+01 ... (remaining 28332 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 5513 0.048 - 0.096: 1299 0.096 - 0.144: 394 0.144 - 0.191: 38 0.191 - 0.239: 7 Chirality restraints: 7251 Sorted by residual: chirality pdb=" CA ALA E 12 " pdb=" N ALA E 12 " pdb=" C ALA E 12 " pdb=" CB ALA E 12 " both_signs ideal model delta sigma weight residual False 2.48 2.25 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA VAL D 30 " pdb=" N VAL D 30 " pdb=" C VAL D 30 " pdb=" CB VAL D 30 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA ILE c 420 " pdb=" N ILE c 420 " pdb=" C ILE c 420 " pdb=" CB ILE c 420 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 7248 not shown) Planarity restraints: 8400 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP Y 413 " -0.064 5.00e-02 4.00e+02 9.65e-02 1.49e+01 pdb=" N PRO Y 414 " 0.167 5.00e-02 4.00e+02 pdb=" CA PRO Y 414 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO Y 414 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR I 118 " 0.028 2.00e-02 2.50e+03 2.10e-02 8.82e+00 pdb=" CG TYR I 118 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR I 118 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR I 118 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR I 118 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR I 118 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR I 118 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR I 118 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU D 150 " -0.041 5.00e-02 4.00e+02 5.98e-02 5.73e+00 pdb=" N PRO D 151 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO D 151 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 151 " -0.034 5.00e-02 4.00e+02 ... (remaining 8397 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3238 2.74 - 3.28: 44324 3.28 - 3.82: 79864 3.82 - 4.36: 94799 4.36 - 4.90: 166365 Nonbonded interactions: 388590 Sorted by model distance: nonbonded pdb=" O ALA A 34 " pdb=" OH TYR A 171 " model vdw 2.197 2.440 nonbonded pdb=" OG SER E 29 " pdb=" O GLY E 157 " model vdw 2.198 2.440 nonbonded pdb=" O ALA G 166 " pdb=" OG SER G 170 " model vdw 2.204 2.440 nonbonded pdb=" OG1 THR A 142 " pdb=" OD1 ASP A 144 " model vdw 2.207 2.440 nonbonded pdb=" NH2 ARG R 329 " pdb=" O ASP a 476 " model vdw 2.209 2.520 ... (remaining 388585 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } ncs_group { reference = (chain 'P' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'Q' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'R' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'S' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = chain 'T' selection = (chain 'U' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'V' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'W' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'X' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'Y' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'Z' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'a' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'b' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'c' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) } ncs_group { reference = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.790 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: 0.040 Extract box with map and model: 31.310 Check model and map are aligned: 0.720 Set scattering table: 0.460 Process input model: 120.500 Find NCS groups from input model: 3.520 Set up NCS constraints: 0.390 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:10.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 174.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 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 : 0.004 0.117 47066 Z= 0.248 Angle : 0.599 9.244 63704 Z= 0.349 Chirality : 0.045 0.239 7251 Planarity : 0.004 0.096 8400 Dihedral : 15.251 89.932 17177 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.53 % Allowed : 13.28 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.11), residues: 6048 helix: 2.27 (0.10), residues: 2520 sheet: 0.79 (0.13), residues: 1526 loop : -0.21 (0.13), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP V 429 HIS 0.004 0.001 HIS X 365 PHE 0.032 0.002 PHE M 71 TYR 0.049 0.001 TYR I 118 ARG 0.008 0.000 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 4641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 659 time to evaluate : 5.350 Fit side-chains revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8122 (mt0) cc_final: 0.7908 (mt0) REVERT: A 90 ASP cc_start: 0.8403 (t70) cc_final: 0.8159 (t70) REVERT: C 80 GLN cc_start: 0.7996 (tm-30) cc_final: 0.7367 (mt0) REVERT: C 118 TYR cc_start: 0.7446 (m-10) cc_final: 0.7167 (m-10) REVERT: C 135 ARG cc_start: 0.7171 (ttm110) cc_final: 0.6532 (mtt90) REVERT: D 134 LYS cc_start: 0.7240 (tmtt) cc_final: 0.6768 (pptt) REVERT: E 80 GLN cc_start: 0.7959 (tp40) cc_final: 0.7745 (mm-40) REVERT: E 137 GLU cc_start: 0.6971 (mp0) cc_final: 0.6747 (pm20) REVERT: F 21 ARG cc_start: 0.6183 (ptp90) cc_final: 0.5843 (ttp-170) REVERT: F 53 ILE cc_start: 0.8437 (mm) cc_final: 0.8173 (mt) REVERT: F 209 GLU cc_start: 0.6787 (tt0) cc_final: 0.6559 (tt0) REVERT: G 26 ARG cc_start: 0.6949 (ptt-90) cc_final: 0.6669 (ptt180) REVERT: G 169 GLU cc_start: 0.6172 (mm-30) cc_final: 0.4988 (tp30) REVERT: H 67 LYS cc_start: 0.7607 (tttt) cc_final: 0.7362 (tttm) REVERT: H 121 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7238 (tm-30) REVERT: H 152 HIS cc_start: 0.7231 (m90) cc_final: 0.6462 (m90) REVERT: I 70 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.7012 (mt-10) REVERT: I 153 PHE cc_start: 0.6840 (p90) cc_final: 0.6383 (p90) REVERT: I 159 THR cc_start: 0.6372 (p) cc_final: 0.5644 (t) REVERT: J 182 ARG cc_start: 0.6043 (mtt90) cc_final: 0.5784 (tpp-160) REVERT: J 214 ASP cc_start: 0.7895 (t0) cc_final: 0.7450 (t70) REVERT: M 13 MET cc_start: 0.7915 (mmm) cc_final: 0.7450 (mmp) REVERT: N 54 SER cc_start: 0.9163 (OUTLIER) cc_final: 0.8846 (p) REVERT: N 168 LYS cc_start: 0.7997 (ttmt) cc_final: 0.7153 (tppt) REVERT: R 354 GLU cc_start: 0.7527 (tt0) cc_final: 0.7246 (tt0) REVERT: T 339 ASP cc_start: 0.7866 (OUTLIER) cc_final: 0.7479 (m-30) REVERT: U 386 MET cc_start: 0.8922 (ttm) cc_final: 0.8692 (ttm) REVERT: V 364 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7587 (mt-10) REVERT: X 325 MET cc_start: 0.8055 (ttp) cc_final: 0.7575 (tpp) REVERT: Y 341 THR cc_start: 0.8949 (p) cc_final: 0.8674 (t) REVERT: Y 500 ASP cc_start: 0.8123 (m-30) cc_final: 0.7843 (m-30) REVERT: Z 324 ASN cc_start: 0.7863 (m-40) cc_final: 0.7504 (p0) REVERT: Z 500 ASP cc_start: 0.8269 (m-30) cc_final: 0.8044 (m-30) REVERT: c 325 MET cc_start: 0.8126 (ttp) cc_final: 0.7897 (tmt) outliers start: 71 outliers final: 23 residues processed: 708 average time/residue: 1.6014 time to fit residues: 1399.2951 Evaluate side-chains 558 residues out of total 4641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 531 time to evaluate : 5.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain H residue 121 GLU Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain I residue 70 GLU Chi-restraints excluded: chain I residue 209 GLU Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 133 THR Chi-restraints excluded: chain N residue 159 THR Chi-restraints excluded: chain N residue 226 THR Chi-restraints excluded: chain T residue 339 ASP Chi-restraints excluded: chain U residue 301 THR Chi-restraints excluded: chain W residue 301 THR Chi-restraints excluded: chain W residue 409 ILE Chi-restraints excluded: chain X residue 401 LEU Chi-restraints excluded: chain Y residue 330 ASP Chi-restraints excluded: chain a residue 416 SER Chi-restraints excluded: chain a residue 503 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 508 optimal weight: 4.9990 chunk 456 optimal weight: 7.9990 chunk 253 optimal weight: 6.9990 chunk 155 optimal weight: 8.9990 chunk 307 optimal weight: 1.9990 chunk 243 optimal weight: 2.9990 chunk 471 optimal weight: 4.9990 chunk 182 optimal weight: 10.0000 chunk 286 optimal weight: 0.9980 chunk 351 optimal weight: 0.8980 chunk 546 optimal weight: 4.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 105 GLN C 73 ASN D 11 GLN D 51 GLN E 105 GLN E 165 ASN F 45 ASN F 51 GLN G 73 ASN H 80 GLN J 11 GLN J 73 ASN J 165 ASN K 129 HIS K 216 ASN L 105 GLN L 165 ASN L 174 ASN M 105 GLN N 45 ASN N 80 GLN P 322 GLN P 390 ASN Q 390 ASN S 324 ASN S 390 ASN T 437 GLN U 365 HIS U 437 GLN V 437 GLN ** X 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 456 GLN Y 437 GLN Z 365 HIS b 324 ASN b 390 ASN c 322 GLN c 396 GLN d 172 GLN O 152 HIS O 231 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 47066 Z= 0.271 Angle : 0.542 8.951 63704 Z= 0.288 Chirality : 0.044 0.224 7251 Planarity : 0.004 0.066 8400 Dihedral : 4.841 110.364 6894 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.21 % Allowed : 14.94 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.11), residues: 6048 helix: 2.48 (0.10), residues: 2548 sheet: 0.84 (0.13), residues: 1526 loop : -0.11 (0.14), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Z 429 HIS 0.005 0.001 HIS R 410 PHE 0.034 0.003 PHE L 71 TYR 0.014 0.001 TYR J 171 ARG 0.011 0.000 ARG E 14 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 709 residues out of total 4641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 560 time to evaluate : 5.340 Fit side-chains revert: symmetry clash REVERT: A 161 GLU cc_start: 0.7576 (mm-30) cc_final: 0.6980 (mp0) REVERT: C 80 GLN cc_start: 0.8206 (tm-30) cc_final: 0.7530 (mt0) REVERT: D 113 GLU cc_start: 0.6302 (mt-10) cc_final: 0.5973 (mp0) REVERT: D 134 LYS cc_start: 0.7310 (tmtt) cc_final: 0.6920 (pptt) REVERT: D 203 LEU cc_start: 0.5788 (OUTLIER) cc_final: 0.5333 (tp) REVERT: E 13 MET cc_start: 0.6275 (mmm) cc_final: 0.5088 (mmp) REVERT: E 80 GLN cc_start: 0.8160 (tp40) cc_final: 0.7833 (tp-100) REVERT: E 113 GLU cc_start: 0.5846 (tt0) cc_final: 0.5302 (mt-10) REVERT: E 121 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.7051 (mm-30) REVERT: E 165 ASN cc_start: 0.5803 (m-40) cc_final: 0.5476 (m110) REVERT: F 29 SER cc_start: 0.6716 (m) cc_final: 0.6413 (p) REVERT: F 70 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7293 (mm-30) REVERT: F 80 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7653 (tm-30) REVERT: F 116 LYS cc_start: 0.6057 (OUTLIER) cc_final: 0.5460 (tmmt) REVERT: G 176 SER cc_start: 0.7620 (m) cc_final: 0.7050 (p) REVERT: H 33 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7376 (pp) REVERT: H 152 HIS cc_start: 0.7301 (m90) cc_final: 0.6453 (m90) REVERT: I 70 