Starting phenix.real_space_refine on Sat Feb 24 20:59:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d6v_27223/02_2024/8d6v_27223.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d6v_27223/02_2024/8d6v_27223.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d6v_27223/02_2024/8d6v_27223.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d6v_27223/02_2024/8d6v_27223.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d6v_27223/02_2024/8d6v_27223.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d6v_27223/02_2024/8d6v_27223.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 112 5.16 5 C 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 113": "OE1" <-> "OE2" Residue "A GLU 173": "OE1" <-> "OE2" Residue "C GLU 18": "OE1" <-> "OE2" Residue "C GLU 132": "OE1" <-> "OE2" Residue "C GLU 150": "OE1" <-> "OE2" Residue "C GLU 161": "OE1" <-> "OE2" Residue "C GLU 169": "OE1" <-> "OE2" Residue "C GLU 209": "OE1" <-> "OE2" Residue "D PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 70": "OE1" <-> "OE2" Residue "D GLU 119": "OE1" <-> "OE2" Residue "D GLU 121": "OE1" <-> "OE2" Residue "D GLU 137": "OE1" <-> "OE2" Residue "D GLU 173": "OE1" <-> "OE2" Residue "D GLU 209": "OE1" <-> "OE2" Residue "E GLU 15": "OE1" <-> "OE2" Residue "E TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 113": "OE1" <-> "OE2" Residue "E GLU 173": "OE1" <-> "OE2" Residue "F GLU 18": "OE1" <-> "OE2" Residue "F GLU 169": "OE1" <-> "OE2" Residue "F GLU 209": "OE1" <-> "OE2" Residue "G GLU 18": "OE1" <-> "OE2" Residue "G PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 119": "OE1" <-> "OE2" Residue "H GLU 121": "OE1" <-> "OE2" Residue "H GLU 137": "OE1" <-> "OE2" Residue "H GLU 161": "OE1" <-> "OE2" Residue "H GLU 169": "OE1" <-> "OE2" Residue "I GLU 18": "OE1" <-> "OE2" Residue "I GLU 44": "OE1" <-> "OE2" Residue "I GLU 121": "OE1" <-> "OE2" Residue "I GLU 209": "OE1" <-> "OE2" Residue "J PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 150": "OE1" <-> "OE2" Residue "J GLU 173": "OE1" <-> "OE2" Residue "K PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 113": "OE1" <-> "OE2" Residue "K GLU 150": "OE1" <-> "OE2" Residue "K GLU 173": "OE1" <-> "OE2" Residue "L GLU 18": "OE1" <-> "OE2" Residue "L GLU 137": "OE1" <-> "OE2" Residue "L GLU 161": "OE1" <-> "OE2" Residue "M GLU 10": "OE1" <-> "OE2" Residue "M GLU 18": "OE1" <-> "OE2" Residue "M GLU 119": "OE1" <-> "OE2" Residue "M GLU 137": "OE1" <-> "OE2" Residue "M GLU 150": "OE1" <-> "OE2" Residue "N GLU 10": "OE1" <-> "OE2" Residue "N GLU 15": "OE1" <-> "OE2" Residue "N GLU 44": "OE1" <-> "OE2" Residue "N PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 70": "OE1" <-> "OE2" Residue "N GLU 137": "OE1" <-> "OE2" Residue "N GLU 150": "OE1" <-> "OE2" Residue "N GLU 169": "OE1" <-> "OE2" Residue "P GLU 367": "OE1" <-> "OE2" Residue "P GLU 370": "OE1" <-> "OE2" Residue "P TYR 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 432": "OE1" <-> "OE2" Residue "P GLU 434": "OE1" <-> "OE2" Residue "P GLU 507": "OE1" <-> "OE2" Residue "Q GLU 354": "OE1" <-> "OE2" Residue "Q GLU 364": "OE1" <-> "OE2" Residue "Q GLU 434": "OE1" <-> "OE2" Residue "R GLU 354": "OE1" <-> "OE2" Residue "R GLU 364": "OE1" <-> "OE2" Residue "S TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 354": "OE1" <-> "OE2" Residue "S GLU 362": "OE1" <-> "OE2" Residue "S GLU 367": "OE1" <-> "OE2" Residue "S GLU 432": "OE1" <-> "OE2" Residue "T GLU 354": "OE1" <-> "OE2" Residue "T GLU 364": "OE1" <-> "OE2" Residue "T GLU 370": "OE1" <-> "OE2" Residue "T GLU 507": "OE1" <-> "OE2" Residue "U GLU 362": "OE1" <-> "OE2" Residue "U GLU 364": "OE1" <-> "OE2" Residue "U GLU 367": "OE1" <-> "OE2" Residue "U GLU 434": "OE1" <-> "OE2" Residue "U GLU 507": "OE1" <-> "OE2" Residue "U GLU 512": "OE1" <-> "OE2" Residue "V GLU 434": "OE1" <-> "OE2" Residue "W GLU 362": "OE1" <-> "OE2" Residue "W GLU 367": "OE1" <-> "OE2" Residue "W GLU 469": "OE1" <-> "OE2" Residue "W GLU 507": "OE1" <-> "OE2" Residue "X ASP 338": "OD1" <-> "OD2" Residue "X GLU 433": "OE1" <-> "OE2" Residue "X GLU 434": "OE1" <-> "OE2" Residue "X GLU 519": "OE1" <-> "OE2" Residue "Y GLU 362": "OE1" <-> "OE2" Residue "Y GLU 364": "OE1" <-> "OE2" Residue "Y GLU 432": "OE1" <-> "OE2" Residue "Y GLU 433": "OE1" <-> "OE2" Residue "Z ASP 338": "OD1" <-> "OD2" Residue "Z GLU 367": "OE1" <-> "OE2" Residue "Z GLU 432": "OE1" <-> "OE2" Residue "Z GLU 469": "OE1" <-> "OE2" Residue "Z GLU 507": "OE1" <-> "OE2" Residue "a GLU 354": "OE1" <-> "OE2" Residue "a GLU 362": "OE1" <-> "OE2" Residue "a GLU 367": "OE1" <-> "OE2" Residue "a GLU 370": "OE1" <-> "OE2" Residue "a GLU 434": "OE1" <-> "OE2" Residue "b GLU 354": "OE1" <-> "OE2" Residue "b GLU 364": "OE1" <-> "OE2" Residue "b GLU 370": "OE1" <-> "OE2" Residue "b GLU 432": "OE1" <-> "OE2" Residue "b GLU 469": "OE1" <-> "OE2" Residue "b GLU 507": "OE1" <-> "OE2" Residue "c GLU 432": "OE1" <-> "OE2" Residue "c GLU 433": "OE1" <-> "OE2" Residue "c ASP 504": "OD1" <-> "OD2" Residue "c GLU 507": "OE1" <-> "OE2" Residue "c GLU 519": "OE1" <-> "OE2" Residue "O GLU 10": "OE1" <-> "OE2" Residue "O GLU 44": "OE1" <-> "OE2" Residue "O GLU 150": "OE1" <-> "OE2" Residue "O GLU 173": "OE1" <-> "OE2" 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: 23.51, per 1000 atoms: 0.51 Number of scatterers: 46380 At special positions: 0 Unit cell: (133.4, 136.88, 175.16, 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: 18.23 Conformation dependent library (CDL) restraints added in 8.4 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: 207 helices and 70 sheets defined 46.6% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.13 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 Processing helix chain 'A' and resid 95 through 114 removed outlier: 3.547A pdb=" N LEU A 99 " --> pdb=" O THR A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 171 removed outlier: 4.399A pdb=" N ILE A 163 " --> pdb=" O THR A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 190 removed outlier: 3.810A pdb=" N ALA A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 234 Processing helix chain 'C' and resid 9 through 26 Processing helix chain 'C' and resid 67 through 89 Processing helix chain 'C' and resid 95 through 114 removed outlier: 3.552A pdb=" N LEU C 99 " --> pdb=" O THR C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 171 removed outlier: 4.629A 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 114 removed outlier: 3.522A pdb=" N LEU D 99 " --> pdb=" O THR D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 171 removed outlier: 4.557A pdb=" N ILE D 163 " --> pdb=" O THR D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 190 removed outlier: 3.660A 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: 4.660A pdb=" N ILE E 163 " --> pdb=" O THR E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 190 removed outlier: 3.618A pdb=" N ALA E 190 " --> pdb=" O ALA E 186 " (cutoff:3.500A) 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 Processing helix chain 'F' and resid 95 through 114 removed outlier: 3.516A pdb=" N LEU F 99 " --> pdb=" O THR F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 171 removed outlier: 4.278A pdb=" N ILE F 163 " --> pdb=" O THR F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 190 removed outlier: 3.538A pdb=" N ALA F 190 " --> pdb=" O ALA F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 234 Processing helix chain 'G' and resid 9 through 26 Processing helix chain 'G' and resid 67 through 89 Processing helix chain 'G' and resid 95 through 114 Processing helix chain 'G' and resid 159 through 171 removed outlier: 4.552A pdb=" N ILE G 163 " --> pdb=" O THR G 159 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 190 Processing helix chain 'G' and resid 227 through 234 Processing helix chain 'H' and resid 9 through 26 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 Processing helix chain 'H' and resid 159 through 171 removed outlier: 4.183A pdb=" N ILE H 163 " --> pdb=" O THR H 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 