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7295 (mm-30) REVERT: K 168 LYS cc_start: 0.7879 (mtpp) cc_final: 0.7275 (mttt) REVERT: M 80 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.7761 (tm-30) REVERT: M 137 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7792 (mt-10) REVERT: M 149 ASP cc_start: 0.7753 (t0) cc_final: 0.7517 (t0) REVERT: N 14 ARG cc_start: 0.6678 (ttp-110) cc_final: 0.6407 (ttp80) REVERT: N 21 ARG cc_start: 0.7331 (ttp-110) cc_final: 0.7005 (ttm-80) REVERT: N 168 LYS cc_start: 0.7996 (ttmt) cc_final: 0.7151 (tppt) REVERT: P 339 ASP cc_start: 0.7958 (t0) cc_final: 0.7625 (t0) REVERT: P 413 ASP cc_start: 0.7424 (OUTLIER) cc_final: 0.6979 (p0) REVERT: Q 357 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.7631 (mtp85) REVERT: S 361 VAL cc_start: 0.9030 (t) cc_final: 0.8744 (t) REVERT: T 339 ASP cc_start: 0.8126 (m-30) cc_final: 0.7856 (m-30) REVERT: U 395 MET cc_start: 0.7012 (OUTLIER) cc_final: 0.6320 (mpt) REVERT: X 325 MET cc_start: 0.8226 (ttp) cc_final: 0.7748 (tpp) REVERT: X 512 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7636 (mt-10) REVERT: Z 500 ASP cc_start: 0.8443 (m-30) cc_final: 0.8224 (m-30) REVERT: a 325 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.7696 (tmm) REVERT: O 15 GLU cc_start: 0.6914 (OUTLIER) cc_final: 0.6085 (mt-10) REVERT: O 51 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7728 (mm-40) outliers start: 149 outliers final: 51 residues processed: 648 average time/residue: 1.5976 time to fit residues: 1278.3915 Evaluate side-chains 593 residues out of total 4641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 526 time to evaluate : 4.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain E residue 22 LYS Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain E residue 153 PHE Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 80 GLN Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 144 ASP Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain G residue 174 ASN Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 73 ASN Chi-restraints excluded: chain I residue 70 GLU Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain J residue 178 THR Chi-restraints excluded: chain K residue 226 THR Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 160 THR Chi-restraints excluded: chain L residue 163 ILE Chi-restraints excluded: chain M residue 80 GLN Chi-restraints excluded: chain M residue 137 GLU Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 114 GLN Chi-restraints excluded: chain N residue 179 ASP Chi-restraints excluded: chain P residue 301 THR Chi-restraints excluded: chain P residue 354 GLU Chi-restraints excluded: chain P residue 413 ASP Chi-restraints excluded: chain Q residue 357 ARG Chi-restraints excluded: chain Q residue 401 LEU Chi-restraints excluded: chain S residue 503 VAL Chi-restraints excluded: chain T residue 430 ASN Chi-restraints excluded: chain U residue 301 THR Chi-restraints excluded: chain U residue 325 MET Chi-restraints excluded: chain U residue 355 PHE Chi-restraints excluded: chain U residue 395 MET Chi-restraints excluded: chain U residue 430 ASN Chi-restraints excluded: chain V residue 301 THR Chi-restraints excluded: chain V residue 364 GLU Chi-restraints excluded: chain V residue 433 GLU Chi-restraints excluded: chain W residue 401 LEU Chi-restraints excluded: chain X residue 301 THR Chi-restraints excluded: chain X residue 330 ASP Chi-restraints excluded: chain X residue 409 ILE Chi-restraints excluded: chain X residue 512 GLU Chi-restraints excluded: chain Y residue 313 VAL Chi-restraints excluded: chain Y residue 330 ASP Chi-restraints excluded: chain Y residue 339 ASP Chi-restraints excluded: chain Y residue 355 PHE Chi-restraints excluded: chain Y residue 401 LEU Chi-restraints excluded: chain Y residue 503 VAL Chi-restraints excluded: chain Z residue 321 THR Chi-restraints excluded: chain Z residue 512 GLU Chi-restraints excluded: chain a residue 325 MET Chi-restraints excluded: chain a residue 339 ASP Chi-restraints excluded: chain c residue 430 ASN Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain O residue 51 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 303 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 454 optimal weight: 2.9990 chunk 372 optimal weight: 8.9990 chunk 150 optimal weight: 0.7980 chunk 547 optimal weight: 9.9990 chunk 591 optimal weight: 9.9990 chunk 487 optimal weight: 0.9980 chunk 543 optimal weight: 0.9990 chunk 186 optimal weight: 10.0000 chunk 439 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN C 73 ASN D 51 GLN F 45 ASN F 51 GLN F 101 ASN H 80 GLN J 73 ASN K 216 ASN L 165 ASN L 174 ASN M 105 GLN M 216 ASN N 45 ASN N 80 GLN P 322 GLN P 390 ASN S 324 ASN X 322 GLN b 390 ASN c 322 GLN O 80 GLN O 231 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 47066 Z= 0.210 Angle : 0.490 7.472 63704 Z= 0.260 Chirality : 0.043 0.175 7251 Planarity : 0.004 0.057 8400 Dihedral : 4.365 108.123 6865 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.28 % Allowed : 16.16 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.11), residues: 6048 helix: 2.75 (0.10), residues: 2534 sheet: 0.86 (0.14), residues: 1526 loop : -0.02 (0.14), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP c 429 HIS 0.004 0.001 HIS Q 365 PHE 0.033 0.002 PHE M 71 TYR 0.011 0.001 TYR C 143 ARG 0.011 0.000 ARG E 14 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 4641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 554 time to evaluate : 5.761 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 161 GLU cc_start: 0.7567 (mm-30) cc_final: 0.6981 (mp0) REVERT: C 18 GLU cc_start: 0.6833 (OUTLIER) cc_final: 0.6571 (pt0) REVERT: C 132 GLU cc_start: 0.6963 (OUTLIER) cc_final: 0.6268 (mt-10) REVERT: D 13 MET cc_start: 0.6183 (tpp) cc_final: 0.5463 (tmm) REVERT: D 52 LYS cc_start: 0.7842 (OUTLIER) cc_final: 0.7611 (mtpm) REVERT: D 113 GLU cc_start: 0.6347 (mt-10) cc_final: 0.6010 (mp0) REVERT: D 134 LYS cc_start: 0.7270 (tmtt) cc_final: 0.6783 (pptt) REVERT: D 135 ARG cc_start: 0.6577 (OUTLIER) cc_final: 0.6325 (ttp80) REVERT: E 13 MET cc_start: 0.6226 (mmm) cc_final: 0.4938 (mmp) REVERT: E 21 ARG cc_start: 0.6436 (OUTLIER) cc_final: 0.6218 (tmm160) REVERT: E 80 GLN cc_start: 0.8147 (tp40) cc_final: 0.7797 (tp-100) REVERT: E 113 GLU cc_start: 0.5749 (tt0) cc_final: 0.5275 (mt-10) REVERT: E 165 ASN cc_start: 0.5673 (m-40) cc_final: 0.5392 (m-40) REVERT: F 29 SER cc_start: 0.6844 (m) cc_final: 0.6520 (p) REVERT: F 70 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7224 (mm-30) REVERT: F 116 LYS cc_start: 0.6014 (OUTLIER) cc_final: 0.5300 (tmmt) REVERT: G 97 ARG cc_start: 0.7764 (OUTLIER) cc_final: 0.7055 (ttm170) REVERT: G 112 THR cc_start: 0.7495 (m) cc_final: 0.7028 (p) REVERT: G 169 GLU cc_start: 0.6803 (OUTLIER) cc_final: 0.5292 (tp30) REVERT: H 33 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7315 (pp) REVERT: H 152 HIS cc_start: 0.7379 (m90) cc_final: 0.6540 (m90) REVERT: I 159 THR cc_start: 0.6426 (OUTLIER) cc_final: 0.5707 (t) REVERT: M 80 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.7770 (tm-30) REVERT: M 105 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.8177 (mp-120) REVERT: M 149 ASP cc_start: 0.7711 (t0) cc_final: 0.7439 (t0) REVERT: N 14 ARG cc_start: 0.6649 (ttp-110) cc_final: 0.6340 (ttp80) REVERT: N 21 ARG cc_start: 0.7442 (ttp-110) cc_final: 0.7135 (ttm-80) REVERT: N 168 LYS cc_start: 0.8045 (ttmt) cc_final: 0.7230 (tptp) REVERT: P 521 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7850 (mpt-90) REVERT: Q 357 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.7658 (ttp80) REVERT: S 361 VAL cc_start: 0.9019 (t) cc_final: 0.8752 (t) REVERT: T 339 ASP cc_start: 0.8137 (m-30) cc_final: 0.7869 (m-30) REVERT: T 430 ASN cc_start: 0.8023 (OUTLIER) cc_final: 0.7782 (m110) REVERT: T 509 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.6800 (tpt-90) REVERT: U 395 MET cc_start: 0.7108 (OUTLIER) cc_final: 0.6435 (mpt) REVERT: U 401 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8173 (tt) REVERT: W 509 ARG cc_start: 0.7707 (OUTLIER) cc_final: 0.7054 (ttp-170) REVERT: X 512 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7676 (mt-10) REVERT: Z 432 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7359 (mp0) REVERT: Z 500 ASP cc_start: 0.8523 (m-30) cc_final: 0.8319 (m-30) REVERT: O 15 GLU cc_start: 0.6850 (OUTLIER) cc_final: 0.6047 (mt-10) REVERT: O 51 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7748 (mm-40) outliers start: 152 outliers final: 57 residues processed: 637 average time/residue: 1.6490 time to fit residues: 1292.0949 Evaluate side-chains 614 residues out of total 4641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 533 time to evaluate : 5.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 52 LYS Chi-restraints excluded: chain D residue 135 ARG Chi-restraints excluded: chain E residue 21 ARG Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 146 SER Chi-restraints excluded: chain G residue 97 ARG Chi-restraints excluded: chain G residue 169 GLU Chi-restraints excluded: chain G residue 174 ASN Chi-restraints excluded: chain G residue 209 GLU Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 168 LYS Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 159 THR Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain J residue 178 THR Chi-restraints excluded: chain K residue 226 THR Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 54 SER Chi-restraints excluded: chain M residue 80 GLN Chi-restraints excluded: chain M residue 105 GLN Chi-restraints excluded: chain N residue 179 ASP Chi-restraints excluded: chain P residue 301 THR Chi-restraints excluded: chain P residue 354 GLU Chi-restraints excluded: chain P residue 372 VAL Chi-restraints excluded: chain P residue 521 ARG Chi-restraints excluded: chain Q residue 357 ARG Chi-restraints excluded: chain Q residue 401 LEU Chi-restraints excluded: chain S residue 401 LEU Chi-restraints excluded: chain S residue 503 VAL Chi-restraints excluded: chain T residue 430 ASN Chi-restraints excluded: chain T residue 509 ARG Chi-restraints excluded: chain U residue 301 THR Chi-restraints excluded: chain U residue 325 MET Chi-restraints excluded: chain U residue 354 GLU Chi-restraints excluded: chain U residue 355 PHE Chi-restraints excluded: chain U residue 395 MET Chi-restraints excluded: chain U residue 401 LEU Chi-restraints excluded: chain V residue 301 THR Chi-restraints excluded: chain V residue 364 GLU Chi-restraints excluded: chain V residue 433 GLU Chi-restraints excluded: chain W residue 330 ASP Chi-restraints excluded: chain W residue 401 LEU Chi-restraints excluded: chain W residue 509 ARG Chi-restraints excluded: chain X residue 301 THR Chi-restraints excluded: chain X residue 355 PHE Chi-restraints excluded: chain X residue 401 LEU Chi-restraints excluded: chain X residue 409 ILE Chi-restraints excluded: chain X residue 512 GLU Chi-restraints excluded: chain Y residue 313 VAL Chi-restraints excluded: chain Y residue 325 MET Chi-restraints excluded: chain Y residue 330 ASP Chi-restraints excluded: chain Z residue 330 ASP Chi-restraints excluded: chain Z residue 432 GLU Chi-restraints excluded: chain Z residue 512 GLU Chi-restraints excluded: chain a residue 339 ASP Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain a residue 430 ASN Chi-restraints excluded: chain a residue 504 ASP Chi-restraints excluded: chain c residue 364 GLU Chi-restraints excluded: chain c residue 430 ASN Chi-restraints excluded: chain c residue 500 ASP Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain O residue 51 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 541 optimal weight: 10.0000 chunk 411 optimal weight: 1.9990 chunk 284 optimal weight: 8.9990 chunk 60 optimal weight: 9.9990 chunk 261 optimal weight: 0.8980 chunk 367 optimal weight: 8.9990 chunk 549 optimal weight: 0.8980 chunk 581 optimal weight: 0.5980 chunk 287 optimal weight: 0.8980 chunk 520 optimal weight: 6.9990 chunk 156 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN D 51 GLN F 45 ASN H 80 GLN J 165 ASN K 216 ASN L 165 ASN L 174 ASN N 45 ASN N 80 GLN P 322 GLN P 390 ASN P 415 GLN S 324 ASN X 322 GLN b 390 ASN c 322 GLN h 172 GLN O 80 GLN O 231 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 47066 Z= 0.138 Angle : 0.450 7.069 63704 Z= 0.241 Chirality : 0.042 0.168 7251 Planarity : 0.003 0.050 8400 Dihedral : 3.894 73.142 6860 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.06 % Allowed : 17.41 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.11), residues: 6048 helix: 2.95 (0.10), residues: 2548 sheet: 0.92 (0.14), residues: 1526 loop : 0.04 (0.14), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP T 429 HIS 0.003 0.001 HIS Q 365 PHE 0.031 0.002 PHE D 71 TYR 0.013 0.001 TYR C 143 ARG 0.013 0.000 ARG E 14 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 719 residues out of total 4641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 577 time to evaluate : 5.374 Fit side-chains revert: symmetry clash REVERT: A 51 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.8141 (mm-40) REVERT: A 161 GLU cc_start: 0.7555 (mm-30) cc_final: 0.6992 (mp0) REVERT: C 132 GLU cc_start: 0.6957 (OUTLIER) cc_final: 0.6293 (mt-10) REVERT: D 13 MET cc_start: 0.6279 (tpp) cc_final: 0.5504 (tmm) REVERT: D 113 GLU cc_start: 0.6380 (mt-10) cc_final: 0.6035 (mp0) REVERT: D 135 ARG cc_start: 0.6714 (OUTLIER) cc_final: 0.6362 (ttp80) REVERT: E 13 MET cc_start: 0.6135 (mmm) cc_final: 0.4963 (mmp) REVERT: E 80 GLN cc_start: 0.8130 (tp40) cc_final: 0.7814 (tp40) REVERT: E 113 GLU cc_start: 0.5645 (tt0) cc_final: 0.5057 (mt-10) REVERT: E 121 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7168 (mm-30) REVERT: E 135 ARG cc_start: 0.7132 (ptm160) cc_final: 0.6735 (ptm160) REVERT: E 165 ASN cc_start: 0.5645 (m-40) cc_final: 0.5371 (m-40) REVERT: F 29 SER cc_start: 0.6870 (m) cc_final: 0.6532 (p) REVERT: F 116 LYS cc_start: 0.6066 (OUTLIER) cc_final: 0.5421 (tmmt) REVERT: G 97 ARG cc_start: 0.7711 (OUTLIER) cc_final: 0.6987 (ttm170) REVERT: G 169 GLU cc_start: 0.6884 (OUTLIER) cc_final: 0.5918 (mm-30) REVERT: G 176 SER cc_start: 0.7571 (m) cc_final: 0.7029 (p) REVERT: H 33 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7283 (pp) REVERT: H 152 HIS cc_start: 0.7311 (m90) cc_final: 0.6509 (m90) REVERT: I 70 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7313 (mm-30) REVERT: K 48 ARG cc_start: 0.7399 (OUTLIER) cc_final: 0.6645 (mmp-170) REVERT: K 168 LYS cc_start: 0.7874 (mtpp) cc_final: 0.7261 (mttt) REVERT: K 203 LEU cc_start: 0.6704 (mp) cc_final: 0.5762 (mt) REVERT: M 149 ASP cc_start: 0.7693 (t0) cc_final: 0.7400 (t0) REVERT: N 13 MET cc_start: 0.7515 (tpp) cc_final: 0.6318 (mpp) REVERT: N 14 ARG cc_start: 0.6661 (ttp-110) cc_final: 0.6449 (ttp80) REVERT: N 21 ARG cc_start: 0.7385 (ttp-110) cc_final: 0.7103 (ttm-80) REVERT: P 330 ASP cc_start: 0.8314 (OUTLIER) cc_final: 0.8055 (p0) REVERT: P 413 ASP cc_start: 0.7313 (OUTLIER) cc_final: 0.6820 (p0) REVERT: P 433 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6782 (tp30) REVERT: Q 357 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.7651 (ttp80) REVERT: S 361 VAL cc_start: 0.8963 (t) cc_final: 0.8700 (t) REVERT: T 339 ASP cc_start: 0.8122 (m-30) cc_final: 0.7684 (m-30) REVERT: T 430 ASN cc_start: 0.7977 (OUTLIER) cc_final: 0.7734 (m110) REVERT: T 509 ARG cc_start: 0.7721 (OUTLIER) cc_final: 0.6643 (tpt-90) REVERT: U 395 MET cc_start: 0.7100 (OUTLIER) cc_final: 0.6484 (mpt) REVERT: W 509 ARG cc_start: 0.7729 (OUTLIER) cc_final: 0.6894 (ttp-170) REVERT: X 512 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7715 (mt-10) REVERT: Z 424 ASP cc_start: 0.8118 (p0) cc_final: 0.7882 (p0) REVERT: Z 500 ASP cc_start: 0.8552 (m-30) cc_final: 0.8339 (m-30) REVERT: O 15 GLU cc_start: 0.6831 (OUTLIER) cc_final: 0.6060 (mt-10) REVERT: O 51 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7746 (mm-40) outliers start: 142 outliers final: 56 residues processed: 660 average time/residue: 1.6110 time to fit residues: 1308.9612 Evaluate side-chains 623 residues out of total 4641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 546 time to evaluate : 5.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 135 ARG Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 144 ASP Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain G residue 97 ARG Chi-restraints excluded: chain G residue 169 GLU Chi-restraints excluded: chain G residue 209 GLU Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 168 LYS Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain I residue 70 GLU Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain J residue 178 THR Chi-restraints excluded: chain K residue 44 GLU Chi-restraints excluded: chain K residue 48 ARG Chi-restraints excluded: chain K residue 226 THR Chi-restraints excluded: chain L residue 160 THR Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 54 SER Chi-restraints excluded: chain M residue 119 GLU Chi-restraints excluded: chain N residue 114 GLN Chi-restraints excluded: chain P residue 301 THR Chi-restraints excluded: chain P residue 330 ASP Chi-restraints excluded: chain P residue 372 VAL Chi-restraints excluded: chain P residue 413 ASP Chi-restraints excluded: chain P residue 433 GLU Chi-restraints excluded: chain Q residue 357 ARG Chi-restraints excluded: chain S residue 313 VAL Chi-restraints excluded: chain S residue 401 LEU Chi-restraints excluded: chain S residue 503 VAL Chi-restraints excluded: chain T residue 430 ASN Chi-restraints excluded: chain T residue 509 ARG Chi-restraints excluded: chain U residue 301 THR Chi-restraints excluded: chain U residue 395 MET Chi-restraints excluded: chain V residue 301 THR Chi-restraints excluded: chain V residue 364 GLU Chi-restraints excluded: chain V residue 433 GLU Chi-restraints excluded: chain W residue 330 ASP Chi-restraints excluded: chain W residue 401 LEU Chi-restraints excluded: chain W residue 509 ARG Chi-restraints excluded: chain X residue 301 THR Chi-restraints excluded: chain X residue 330 ASP Chi-restraints excluded: chain X residue 409 ILE Chi-restraints excluded: chain X residue 512 GLU Chi-restraints excluded: chain Y residue 313 VAL Chi-restraints excluded: chain Y residue 325 MET Chi-restraints excluded: chain Y residue 330 ASP Chi-restraints excluded: chain Y residue 503 VAL Chi-restraints excluded: chain Z residue 330 ASP Chi-restraints excluded: chain Z residue 509 ARG Chi-restraints excluded: chain Z residue 512 GLU Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain a residue 430 ASN Chi-restraints excluded: chain a residue 504 ASP Chi-restraints excluded: chain c residue 364 GLU Chi-restraints excluded: chain c residue 430 ASN Chi-restraints excluded: chain c residue 500 ASP Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain O residue 51 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 484 optimal weight: 3.9990 chunk 330 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 433 optimal weight: 3.9990 chunk 240 optimal weight: 5.9990 chunk 496 optimal weight: 0.3980 chunk 402 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 297 optimal weight: 0.8980 chunk 522 optimal weight: 1.9990 chunk 146 optimal weight: 9.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 216 ASN C 73 ASN D 51 GLN F 45 ASN H 80 GLN J 165 ASN K 216 ASN L 98 GLN L 165 ASN L 174 ASN N 45 ASN N 80 GLN P 322 GLN P 390 ASN P 415 GLN S 324 ASN X 322 GLN b 390 ASN c 322 GLN O 80 GLN O 231 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 47066 Z= 0.248 Angle : 0.501 7.407 63704 Z= 0.266 Chirality : 0.043 0.235 7251 Planarity : 0.004 0.048 8400 Dihedral : 4.029 69.831 6857 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.60 % Allowed : 17.28 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.11), residues: 6048 helix: 2.87 (0.10), residues: 2534 sheet: 0.91 (0.14), residues: 1526 loop : 0.02 (0.14), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP c 429 HIS 0.004 0.001 HIS Y 365 PHE 0.033 0.002 PHE M 71 TYR 0.012 0.001 TYR N 118 ARG 0.011 0.000 ARG E 14 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 4641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 555 time to evaluate : 5.515 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.8129 (mm-40) REVERT: A 161 GLU cc_start: 0.7585 (mm-30) cc_final: 0.6982 (mp0) REVERT: C 126 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7441 (tt0) REVERT: C 132 GLU cc_start: 0.7003 (OUTLIER) cc_final: 0.6298 (mt-10) REVERT: D 13 MET cc_start: 0.6254 (tpp) cc_final: 0.5542 (tmm) REVERT: D 135 ARG cc_start: 0.6706 (OUTLIER) cc_final: 0.6398 (ttp80) REVERT: E 13 MET cc_start: 0.6081 (mmm) cc_final: 0.4903 (mmp) REVERT: E 80 GLN cc_start: 0.8169 (tp40) cc_final: 0.7849 (tp40) REVERT: E 135 ARG cc_start: 0.7110 (ptm160) cc_final: 0.6749 (ptm160) REVERT: E 165 ASN cc_start: 0.5628 (m-40) cc_final: 0.5422 (m-40) REVERT: F 29 SER cc_start: 0.6878 (m) cc_final: 0.6532 (p) REVERT: F 80 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7674 (tm-30) REVERT: F 116 LYS cc_start: 0.5966 (OUTLIER) cc_final: 0.5368 (tmmt) REVERT: F 234 LEU cc_start: 0.6635 (OUTLIER) cc_final: 