190 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 Processing helix chain 'I' and resid 90 through 94 Processing helix chain 'I' and resid 95 through 114 removed outlier: 3.507A pdb=" N LEU I 99 " --> pdb=" O THR I 95 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 171 removed outlier: 4.383A pdb=" N ILE I 163 " --> pdb=" O THR I 159 " (cutoff:3.500A) Processing helix chain 'I' and resid 176 through 190 removed outlier: 3.694A 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: 3.592A pdb=" N LEU J 99 " --> pdb=" O THR J 95 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 171 removed outlier: 4.399A pdb=" N ILE J 163 " --> pdb=" O THR J 159 " (cutoff:3.500A) Processing helix chain 'J' and resid 176 through 190 removed outlier: 3.617A pdb=" N ALA J 190 " --> pdb=" O ALA J 186 " (cutoff:3.500A) 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: 3.520A pdb=" N LEU K 99 " --> pdb=" O THR K 95 " (cutoff:3.500A) Processing helix chain 'K' and resid 159 through 171 removed outlier: 4.519A 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 227 through 234 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: 3.594A pdb=" N LEU L 99 " --> pdb=" O THR L 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 159 through 171 removed outlier: 4.430A pdb=" N ILE L 163 " --> pdb=" O THR L 159 " (cutoff:3.500A) 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: 3.502A pdb=" N LEU M 99 " --> pdb=" O THR M 95 " (cutoff:3.500A) Processing helix chain 'M' and resid 159 through 171 removed outlier: 4.592A 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 227 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 90 through 94 Processing helix chain 'N' and resid 95 through 114 removed outlier: 3.549A pdb=" N LEU N 99 " --> pdb=" O THR N 95 " (cutoff:3.500A) Processing helix chain 'N' and resid 160 through 171 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 390 Processing helix chain 'P' and resid 390 through 395 Processing helix chain 'P' and resid 413 through 416 removed outlier: 3.540A pdb=" N SER P 416 " --> pdb=" O ASP P 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 413 through 416' Processing helix chain 'P' and resid 442 through 454 removed outlier: 3.871A 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: 3.666A 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 390 removed outlier: 3.524A pdb=" N ASN Q 390 " --> pdb=" O MET Q 386 " (cutoff:3.500A) Processing helix chain 'Q' and resid 390 through 396 removed outlier: 3.517A pdb=" N GLN Q 396 " --> pdb=" O ALA Q 392 " (cutoff:3.500A) Processing helix chain 'Q' and resid 442 through 454 removed outlier: 3.734A 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: 3.631A 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 390 removed outlier: 3.511A pdb=" N ASN R 390 " --> pdb=" O MET R 386 " (cutoff:3.500A) Processing helix chain 'R' and resid 390 through 395 Processing helix chain 'R' and resid 413 through 416 Processing helix chain 'R' and resid 442 through 454 removed outlier: 3.770A 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: 3.573A pdb=" N ILE R 510 " --> pdb=" O PRO R 506 " (cutoff:3.500A) Processing helix chain 'S' and resid 348 through 371 Processing helix chain 'S' and resid 375 through 390 removed outlier: 3.523A pdb=" N ASN S 390 " --> pdb=" O MET S 386 " (cutoff:3.500A) 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: 3.764A 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: 3.524A 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 396 removed outlier: 3.709A pdb=" N GLN T 396 " --> pdb=" O ALA T 392 " (cutoff:3.500A) Processing helix chain 'T' and resid 413 through 416 Processing helix chain 'T' and resid 442 through 454 removed outlier: 3.825A 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: 3.678A 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 395 Processing helix chain 'U' and resid 413 through 416 Processing helix chain 'U' and resid 442 through 454 removed outlier: 3.853A 