0.6358 (pp) REVERT: G 97 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.6984 (ttm170) REVERT: G 176 SER cc_start: 0.7578 (m) cc_final: 0.7039 (p) REVERT: H 33 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7337 (pp) REVERT: H 152 HIS cc_start: 0.7421 (m90) cc_final: 0.6544 (m90) REVERT: I 70 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7380 (mm-30) REVERT: I 159 THR cc_start: 0.6493 (OUTLIER) cc_final: 0.5686 (t) REVERT: K 48 ARG cc_start: 0.7366 (OUTLIER) cc_final: 0.6629 (mmp-170) REVERT: K 203 LEU cc_start: 0.6690 (mp) cc_final: 0.5778 (mt) REVERT: M 80 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.7737 (tm-30) REVERT: M 149 ASP cc_start: 0.7679 (t0) cc_final: 0.7405 (t0) REVERT: N 13 MET cc_start: 0.7543 (tpp) cc_final: 0.6395 (mpp) REVERT: N 14 ARG cc_start: 0.6621 (ttp-110) cc_final: 0.6290 (ttp80) REVERT: N 21 ARG cc_start: 0.7371 (ttp-110) cc_final: 0.7071 (ttm-80) REVERT: N 24 ILE cc_start: 0.8164 (mm) cc_final: 0.7927 (mt) REVERT: P 330 ASP cc_start: 0.8345 (OUTLIER) cc_final: 0.8087 (p0) REVERT: P 413 ASP cc_start: 0.7327 (OUTLIER) cc_final: 0.6872 (p0) REVERT: P 433 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6847 (tp30) REVERT: P 521 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7839 (mpt-90) REVERT: Q 357 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.7611 (ttp80) REVERT: R 325 MET cc_start: 0.8358 (OUTLIER) cc_final: 0.8038 (ttt) REVERT: R 432 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.6856 (mp0) REVERT: S 361 VAL cc_start: 0.9022 (t) cc_final: 0.8755 (t) REVERT: S 509 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.7189 (ttt180) REVERT: T 339 ASP cc_start: 0.8118 (m-30) cc_final: 0.7655 (m-30) REVERT: T 430 ASN cc_start: 0.8002 (OUTLIER) cc_final: 0.7748 (m110) REVERT: U 395 MET cc_start: 0.7176 (OUTLIER) cc_final: 0.6515 (mpt) REVERT: U 401 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8223 (tt) REVERT: V 461 ASP cc_start: 0.7896 (OUTLIER) cc_final: 0.7668 (t0) REVERT: W 430 ASN cc_start: 0.8274 (OUTLIER) cc_final: 0.7927 (t0) REVERT: W 509 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.6920 (ttp-110) REVERT: X 512 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7693 (mt-10) REVERT: Z 500 ASP cc_start: 0.8550 (m-30) cc_final: 0.8347 (m-30) REVERT: Z 507 GLU cc_start: 0.7521 (tp30) cc_final: 0.7315 (tp30) REVERT: a 325 MET cc_start: 0.8131 (OUTLIER) cc_final: 0.7712 (tmm) REVERT: O 15 GLU cc_start: 0.6852 (OUTLIER) cc_final: 0.5935 (mt-10) REVERT: O 51 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7797 (mm-40) outliers start: 167 outliers final: 79 residues processed: 658 average time/residue: 1.6827 time to fit residues: 1362.2116 Evaluate side-chains 653 residues out of total 4641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 543 time to evaluate : 5.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 91 ARG Chi-restraints excluded: chain D residue 135 ARG Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 80 GLN Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 144 ASP Chi-restraints excluded: chain F residue 146 SER Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 97 ARG Chi-restraints excluded: chain G residue 174 ASN Chi-restraints excluded: chain G residue 209 GLU Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 168 LYS Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain I residue 70 GLU Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain I residue 159 THR Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 209 GLU Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain K residue 44 GLU Chi-restraints excluded: chain K residue 48 ARG Chi-restraints excluded: chain K residue 226 THR Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 160 THR Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 54 SER Chi-restraints excluded: chain M residue 80 GLN Chi-restraints excluded: chain M residue 119 GLU Chi-restraints excluded: chain M residue 226 THR Chi-restraints excluded: chain N residue 114 GLN Chi-restraints excluded: chain N residue 179 ASP Chi-restraints excluded: chain P residue 301 THR Chi-restraints excluded: chain P residue 330 ASP Chi-restraints excluded: chain P residue 372 VAL Chi-restraints excluded: chain P residue 413 ASP Chi-restraints excluded: chain P residue 433 GLU Chi-restraints excluded: chain P residue 521 ARG Chi-restraints excluded: chain Q residue 357 ARG Chi-restraints excluded: chain Q residue 401 LEU Chi-restraints excluded: chain R residue 325 MET Chi-restraints excluded: chain R residue 432 GLU Chi-restraints excluded: chain S residue 401 LEU Chi-restraints excluded: chain S residue 503 VAL Chi-restraints excluded: chain S residue 509 ARG Chi-restraints excluded: chain T residue 430 ASN Chi-restraints excluded: chain U residue 301 THR Chi-restraints excluded: chain U residue 325 MET Chi-restraints excluded: chain U residue 354 GLU Chi-restraints excluded: chain U residue 355 PHE Chi-restraints excluded: chain U residue 395 MET Chi-restraints excluded: chain U residue 401 LEU Chi-restraints excluded: chain V residue 301 THR Chi-restraints excluded: chain V residue 364 GLU Chi-restraints excluded: chain V residue 433 GLU Chi-restraints excluded: chain V residue 461 ASP Chi-restraints excluded: chain W residue 301 THR Chi-restraints excluded: chain W residue 330 ASP Chi-restraints excluded: chain W residue 401 LEU Chi-restraints excluded: chain W residue 430 ASN Chi-restraints excluded: chain W residue 509 ARG Chi-restraints excluded: chain X residue 301 THR Chi-restraints excluded: chain X residue 330 ASP Chi-restraints excluded: chain X residue 401 LEU Chi-restraints excluded: chain X residue 409 ILE Chi-restraints excluded: chain X residue 512 GLU Chi-restraints excluded: chain Y residue 313 VAL Chi-restraints excluded: chain Y residue 325 MET Chi-restraints excluded: chain Y residue 330 ASP Chi-restraints excluded: chain Y residue 355 PHE Chi-restraints excluded: chain Y residue 396 GLN Chi-restraints excluded: chain Y residue 431 ILE Chi-restraints excluded: chain Y residue 503 VAL Chi-restraints excluded: chain Z residue 321 THR Chi-restraints excluded: chain Z residue 325 MET Chi-restraints excluded: chain Z residue 330 ASP Chi-restraints excluded: chain Z residue 362 GLU Chi-restraints excluded: chain Z residue 512 GLU Chi-restraints excluded: chain a residue 325 MET Chi-restraints excluded: chain a residue 430 ASN Chi-restraints excluded: chain a residue 504 ASP Chi-restraints excluded: chain a residue 507 GLU Chi-restraints excluded: chain b residue 343 THR Chi-restraints excluded: chain b residue 351 VAL Chi-restraints excluded: chain c residue 364 GLU Chi-restraints excluded: chain c residue 500 ASP Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain O residue 51 GLN Chi-restraints excluded: chain O residue 205 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 195 optimal weight: 1.9990 chunk 524 optimal weight: 8.9990 chunk 115 optimal weight: 6.9990 chunk 341 optimal weight: 5.9990 chunk 143 optimal weight: 5.9990 chunk 582 optimal weight: 7.9990 chunk 483 optimal weight: 2.9990 chunk 269 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 192 optimal weight: 0.8980 chunk 305 optimal weight: 6.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN C 73 ASN D 51 GLN F 45 ASN F 51 GLN F 165 ASN G 152 HIS H 80 GLN J 165 ASN K 216 ASN L 165 ASN L 174 ASN M 105 GLN M 216 ASN N 80 GLN P 322 GLN P 390 ASN P 415 GLN R 390 ASN S 324 ASN X 322 GLN b 390 ASN c 322 GLN O 80 GLN ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 231 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 47066 Z= 0.276 Angle : 0.518 7.695 63704 Z= 0.275 Chirality : 0.044 0.188 7251 Planarity : 0.004 0.049 8400 Dihedral : 4.126 65.586 6857 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.64 % Allowed : 17.93 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.11), residues: 6048 helix: 2.77 (0.10), residues: 2534 sheet: 0.90 (0.14), residues: 1526 loop : -0.03 (0.14), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP c 429 HIS 0.004 0.001 HIS b 410 PHE 0.034 0.003 PHE M 71 TYR 0.017 0.001 TYR N 118 ARG 0.011 0.000 ARG E 14 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 726 residues out of total 4641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 557 time to evaluate : 5.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 161 GLU cc_start: 0.7562 (mm-30) cc_final: 0.6973 (mp0) REVERT: C 126 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7532 (tt0) REVERT: C 132 GLU cc_start: 0.7031 (OUTLIER) cc_final: 0.6319 (mt-10) REVERT: D 13 MET cc_start: 0.6246 (tpp) cc_final: 0.5463 (tmm) REVERT: D 52 LYS cc_start: 0.7733 (OUTLIER) cc_final: 0.7483 (mtpm) REVERT: D 113 GLU cc_start: 0.6288 (mt-10) cc_final: 0.5973 (mp0) REVERT: E 13 MET cc_start: 0.6077 (mmm) cc_final: 0.4916 (mmp) REVERT: E 80 GLN cc_start: 0.8174 (tp40) cc_final: 0.7824 (tp-100) REVERT: E 165 ASN cc_start: 0.5594 (m-40) cc_final: 0.5387 (m-40) REVERT: F 80 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7697 (tm-30) REVERT: F 116 LYS cc_start: 0.5970 (OUTLIER) cc_final: 0.5291 (tmmt) REVERT: F 234 LEU cc_start: 0.6615 (OUTLIER) cc_final: 0.6260 (pp) REVERT: G 97 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.6979 (ttm170) REVERT: H 121 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7516 (tt0) REVERT: I 70 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7242 (mm-30) REVERT: I 159 THR cc_start: 0.6554 (OUTLIER) cc_final: 0.6138 (p) REVERT: K 48 ARG cc_start: 0.7433 (OUTLIER) cc_final: 0.6666 (mmp-170) REVERT: K 168 LYS cc_start: 0.7930 (mtpp) cc_final: 0.7326 (mttt) REVERT: K 203 LEU cc_start: 0.6660 (mp) cc_final: 0.5785 (mt) REVERT: M 80 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7733 (tm-30) REVERT: M 149 ASP cc_start: 0.7700 (t0) cc_final: 0.7437 (t0) REVERT: N 13 MET cc_start: 0.7551 (tpp) cc_final: 0.6394 (mpp) REVERT: N 14 ARG cc_start: 0.6667 (ttp-110) cc_final: 0.6339 (ttp80) REVERT: N 21 ARG cc_start: 0.7372 (ttp-110) cc_final: 0.7097 (ttm-80) REVERT: P 330 ASP cc_start: 0.8352 (OUTLIER) cc_final: 0.8092 (p0) REVERT: P 413 ASP cc_start: 0.7312 (OUTLIER) cc_final: 0.6876 (p0) REVERT: P 433 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.6845 (tp30) REVERT: P 521 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7582 (mpt-90) REVERT: Q 357 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.7593 (ttp80) REVERT: R 325 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.8057 (ttt) REVERT: R 432 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.6986 (mp0) REVERT: S 361 VAL cc_start: 0.9070 (t) cc_final: 0.8791 (t) REVERT: T 339 ASP cc_start: 0.8138 (m-30) cc_final: 0.7637 (m-30) REVERT: T 430 ASN cc_start: 0.8011 (OUTLIER) cc_final: 0.7751 (m110) REVERT: T 509 ARG cc_start: 0.7719 (OUTLIER) cc_final: 0.6680 (tpt-90) REVERT: U 395 MET cc_start: 0.7258 (OUTLIER) cc_final: 0.6549 (mpt) REVERT: U 401 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8202 (tt) REVERT: V 461 ASP cc_start: 0.7886 (OUTLIER) cc_final: 0.7639 (t0) REVERT: W 509 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.6947 (ttp-110) REVERT: X 512 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7646 (mt-10) REVERT: Z 386 MET cc_start: 0.9251 (mtp) cc_final: 0.9037 (mtm) REVERT: Z 447 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8526 (mtmp) REVERT: Z 507 GLU cc_start: 0.7571 (tp30) cc_final: 0.7368 (tp30) REVERT: O 15 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.6013 (mt-10) REVERT: O 51 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7772 (mm-40) outliers start: 169 outliers final: 92 residues processed: 662 average time/residue: 1.6494 time to fit residues: 1342.5379 Evaluate side-chains 656 residues out of total 4641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 535 time to evaluate : 5.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 52 LYS Chi-restraints excluded: chain D residue 91 ARG Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 80 GLN Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 146 SER Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 97 ARG Chi-restraints excluded: chain G residue 174 ASN Chi-restraints excluded: chain G residue 209 GLU Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 121 GLU Chi-restraints excluded: chain H residue 168 LYS Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain I residue 70 GLU Chi-restraints excluded: chain I residue 159 THR Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 209 GLU Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain K residue 44 GLU Chi-restraints excluded: chain K residue 48 ARG Chi-restraints excluded: chain K residue 119 GLU Chi-restraints excluded: chain K residue 226 THR Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 160 THR Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 54 SER Chi-restraints excluded: chain M residue 80 GLN Chi-restraints excluded: chain M residue 112 THR Chi-restraints excluded: chain M residue 119 GLU Chi-restraints excluded: chain M residue 226 THR Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 114 GLN Chi-restraints excluded: chain P residue 301 THR Chi-restraints excluded: chain P residue 330 ASP Chi-restraints excluded: chain P residue 372 VAL Chi-restraints excluded: chain P residue 413 ASP Chi-restraints excluded: chain P residue 433 GLU Chi-restraints excluded: chain P residue 521 ARG Chi-restraints excluded: chain Q residue 357 ARG Chi-restraints excluded: chain Q residue 401 LEU Chi-restraints excluded: chain R residue 306 LEU Chi-restraints excluded: chain R residue 321 THR Chi-restraints excluded: chain R residue 325 MET Chi-restraints excluded: chain R residue 432 GLU Chi-restraints excluded: chain S residue 313 VAL Chi-restraints excluded: chain S residue 325 MET Chi-restraints excluded: chain S residue 401 LEU Chi-restraints excluded: chain S residue 503 VAL Chi-restraints excluded: chain T residue 430 ASN Chi-restraints excluded: chain T residue 509 ARG Chi-restraints excluded: chain U residue 301 THR Chi-restraints excluded: chain U residue 325 MET Chi-restraints excluded: chain U residue 395 MET Chi-restraints excluded: chain U residue 401 LEU Chi-restraints excluded: chain V residue 301 THR Chi-restraints excluded: chain V residue 313 VAL Chi-restraints excluded: chain V residue 348 THR Chi-restraints excluded: chain V residue 364 GLU Chi-restraints excluded: chain V residue 433 GLU Chi-restraints excluded: chain V residue 461 ASP Chi-restraints excluded: chain W residue 301 THR Chi-restraints excluded: chain W residue 325 MET Chi-restraints excluded: chain W residue 330 ASP Chi-restraints excluded: chain W residue 401 LEU Chi-restraints excluded: chain W residue 509 ARG Chi-restraints excluded: chain X residue 301 THR Chi-restraints excluded: chain X residue 330 ASP Chi-restraints excluded: chain X residue 401 LEU Chi-restraints excluded: chain X residue 409 ILE Chi-restraints excluded: chain X residue 512 GLU Chi-restraints excluded: chain Y residue 313 VAL Chi-restraints excluded: chain Y residue 325 MET Chi-restraints excluded: chain Y residue 330 ASP Chi-restraints excluded: chain Y residue 339 ASP Chi-restraints excluded: chain Y residue 348 THR Chi-restraints excluded: chain Y residue 355 PHE Chi-restraints excluded: chain Y residue 401 LEU Chi-restraints excluded: chain Y residue 431 ILE Chi-restraints excluded: chain Y residue 503 VAL Chi-restraints excluded: chain Z residue 321 THR Chi-restraints excluded: chain Z residue 325 MET Chi-restraints excluded: chain Z residue 330 ASP Chi-restraints excluded: chain Z residue 362 GLU Chi-restraints excluded: chain Z residue 447 LYS Chi-restraints excluded: chain Z residue 512 GLU Chi-restraints excluded: chain a residue 391 LEU Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain a residue 430 ASN Chi-restraints excluded: chain a residue 447 LYS Chi-restraints excluded: chain a residue 504 ASP Chi-restraints excluded: chain a residue 507 GLU Chi-restraints excluded: chain b residue 322 GLN Chi-restraints excluded: chain b residue 343 THR Chi-restraints excluded: chain b residue 351 VAL Chi-restraints excluded: chain c residue 500 ASP Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain O residue 51 GLN Chi-restraints excluded: chain O residue 205 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 561 optimal weight: 6.9990 chunk 65 optimal weight: 20.0000 chunk 331 optimal weight: 1.9990 chunk 425 optimal weight: 0.0570 chunk 329 optimal weight: 2.9990 chunk 490 optimal weight: 2.9990 chunk 325 optimal weight: 0.7980 chunk 580 optimal weight: 3.9990 chunk 363 optimal weight: 1.9990 chunk 353 optimal weight: 0.8980 chunk 267 optimal weight: 7.9990 overall best weight: 1.1502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 216 ASN C 73 ASN D 51 GLN F 45 ASN H 80 GLN K 216 ASN L 165 ASN L 174 ASN M 45 ASN M 105 GLN M 216 ASN N 45 ASN N 80 GLN P 322 GLN P 390 ASN P 415 GLN S 324 ASN b 390 ASN c 322 GLN d 172 GLN O 80 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.118 47066 Z= 0.165 Angle : 0.464 8.455 63704 Z= 0.248 Chirality : 0.042 0.205 7251 Planarity : 0.003 0.046 8400 Dihedral : 3.890 60.867 6857 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.93 % Allowed : 19.31 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.11), residues: 6048 helix: 3.00 (0.10), residues: 2534 sheet: 0.93 (0.14), residues: 1526 loop : 0.05 (0.14), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP c 429 HIS 0.003 0.001 HIS Q 365 PHE 0.031 0.002 PHE C 71 TYR 0.015 0.001 TYR C 143 ARG 0.012 0.000 ARG E 14 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 708 residues out of total 4641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 572 time to evaluate : 5.987 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.8005 (mm-40) REVERT: A 121 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8107 (tm-30) REVERT: A 161 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7009 (mp0) REVERT: C 126 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7377 (tt0) REVERT: C 132 GLU cc_start: 0.7010 (OUTLIER) cc_final: 0.6344 (mt-10) REVERT: D 13 MET cc_start: 0.6288 (tpp) cc_final: 0.5454 (tmm) REVERT: D 113 GLU cc_start: 0.6215 (mt-10) cc_final: 0.5869 (mp0) REVERT: E 13 MET cc_start: 0.6020 (mmm) cc_final: 0.4917 (mmp) REVERT: E 80 GLN cc_start: 0.8159 (tp40) cc_final: 0.7813 (tp-100) REVERT: E 121 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7169 (mm-30) REVERT: E 135 ARG cc_start: 0.7160 (ptm160) cc_final: 0.6775 (ptm160) REVERT: E 165 ASN cc_start: 0.5617 (m-40) cc_final: 0.5399 (m-40) REVERT: F 80 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7681 (tm-30) REVERT: F 116 LYS cc_start: 0.5884 (OUTLIER) cc_final: 0.5256 (tmmt) REVERT: G 73 ASN cc_start: 0.7420 (m110) cc_final: 0.7219 (m110) REVERT: G 97 ARG cc_start: 0.7661 (OUTLIER) cc_final: 0.6940 (ttm170) REVERT: H 33 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.7359 (pp) REVERT: H 44 GLU cc_start: 0.6459 (OUTLIER) cc_final: 0.5627 (pp20) REVERT: I 13 MET cc_start: 0.6575 (OUTLIER) cc_final: 0.6265 (mmt) REVERT: I 70 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7211 (mm-30) REVERT: I 159 THR cc_start: 0.6455 (p) cc_final: 0.6066 (p) REVERT: K 48 ARG cc_start: 0.7411 (OUTLIER) cc_final: 0.6649 (mmp-170) REVERT: K 168 LYS cc_start: 0.7991 (mtpp) cc_final: 0.7369 (mttt) REVERT: K 203 LEU cc_start: 0.6596 (mp) cc_final: 0.5724 (mt) REVERT: L 28 LYS cc_start: 0.8329 (mttt) cc_final: 0.8016 (mttm) REVERT: L 233 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7745 (tt) REVERT: M 149 ASP cc_start: 0.7663 (t0) cc_final: 0.7403 (t0) REVERT: N 13 MET cc_start: 0.7545 (tpp) cc_final: 0.6451 (mpp) REVERT: N 14 ARG cc_start: 0.6688 (ttp-110) cc_final: 0.6447 (ttp80) REVERT: N 21 ARG cc_start: 0.7387 (ttp-110) cc_final: 0.7118 (ttm-80) REVERT: P 413 ASP cc_start: 0.7295 (OUTLIER) cc_final: 0.6873 (p0) REVERT: P 433 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.6923 (tp30) REVERT: Q 357 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.7679 (ttp80) REVERT: S 361 VAL cc_start: 0.9003 (t) cc_final: 0.8743 (t) REVERT: S 509 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.7116 (ttt180) REVERT: T 339 ASP cc_start: 0.8093 (m-30) cc_final: 0.7681 (m-30) REVERT: T 430 ASN cc_start: 0.7999 (OUTLIER) cc_final: 0.7755 (m110) REVERT: T 509 ARG cc_start: 0.7689 (OUTLIER) cc_final: 0.6664 (tpt-90) REVERT: U 395 MET cc_start: 0.7257 (OUTLIER) cc_final: 0.6612 (mpt) REVERT: U 401 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8221 (tt) REVERT: V 461 ASP cc_start: 0.7856 (OUTLIER) cc_final: 0.7629 (t0) REVERT: W 509 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.6894 (ttp-170) REVERT: X 512 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7678 (mt-10) REVERT: Z 386 MET cc_start: 0.9256 (mtp) cc_final: 0.9048 (mtm) REVERT: Z 432 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7117 (tp30) REVERT: Z 507 GLU cc_start: 0.7530 (tp30) cc_final: 0.7324 (tp30) REVERT: O 15 GLU cc_start: 0.6880 (OUTLIER) cc_final: 0.6053 (mt-10) REVERT: O 51 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.7788 (mm-40) outliers start: 136 outliers final: 69 residues processed: 652 average time/residue: 1.6439 time to fit residues: 1320.3499 Evaluate side-chains 639 residues out of total 4641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 542 time to evaluate : 5.