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: 3.648A 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 removed outlier: 3.518A pdb=" N ASN V 390 " --> pdb=" O MET V 386 " (cutoff:3.500A) Processing helix chain 'V' and resid 390 through 395 Processing helix chain 'V' and resid 413 through 416 Processing helix chain 'V' and resid 442 through 454 removed outlier: 3.769A 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: 3.681A 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 removed outlier: 3.586A pdb=" N ASN W 390 " --> pdb=" O MET W 386 " (cutoff:3.500A) 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: 3.839A 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: 3.646A 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 390 Processing helix chain 'X' and resid 390 through 396 Processing helix chain 'X' and resid 413 through 416 Processing helix chain 'X' and resid 442 through 454 removed outlier: 3.706A pdb=" N LYS X 452 " --> pdb=" O SER X 448 " (cutoff:3.500A) Processing helix chain 'X' and resid 455 through 457 No H-bonds generated for 'chain 'X' and resid 455 through 457' Processing helix chain 'X' and resid 459 through 478 Processing helix chain 'X' and resid 506 through 522 removed outlier: 3.631A 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 396 Processing helix chain 'Y' and resid 413 through 416 Processing helix chain 'Y' and resid 442 through 454 removed outlier: 3.780A 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 522 removed outlier: 3.635A 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 390 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: 3.791A 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: 3.625A 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 390 removed outlier: 3.511A pdb=" N ASN a 390 " --> pdb=" O MET a 386 " (cutoff:3.500A) Processing helix chain 'a' and resid 390 through 395 Processing helix chain 'a' and resid 413 through 416 Processing helix chain 'a' and resid 442 through 454 removed outlier: 3.797A 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: 3.597A pdb=" N ILE a 510 " --> pdb=" O PRO a 506 " (cutoff:3.500A) Processing helix chain 'b' and resid 348 through 371 Processing helix chain 'b' and resid 375 through 390 removed outlier: 3.504A pdb=" N ASN b 390 " --> pdb=" O MET b 386 " (cutoff:3.500A) Processing helix chain 'b' and resid 390 through 395 Processing helix chain 'b' and resid 413 through 416 Processing helix chain 'b' and resid 442 through 454 removed outlier: 3.784A 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: 3.634A 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 395 Processing helix chain 'c' and resid 413 through 416 Processing helix chain 'c' and resid 442 through 454 removed outlier: 3.782A 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: 3.621A pdb=" N ILE c 510 " --> pdb=" O PRO c 506 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 26 removed outlier: 3.610A pdb=" N LEU O 19 " --> pdb=" O GLU O 15 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 89 Processing helix chain 'O' and resid 90 through 94 Processing helix chain 'O' and resid 95 through 114 removed outlier: 3.593A pdb=" N LEU O 99 " --> pdb=" O THR O 95 " (cutoff:3.500A) Processing helix chain 'O' and resid 159 through 171 removed outlier: 4.669A 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: 6.503A pdb=" N VAL A 60 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU A 138 " --> pdb=" O GLU A 150 " (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: 6.533A pdb=" N VAL C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 3.740A 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 Processing sheet with id=AA6, first strand: chain 'D' and resid 53 through 57 removed outlier: 6.482A pdb=" N VAL D 60 " --> pdb=" O LEU D 56 " (cutoff:3.500A) removed outlier: 3.996A 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: 6.504A pdb=" N VAL E 60 " --> pdb=" O LEU E 56 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU E 138 " --> pdb=" O GLU E 150 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 153 through 156 Processing sheet with id=AB1, first strand: chain 'F' and resid 53 through 57 removed outlier: 6.499A 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: 6.515A pdb=" N VAL G 60 " --> pdb=" O LEU G 56 " (cutoff:3.500A) removed outlier: 3.766A 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: 6.179A pdb=" N ILE H 53 " --> pdb=" O ALA H 64 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ALA H 64 " --> pdb=" O ILE H 53 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N GLU H 55 " --> pdb=" O PHE H 62 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N PHE H 62 " --> pdb=" O GLU H 55 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU H 138 " --> pdb=" O GLU H 150 " (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: 6.488A pdb=" N VAL I 60 " --> pdb=" O LEU I 56 " (cutoff:3.500A) removed outlier: 3.823A 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: 6.458A pdb=" N VAL J 60 " --> pdb=" O LEU J 56 " (cutoff:3.500A) removed outlier: 3.846A 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 Processing sheet with id=AC2, first strand: chain 'K' and resid 53 through 57 removed outlier: 6.487A pdb=" N VAL K 60 " --> pdb=" O LEU K 56 " (cutoff:3.500A) removed outlier: 3.859A 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 Processing sheet with id=AC4, first strand: chain 'L' and resid 53 through 57 removed outlier: 6.559A pdb=" N VAL L 60 " --> pdb=" O LEU L 56 " (cutoff:3.500A) removed outlier: 3.731A 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: 4.293A 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: 6.498A pdb=" N VAL M 60 " --> pdb=" O LEU M 56 " (cutoff:3.500A) removed outlier: 3.825A 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 Processing sheet with id=AC8, first strand: chain 'N' and resid 53 through 57 removed outlier: 6.535A pdb=" N VAL N 60 " --> pdb=" O LEU N 56 " (cutoff:3.500A) removed outlier: 3.848A 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: 6.511A pdb=" N SER P 320 " --> pdb=" O SER P 327 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET P 325 " --> pdb=" O GLN P 322 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'P' and resid 334 through 338 removed outlier: 6.780A pdb=" N VAL P 334 " --> pdb=" O ILE P 345 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N ILE P 345 " --> pdb=" O VAL P 334 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N ILE P 336 " --> pdb=" O THR P 343 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N THR P 343 " --> pdb=" O ILE P 336 " (cutoff:3.500A) removed outlier: 3.666A 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: 6.564A pdb=" N SER Q 320 " --> pdb=" O SER Q 327 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N MET Q 325 " --> pdb=" O GLN Q 322 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'Q' and resid 334 through 335 removed outlier: 3.720A pdb=" N PHE Q 423 " --> pdb=" O PRO Q 402 " (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: 6.651A pdb=" N SER R 320 " --> pdb=" O SER R 327 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N MET R 325 " --> pdb=" O GLN R 322 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'R' and resid 334 through 338 removed outlier: 6.703A pdb=" N VAL R 334 " --> pdb=" O ILE R 345 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N ILE R 345 " --> pdb=" O VAL R 334 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ILE R 336 " --> pdb=" O THR R 343 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N THR R 343 " --> pdb=" O ILE R 336 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE R 423 " --> pdb=" O PRO R 402 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ILE R 420 " --> pdb=" O GLU R 432 " (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: 6.573A pdb=" N SER S 320 " --> pdb=" O SER S 327 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'S' and resid 334 through 338 removed outlier: 6.703A pdb=" N THR S 