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 80 GLN Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 144 ASP Chi-restraints excluded: chain F residue 146 SER Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 97 ARG Chi-restraints excluded: chain G residue 174 ASN Chi-restraints excluded: chain G residue 209 GLU Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 44 GLU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 168 LYS Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain I residue 70 GLU Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 228 SER Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain K residue 44 GLU Chi-restraints excluded: chain K residue 48 ARG Chi-restraints excluded: chain K residue 119 GLU Chi-restraints excluded: chain K residue 226 THR Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 160 THR Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 54 SER Chi-restraints excluded: chain M residue 226 THR Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 114 GLN Chi-restraints excluded: chain P residue 301 THR Chi-restraints excluded: chain P residue 354 GLU Chi-restraints excluded: chain P residue 372 VAL Chi-restraints excluded: chain P residue 413 ASP Chi-restraints excluded: chain P residue 433 GLU Chi-restraints excluded: chain Q residue 357 ARG Chi-restraints excluded: chain S residue 313 VAL Chi-restraints excluded: chain S residue 401 LEU Chi-restraints excluded: chain S residue 503 VAL Chi-restraints excluded: chain S residue 509 ARG Chi-restraints excluded: chain T residue 430 ASN Chi-restraints excluded: chain T residue 509 ARG Chi-restraints excluded: chain U residue 301 THR Chi-restraints excluded: chain U residue 325 MET Chi-restraints excluded: chain U residue 355 PHE Chi-restraints excluded: chain U residue 395 MET Chi-restraints excluded: chain U residue 401 LEU Chi-restraints excluded: chain V residue 301 THR Chi-restraints excluded: chain V residue 364 GLU Chi-restraints excluded: chain V residue 433 GLU Chi-restraints excluded: chain V residue 461 ASP Chi-restraints excluded: chain W residue 301 THR Chi-restraints excluded: chain W residue 325 MET Chi-restraints excluded: chain W residue 330 ASP Chi-restraints excluded: chain W residue 401 LEU Chi-restraints excluded: chain W residue 509 ARG Chi-restraints excluded: chain X residue 301 THR Chi-restraints excluded: chain X residue 330 ASP Chi-restraints excluded: chain X residue 401 LEU Chi-restraints excluded: chain X residue 409 ILE Chi-restraints excluded: chain X residue 512 GLU Chi-restraints excluded: chain Y residue 313 VAL Chi-restraints excluded: chain Y residue 325 MET Chi-restraints excluded: chain Y residue 330 ASP Chi-restraints excluded: chain Y residue 348 THR Chi-restraints excluded: chain Y residue 503 VAL Chi-restraints excluded: chain Z residue 330 ASP Chi-restraints excluded: chain Z residue 432 GLU Chi-restraints excluded: chain Z residue 512 GLU Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain a residue 430 ASN Chi-restraints excluded: chain a residue 504 ASP Chi-restraints excluded: chain a residue 507 GLU Chi-restraints excluded: chain b residue 351 VAL Chi-restraints excluded: chain c residue 500 ASP Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain O residue 51 GLN Chi-restraints excluded: chain O residue 205 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 358 optimal weight: 2.9990 chunk 231 optimal weight: 5.9990 chunk 346 optimal weight: 0.6980 chunk 174 optimal weight: 0.7980 chunk 114 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 chunk 368 optimal weight: 0.3980 chunk 395 optimal weight: 5.9990 chunk 286 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 456 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 165 ASN C 73 ASN D 51 GLN F 45 ASN H 45 ASN H 80 GLN J 165 ASN K 216 ASN L 101 ASN L 165 ASN L 174 ASN M 45 ASN M 105 GLN M 216 ASN N 45 ASN N 80 GLN P 390 ASN P 415 GLN ** P 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 324 ASN Z 322 GLN b 390 ASN c 322 GLN O 80 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 47066 Z= 0.133 Angle : 0.449 9.107 63704 Z= 0.239 Chirality : 0.041 0.168 7251 Planarity : 0.003 0.049 8400 Dihedral : 3.710 54.981 6857 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.65 % Allowed : 19.63 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.11), residues: 6048 helix: 3.14 (0.10), residues: 2548 sheet: 0.97 (0.14), residues: 1526 loop : 0.08 (0.14), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP T 429 HIS 0.003 0.000 HIS Q 365 PHE 0.031 0.002 PHE C 71 TYR 0.016 0.001 TYR C 143 ARG 0.013 0.000 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 4641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 570 time to evaluate : 5.699 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.8068 (mm-40) REVERT: A 121 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8063 (tm-30) REVERT: A 156 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.7691 (mpp) REVERT: A 161 GLU cc_start: 0.7552 (mm-30) cc_final: 0.6966 (mp0) REVERT: C 126 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7238 (tt0) REVERT: C 132 GLU cc_start: 0.7008 (OUTLIER) cc_final: 0.6361 (mt-10) REVERT: D 13 MET cc_start: 0.6240 (tpp) cc_final: 0.5427 (tmm) REVERT: D 52 LYS cc_start: 0.7801 (OUTLIER) cc_final: 0.7568 (mtpm) REVERT: D 113 GLU cc_start: 0.6237 (mt-10) cc_final: 0.5882 (mp0) REVERT: E 13 MET cc_start: 0.5967 (mmm) cc_final: 0.4916 (mmp) REVERT: E 45 ASN cc_start: 0.6625 (t0) cc_final: 0.6417 (t160) REVERT: E 80 GLN cc_start: 0.8149 (tp40) cc_final: 0.7806 (tp-100) REVERT: E 135 ARG cc_start: 0.7138 (ptm160) cc_final: 0.6776 (ptm160) REVERT: E 165 ASN cc_start: 0.5617 (m-40) cc_final: 0.5404 (m-40) REVERT: F 70 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7071 (mt-10) REVERT: F 116 LYS cc_start: 0.5859 (OUTLIER) cc_final: 0.5182 (tmmt) REVERT: G 73 ASN cc_start: 0.7376 (m110) cc_final: 0.7153 (m110) REVERT: G 97 ARG cc_start: 0.7671 (OUTLIER) cc_final: 0.6931 (ttm170) REVERT: G 119 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7527 (mp0) REVERT: G 176 SER cc_start: 0.7506 (m) cc_final: 0.7028 (p) REVERT: G 233 LEU cc_start: 0.7274 (mp) cc_final: 0.6955 (tp) REVERT: H 44 GLU cc_start: 0.6420 (OUTLIER) cc_final: 0.5547 (pp20) REVERT: H 152 HIS cc_start: 0.7306 (m90) cc_final: 0.7012 (m90) REVERT: I 13 MET cc_start: 0.6428 (OUTLIER) cc_final: 0.6107 (mmt) REVERT: I 70 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7169 (mm-30) REVERT: I 159 THR cc_start: 0.6430 (p) cc_final: 0.6023 (p) REVERT: K 48 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.6653 (mmp-170) REVERT: K 168 LYS cc_start: 0.7920 (mtpp) cc_final: 0.7315 (mttt) REVERT: K 203 LEU cc_start: 0.6507 (mp) cc_final: 0.5681 (mt) REVERT: L 28 LYS cc_start: 0.8324 (mttt) cc_final: 0.8002 (mttm) REVERT: L 233 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7705 (tt) REVERT: M 149 ASP cc_start: 0.7649 (t0) cc_final: 0.7392 (t0) REVERT: N 13 MET cc_start: 0.7547 (tpp) cc_final: 0.6448 (mpp) REVERT: N 14 ARG cc_start: 0.6747 (ttp-110) cc_final: 0.6506 (ttp80) REVERT: N 21 ARG cc_start: 0.7356 (ttp-110) cc_final: 0.7109 (ttm-80) REVERT: P 413 ASP cc_start: 0.7246 (OUTLIER) cc_final: 0.6817 (p0) REVERT: P 433 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6948 (tp30) REVERT: Q 357 ARG cc_start: 0.8839 (OUTLIER) cc_final: 0.7581 (ttp80) REVERT: S 361 VAL cc_start: 0.8981 (t) cc_final: 0.8731 (t) REVERT: S 509 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.7125 (ttt180) REVERT: T 339 ASP cc_start: 0.8106 (m-30) cc_final: 0.7707 (m-30) REVERT: T 461 ASP cc_start: 0.7766 (t0) cc_final: 0.7483 (t0) REVERT: T 509 ARG cc_start: 0.7613 (OUTLIER) cc_final: 0.6643 (tpt-90) REVERT: U 395 MET cc_start: 0.7141 (OUTLIER) cc_final: 0.6516 (mpt) REVERT: W 509 ARG cc_start: 0.7711 (OUTLIER) cc_final: 0.6879 (ttp-170) REVERT: X 512 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7718 (mt-10) REVERT: Z 432 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7127 (tp30) REVERT: Z 507 GLU cc_start: 0.7488 (tp30) cc_final: 0.7238 (tp30) REVERT: b 354 GLU cc_start: 0.7864 (tt0) cc_final: 0.7190 (pt0) REVERT: O 15 GLU cc_start: 0.6898 (OUTLIER) cc_final: 0.6093 (mt-10) REVERT: O 51 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7805 (mm-40) outliers start: 123 outliers final: 66 residues processed: 643 average time/residue: 1.6805 time to fit residues: 1344.7039 Evaluate side-chains 634 residues out of total 4641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 542 time to evaluate : 5.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 52 LYS Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 144 ASP Chi-restraints excluded: chain F residue 146 SER Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 97 ARG Chi-restraints excluded: chain G residue 119 GLU Chi-restraints excluded: chain G residue 174 ASN Chi-restraints excluded: chain G residue 209 GLU Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 44 GLU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain I residue 70 GLU Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 228 SER Chi-restraints excluded: chain K residue 44 GLU Chi-restraints excluded: chain K residue 48 ARG Chi-restraints excluded: chain K residue 226 THR Chi-restraints excluded: chain L residue 160 THR Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 54 SER Chi-restraints excluded: chain M residue 183 ILE Chi-restraints excluded: chain M residue 226 THR Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain P residue 301 THR Chi-restraints excluded: chain P residue 354 GLU Chi-restraints excluded: chain P residue 372 VAL Chi-restraints excluded: chain P residue 413 ASP Chi-restraints excluded: chain P residue 433 GLU Chi-restraints excluded: chain Q residue 357 ARG Chi-restraints excluded: chain R residue 399 LEU Chi-restraints excluded: chain R residue 409 ILE Chi-restraints excluded: chain S residue 313 VAL Chi-restraints excluded: chain S residue 385 ILE Chi-restraints excluded: chain S residue 401 LEU Chi-restraints excluded: chain S residue 503 VAL Chi-restraints excluded: chain S residue 509 ARG Chi-restraints excluded: chain T residue 509 ARG Chi-restraints excluded: chain U residue 325 MET Chi-restraints excluded: chain U residue 355 PHE Chi-restraints excluded: chain U residue 395 MET Chi-restraints excluded: chain V residue 301 THR Chi-restraints excluded: chain V residue 364 GLU Chi-restraints excluded: chain V residue 433 GLU Chi-restraints excluded: chain W residue 301 THR Chi-restraints excluded: chain W residue 330 ASP Chi-restraints excluded: chain W residue 401 LEU Chi-restraints excluded: chain W residue 509 ARG Chi-restraints excluded: chain X residue 301 THR Chi-restraints excluded: chain X residue 330 ASP Chi-restraints excluded: chain X residue 401 LEU Chi-restraints excluded: chain X residue 409 ILE Chi-restraints excluded: chain X residue 512 GLU Chi-restraints excluded: chain Y residue 313 VAL Chi-restraints excluded: chain Y residue 325 MET Chi-restraints excluded: chain Y residue 330 ASP Chi-restraints excluded: chain Y residue 348 THR Chi-restraints excluded: chain Y residue 355 PHE Chi-restraints excluded: chain Z residue 330 ASP Chi-restraints excluded: chain Z residue 432 GLU Chi-restraints excluded: chain Z residue 512 GLU Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain a residue 430 ASN Chi-restraints excluded: chain a residue 504 ASP Chi-restraints excluded: chain a residue 507 GLU Chi-restraints excluded: chain b residue 351 VAL Chi-restraints excluded: chain c residue 500 ASP Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain O residue 51 GLN Chi-restraints excluded: chain O residue 205 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 527 optimal weight: 2.9990 chunk 555 optimal weight: 7.9990 chunk 507 optimal weight: 8.9990 chunk 540 optimal weight: 2.9990 chunk 325 optimal weight: 2.9990 chunk 235 optimal weight: 7.9990 chunk 424 optimal weight: 0.5980 chunk 165 optimal weight: 1.9990 chunk 488 optimal weight: 7.9990 chunk 511 optimal weight: 1.9990 chunk 538 optimal weight: 0.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 165 ASN C 73 ASN D 51 GLN F 45 ASN F 51 GLN H 45 ASN H 80 GLN K 216 ASN L 165 ASN L 174 ASN M 45 ASN M 105 GLN M 216 ASN N 45 ASN N 80 GLN P 322 GLN P 390 ASN P 415 GLN S 324 ASN X 396 GLN Z 322 GLN b 390 ASN c 322 GLN O 80 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 47066 Z= 0.205 Angle : 0.492 11.869 63704 Z= 0.260 Chirality : 0.043 0.265 7251 Planarity : 0.004 0.055 8400 Dihedral : 3.837 50.781 6856 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.56 % Allowed : 19.57 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.11), residues: 6048 helix: 3.06 (0.10), residues: 2534 sheet: 0.98 (0.14), residues: 1526 loop : 0.07 (0.14), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP c 429 HIS 0.003 0.001 HIS Y 365 PHE 0.032 0.002 PHE M 71 TYR 0.016 0.001 TYR C 143 ARG 0.015 0.000 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 4641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 548 time to evaluate : 4.877 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.8062 (mm-40) REVERT: A 121 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8072 (tm-30) REVERT: A 156 MET cc_start: 0.8211 (OUTLIER) cc_final: 0.7705 (mpp) REVERT: A 161 GLU cc_start: 0.7541 (mm-30) cc_final: 0.7028 (mp0) REVERT: C 126 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7344 (tt0) REVERT: C 132 GLU cc_start: 0.7034 (OUTLIER) cc_final: 0.6382 (mt-10) REVERT: D 13 MET cc_start: 0.6192 (tpp) cc_final: 0.5429 (tmm) REVERT: D 52 LYS cc_start: 0.7782 (OUTLIER) cc_final: 0.7540 (mtpm) REVERT: D 113 GLU cc_start: 0.6237 (mt-10) cc_final: 0.5882 (mp0) REVERT: E 13 MET cc_start: 0.5985 (mmm) cc_final: 0.4928 (mmp) REVERT: E 80 GLN cc_start: 0.8162 (tp40) cc_final: 0.7813 (tp-100) REVERT: E 165 ASN cc_start: 0.5583 (m-40) cc_final: 0.5372 (m110) REVERT: F 70 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7091 (mt-10) REVERT: F 80 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7675 (tm-30) REVERT: F 116 LYS cc_start: 0.5857 (OUTLIER) cc_final: 0.5277 (tmmt) REVERT: G 73 ASN cc_start: 0.7390 (m110) cc_final: 0.7163 (m110) REVERT: G 97 ARG cc_start: 0.7675 (OUTLIER) cc_final: 0.6954 (ttm170) REVERT: G 119 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7555 (mp0) REVERT: G 176 SER cc_start: 0.7554 (m) cc_final: 0.6999 (p) REVERT: G 233 LEU cc_start: 0.7291 (mp) cc_final: 0.6970 (tp) REVERT: H 44 GLU cc_start: 0.6573 (OUTLIER) cc_final: 0.5656 (pp20) REVERT: I 13 MET cc_start: 0.6505 (OUTLIER) cc_final: 0.6193 (mmt) REVERT: I 70 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7184 (mm-30) REVERT: I 159 THR cc_start: 0.6429 (p) cc_final: 0.6010 (p) REVERT: K 48 ARG cc_start: 0.7401 (OUTLIER) cc_final: 0.6648 (mmp-170) REVERT: K 168 LYS cc_start: 0.7920 (mtpp) cc_final: 0.7299 (mttt) REVERT: K 203 LEU cc_start: 0.6548 (mp) cc_final: 0.5721 (mt) REVERT: L 28 LYS cc_start: 0.8315 (mttt) cc_final: 0.7985 (mttm) REVERT: L 233 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7671 (tt) REVERT: M 80 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.7800 (tm-30) REVERT: M 149 ASP cc_start: 0.7668 (t0) cc_final: 0.7404 (t0) REVERT: N 13 MET cc_start: 0.7579 (tpp) cc_final: 0.6446 (mpp) REVERT: N 14 ARG cc_start: 0.6728 (ttp-110) cc_final: 0.6385 (ttp80) REVERT: N 21 ARG cc_start: 0.7358 (ttp-110) cc_final: 0.7120 (ttm-80) REVERT: P 330 ASP cc_start: 0.8306 (OUTLIER) cc_final: 0.8071 (p0) REVERT: P 413 ASP cc_start: 0.7256 (OUTLIER) cc_final: 0.6839 (p0) REVERT: P 433 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6899 (tp30) REVERT: Q 357 ARG cc_start: 0.8864 (OUTLIER) cc_final: 0.7647 (ttp80) REVERT: S 361 VAL cc_start: 0.9033 (t) cc_final: 0.8761 (t) REVERT: S 509 ARG cc_start: 0.7900 (OUTLIER) cc_final: 0.7127 (ttt180) REVERT: T 339 ASP cc_start: 0.8078 (m-30) cc_final: 0.7666 (m-30) REVERT: T 509 ARG cc_start: 0.7695 (OUTLIER) cc_final: 0.6673 (tpt-90) REVERT: U 395 MET cc_start: 0.7188 (OUTLIER) cc_final: 0.6571 (mpt) REVERT: W 509 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.6878 (ttp-170) REVERT: X 512 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7701 (mt-10) REVERT: Z 432 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7145 (tp30) REVERT: Z 507 GLU cc_start: 0.7561 (tp30) cc_final: 0.7329 (tp30) REVERT: O 15 GLU cc_start: 0.6909 (OUTLIER) cc_final: 0.6048 (mt-10) REVERT: O 51 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7780 (mm-40) outliers start: 119 outliers final: 71 residues processed: 620 average time/residue: 1.6772 time to fit residues: 1274.6339 Evaluate side-chains 631 residues out of total 4641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 531 time to evaluate : 5.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 52 LYS Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 80 GLN Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 146 SER Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 97 ARG Chi-restraints excluded: chain G residue 119 GLU Chi-restraints excluded: chain G residue 174 ASN Chi-restraints excluded: chain G residue 209 GLU Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 44 GLU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 168 LYS Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain I residue 70 GLU Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 228 SER Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain K residue 44 GLU Chi-restraints excluded: chain K residue 48 ARG Chi-restraints excluded: chain K residue 119 GLU Chi-restraints excluded: chain K residue 226 THR Chi-restraints excluded: chain L residue 160 THR Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 54 SER Chi-restraints excluded: chain M residue 80 GLN Chi-restraints excluded: chain M residue 226 THR Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain P residue 301 THR Chi-restraints excluded: chain P residue 330 ASP Chi-restraints excluded: chain P residue 354 GLU Chi-restraints excluded: chain P residue 372 VAL Chi-restraints excluded: chain P residue 413 ASP Chi-restraints excluded: chain P residue 433 GLU Chi-restraints excluded: chain Q residue 357 ARG Chi-restraints excluded: chain R residue 409 ILE Chi-restraints excluded: chain S residue 313 VAL Chi-restraints excluded: chain S residue 401 LEU Chi-restraints excluded: chain S residue 503 VAL Chi-restraints excluded: chain S residue 509 ARG Chi-restraints excluded: chain T residue 509 ARG Chi-restraints excluded: chain U residue 325 MET Chi-restraints excluded: chain U residue 354 GLU Chi-restraints excluded: chain U residue 355 PHE Chi-restraints excluded: chain U residue 395 MET Chi-restraints excluded: chain V residue 301 THR Chi-restraints excluded: chain V residue 364 GLU Chi-restraints excluded: chain V residue 401 LEU Chi-restraints excluded: chain V residue 433 GLU Chi-restraints excluded: chain W residue 301 THR Chi-restraints excluded: chain W residue 325 MET Chi-restraints excluded: chain W residue 330 ASP Chi-restraints excluded: chain W residue 401 LEU Chi-restraints excluded: chain W residue 509 ARG Chi-restraints excluded: chain X residue 301 THR Chi-restraints excluded: chain X residue 330 ASP Chi-restraints excluded: chain X residue 401 LEU Chi-restraints excluded: chain X residue 409 ILE Chi-restraints excluded: chain X residue 512 GLU Chi-restraints excluded: chain Y residue 313 VAL Chi-restraints excluded: chain Y residue 325 MET Chi-restraints excluded: chain Y residue 330 ASP Chi-restraints excluded: chain Y residue 348 THR Chi-restraints excluded: chain Y residue 355 PHE Chi-restraints excluded: chain Y residue 503 VAL Chi-restraints excluded: chain Z residue 330 ASP Chi-restraints excluded: chain Z residue 432 GLU Chi-restraints excluded: chain Z residue 512 GLU Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain a residue 430 ASN Chi-restraints excluded: chain a residue 504 ASP Chi-restraints excluded: chain a residue 507 GLU Chi-restraints excluded: chain b residue 343 THR Chi-restraints excluded: chain b residue 351 VAL Chi-restraints excluded: chain c residue 364 GLU Chi-restraints excluded: chain c residue 500 ASP Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain O residue 51 GLN Chi-restraints excluded: chain O residue 205 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 355 optimal weight: 0.8980 chunk 571 optimal weight: 0.9980 chunk 348 optimal weight: 7.9990 chunk 271 optimal weight: 4.9990 chunk 397 optimal weight: 5.9990 chunk 599 optimal weight: 0.0970 chunk 551 optimal weight: 6.9990 chunk 477 optimal weight: 8.9990 chunk 49 optimal weight: 5.9990 chunk 368 optimal weight: 0.8980 chunk 292 optimal weight: 5.9990 overall best weight: 1.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 165 ASN C 73 ASN D 51 GLN E 45 ASN F 45 ASN F 51 GLN H 45 ASN H 80 GLN J 165 ASN K 216 ASN L 165 ASN L 174 ASN M 45 ASN M 105 GLN M 216 ASN N 45 ASN N 80 GLN P 322 GLN P 390 ASN P 415 GLN S 324 ASN Z 322 GLN c 322 GLN O 80 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 47066 Z= 0.193 Angle : 0.488 10.767 63704 Z= 0.258 Chirality : 0.042 0.223 7251 Planarity : 0.004 0.058 8400 Dihedral : 3.833 45.601 6856 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.65 % Allowed : 19.63 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.11), residues: 6048 helix: 3.04 (0.10), residues: 2534 sheet: 0.97 (0.14), residues: 1526 loop : 0.08 (0.14), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP c 429 HIS 0.003 0.001 HIS Y 365 PHE 0.031 0.002 PHE M 71 TYR 0.017 0.001 TYR C 143 ARG 0.015 0.000 ARG E 14 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 4641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 544 time to evaluate : 5.552 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.8045 (mm-40) REVERT: A 121 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8057 (tm-30) REVERT: A 156 MET cc_start: 0.8192 (OUTLIER) cc_final: 0.7675 (mpp) REVERT: A 161 GLU cc_start: 0.7532 (mm-30) cc_final: 0.7025 (mp0) REVERT: C 126 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7362 (tt0) REVERT: C 132 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6382 (mt-10) REVERT: D 13 MET cc_start: 0.6250 (tpp) cc_final: 0.5364 (tmm) REVERT: D 52 LYS cc_start: 0.7775 (OUTLIER) cc_final: 0.7532 (mtpm) REVERT: D 113 GLU cc_start: 0.6234 (mt-10) cc_final: 0.5880 (mp0) REVERT: E 13 MET cc_start: 0.5933 (mmm) cc_final: 0.4812 (mmp) REVERT: E 14 ARG cc_start: 0.5862 (mtm110) cc_final: 0.5506 (ptp90) REVERT: E 80 GLN cc_start: 0.8158 (tp40) cc_final: 0.7811 (tp-100) REVERT: E 135 ARG cc_start: 0.7013 (ptm160) cc_final: 0.6734 (ptm160) REVERT: E 165 ASN cc_start: 0.5557 (m-40) cc_final: 0.5327 (m110) REVERT: F 70 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7082 (mt-10) REVERT: F 80 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7697 (tm-30) REVERT: F 116 LYS cc_start: 0.5851 (OUTLIER) cc_final: 0.5201 (tmmt) REVERT: G 73 ASN cc_start: 0.7395 (m110) cc_final: 0.7169 (m110) REVERT: G 97 ARG cc_start: 0.7671 (OUTLIER) cc_final: 0.6928 (ttm170) REVERT: G 119 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7556 (mp0) REVERT: G 176 SER cc_start: 0.7512 (m) cc_final: 0.7006 (p) REVERT: G 233 LEU cc_start: 0.7246 (mp) cc_final: 0.6948 (tp) REVERT: H 44 GLU cc_start: 0.6615 (OUTLIER) cc_final: 0.5650 (pp20) REVERT: H 121 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7222 (tm-30) REVERT: I 70 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7167 (mm-30) REVERT: I 159 THR cc_start: 0.6416 (p) cc_final: 0.6002 (p) REVERT: J 22 LYS cc_start: 0.7672 (mttt) cc_final: 0.7315 (mttm) REVERT: K 48 ARG cc_start: 0.7399 (OUTLIER) cc_final: 0.6649 (mmp-170) REVERT: K 168 LYS cc_start: 0.7919 (mtpp) cc_final: 0.7350 (mttt) REVERT: K 203 LEU cc_start: 0.6522 (mp) cc_final: 0.5714 (mt) REVERT: L 28 LYS cc_start: 0.8317 (mttt) cc_final: 0.7985 (mttm) REVERT: L 233 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7690 (tt) REVERT: M 80 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.7795 (tm-30) REVERT: M 149 ASP cc_start: 0.7661 (t0) cc_final: 0.7398 (t0) REVERT: N 13 MET cc_start: 0.7554 (tpp) cc_final: 0.6439 (mpp) REVERT: N 14 ARG cc_start: 0.6729 (ttp-110) cc_final: 0.6385 (ttp80) REVERT: N 21 ARG cc_start: 0.7348 (ttp-110) cc_final: 0.7115 (ttm-80) REVERT: N 113 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7587 (mp0) REVERT: P 330 ASP cc_start: 0.8306 (OUTLIER) cc_final: 0.8069 (p0) REVERT: P 413 ASP cc_start: 0.7259 (OUTLIER) cc_final: 0.6849 (p0) REVERT: P 433 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6900 (tp30) REVERT: Q 357 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.7657 (ttp80) REVERT: Q 519 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7312 (mp0) REVERT: S 361 VAL cc_start: 0.9056 (t) cc_final: 0.8786 (t) REVERT: S 509 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7132 (ttt180) REVERT: T 339 ASP cc_start: 0.8065 (m-30) cc_final: 0.7663 (m-30) REVERT: T 461 ASP cc_start: 0.7756 (t0) cc_final: 0.7463 (t0) REVERT: T 509 ARG cc_start: 0.7685 (OUTLIER) cc_final: 0.6660 (tpt-90) REVERT: U 395 MET cc_start: 0.7191 (OUTLIER) cc_final: 0.6520 (mpt) REVERT: U 434 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7408 (mp0) REVERT: W 509 ARG cc_start: 0.7713 (OUTLIER) cc_final: 0.6873 (ttp-170) REVERT: X 512 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7708 (mt-10) REVERT: Y 395 MET cc_start: 0.6809 (OUTLIER) cc_final: 0.6069 (mpt) REVERT: Z 432 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7110 (tp30) REVERT: Z 507 GLU cc_start: 0.7558 (tp30) cc_final: 0.7328 (tp30) REVERT: O 15 GLU cc_start: 0.6950 (OUTLIER) cc_final: 0.6105 (mt-10) REVERT: O 51 GLN cc_start: 0.8219 (OUTLIER) cc_final: 0.7772 (mm-40) REVERT: O 135 ARG cc_start: 0.7549 (ttt-90) cc_final: 0.7146 (ttt-90) outliers start: 123 outliers final: 72 residues processed: 617 average time/residue: 1.6838 time to fit residues: 1275.1249 Evaluate side-chains 638 residues out of total 4641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 534 time to evaluate : 5.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 52 LYS Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 80 GLN Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 146 SER Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 97 ARG Chi-restraints excluded: chain G residue 119 GLU Chi-restraints excluded: chain G residue 174 ASN Chi-restraints excluded: chain G residue 209 GLU Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 44 GLU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 121 GLU Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 70 GLU Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 228 SER Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain K residue 44 GLU Chi-restraints excluded: chain K residue 48 ARG Chi-restraints excluded: chain K residue 119 GLU Chi-restraints excluded: chain K residue 226 THR Chi-restraints excluded: chain L residue 160 THR Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 54 SER Chi-restraints excluded: chain M residue 80 GLN Chi-restraints excluded: chain M residue 112 THR Chi-restraints excluded: chain M residue 226 THR Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain P residue 301 THR Chi-restraints excluded: chain P residue 330 ASP Chi-restraints excluded: chain P residue 372 VAL Chi-restraints excluded: chain P residue 413 ASP Chi-restraints excluded: chain P residue 433 GLU Chi-restraints excluded: chain Q residue 357 ARG Chi-restraints excluded: chain Q residue 519 GLU Chi-restraints excluded: chain S residue 351 VAL Chi-restraints excluded: chain S residue 401 LEU Chi-restraints excluded: chain S residue 503 VAL Chi-restraints excluded: chain S residue 509 ARG Chi-restraints excluded: chain T residue 509 ARG Chi-restraints excluded: chain U residue 301 THR Chi-restraints excluded: chain U residue 325 MET Chi-restraints excluded: chain U residue 354 GLU Chi-restraints excluded: chain U residue 355 PHE Chi-restraints excluded: chain U residue 395 MET Chi-restraints excluded: chain U residue 434 GLU Chi-restraints excluded: chain V residue 301 THR Chi-restraints excluded: chain V residue 364 GLU Chi-restraints excluded: chain V residue 401 LEU Chi-restraints excluded: chain W residue 301 THR Chi-restraints excluded: chain W residue 325 MET Chi-restraints excluded: chain W residue 330 ASP Chi-restraints excluded: chain W residue 401 LEU Chi-restraints excluded: chain W residue 509 ARG Chi-restraints excluded: chain X residue 301 THR Chi-restraints excluded: chain X residue 330 ASP Chi-restraints excluded: chain X residue 401 LEU Chi-restraints excluded: chain X residue 409 ILE Chi-restraints excluded: chain X residue 512 GLU Chi-restraints excluded: chain Y residue 313 VAL Chi-restraints excluded: chain Y residue 322 GLN Chi-restraints excluded: chain Y residue 325 MET Chi-restraints excluded: chain Y residue 330 ASP Chi-restraints excluded: chain Y residue 348 THR Chi-restraints excluded: chain Y residue 355 PHE Chi-restraints excluded: chain Y residue 395 MET Chi-restraints excluded: chain Y residue 503 VAL Chi-restraints excluded: chain Z residue 321 THR Chi-restraints excluded: chain Z residue 330 ASP Chi-restraints excluded: chain Z residue 432 GLU Chi-restraints excluded: chain Z residue 512 GLU Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain a residue 430 ASN Chi-restraints excluded: chain a residue 504 ASP Chi-restraints excluded: chain a residue 507 GLU Chi-restraints excluded: chain b residue 351 VAL Chi-restraints excluded: chain c residue 364 GLU Chi-restraints excluded: chain c residue 500 ASP Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain O residue 51 GLN Chi-restraints excluded: chain O residue 205 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 379 optimal weight: 6.9990 chunk 508 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 440 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 chunk 132 optimal weight: 8.9990 chunk 478 optimal weight: 0.7980 chunk 200 optimal weight: 0.9990 chunk 491 optimal weight: 7.9990 chunk 60 optimal weight: 20.0000 chunk 88 optimal weight: 0.0020 overall best weight: 0.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 165 ASN C 73 ASN D 51 GLN F 45 ASN F 105 GLN G 73 ASN H 45 ASN H 80 GLN J 165 ASN K 216 ASN L 165 ASN L 174 ASN M 45 ASN M 105 GLN M 216 ASN N 45 ASN N 80 GLN P 322 GLN P 390 ASN ** P 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 324 ASN V 324 ASN Z 322 GLN c 322 GLN O 80 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.127294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.096295 restraints weight = 55747.511| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 1.63 r_work: 0.2879 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 47066 Z= 0.147 Angle : 0.467 10.399 63704 Z= 0.247 Chirality : 0.042 0.198 7251 Planarity : 0.003 0.061 8400 Dihedral : 3.700 39.960 6856 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.37 % Allowed : 20.04 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.11), residues: 6048 helix: 3.13 (0.10), residues: 2548 sheet: 0.99 (0.14), residues: 1526 loop : 0.09 (0.14), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP c 429 HIS 0.003 0.000 HIS Q 365 PHE 0.031 0.002 PHE C 71 TYR 0.017 0.001 TYR C 143 ARG 0.014 0.000 ARG A 135 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18851.86 seconds wall clock time: 334 minutes 32.64 seconds (20072.64 seconds total)