341 " --> pdb=" O THR S 337 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE S 423 " --> pdb=" O PRO S 402 " (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: 6.525A 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: 6.597A pdb=" N VAL T 334 " --> pdb=" O ILE T 345 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ILE T 345 " --> pdb=" O VAL T 334 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ILE T 336 " --> pdb=" O THR T 343 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N THR T 343 " --> pdb=" O ILE T 336 " (cutoff:3.500A) removed outlier: 3.724A 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: 6.531A pdb=" N SER U 320 " --> pdb=" O SER U 327 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET U 325 " --> pdb=" O GLN U 322 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'U' and resid 334 through 338 removed outlier: 6.625A pdb=" N THR U 341 " --> pdb=" O THR U 337 " (cutoff:3.500A) removed outlier: 3.907A 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: 6.640A pdb=" N SER V 320 " --> pdb=" O SER V 327 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'V' and resid 334 through 338 removed outlier: 6.517A pdb=" N THR V 341 " --> pdb=" O THR V 337 " (cutoff:3.500A) removed outlier: 3.836A 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: 6.530A pdb=" N SER W 320 " --> pdb=" O SER W 327 " (cutoff:3.500A) removed outlier: 3.761A 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: 6.717A pdb=" N VAL W 334 " --> pdb=" O ILE W 345 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ILE W 345 " --> pdb=" O VAL W 334 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ILE W 336 " --> pdb=" O THR W 343 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N THR W 343 " --> pdb=" O ILE W 336 " (cutoff:3.500A) removed outlier: 3.752A 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: 6.630A pdb=" N GLN X 322 " --> pdb=" O ILE X 326 " (cutoff:3.500A) removed outlier: 6.075A 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 335 removed outlier: 3.870A 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: 6.593A 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: 6.652A pdb=" N THR Y 341 " --> pdb=" O THR Y 337 " (cutoff:3.500A) removed outlier: 3.811A 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: 6.425A pdb=" N GLN Z 322 " --> pdb=" O ILE Z 326 " (cutoff:3.500A) removed outlier: 5.316A 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 335 removed outlier: 3.767A 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: 6.426A pdb=" N SER a 320 " --> pdb=" O SER a 327 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'a' and resid 334 through 338 removed outlier: 6.643A pdb=" N VAL a 334 " --> pdb=" O ILE a 345 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N ILE a 345 " --> pdb=" O VAL a 334 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ILE a 336 " --> pdb=" O THR a 343 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N THR a 343 " --> pdb=" O ILE a 336 " (cutoff:3.500A) removed outlier: 3.768A 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: 6.558A 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: 6.541A pdb=" N THR b 341 " --> pdb=" O THR b 337 " (cutoff:3.500A) removed outlier: 3.674A 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: 6.548A pdb=" N SER c 320 " --> pdb=" O SER c 327 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET c 325 " --> pdb=" O GLN c 322 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'c' and resid 334 through 338 removed outlier: 6.697A pdb=" N VAL c 334 " --> pdb=" O ILE c 345 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ILE c 345 " --> pdb=" O VAL c 334 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ILE c 336 " --> pdb=" O THR c 343 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR c 343 " --> pdb=" O ILE c 336 " (cutoff:3.500A) removed outlier: 3.835A 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 Processing sheet with id=AH7, first strand: chain 'O' and resid 53 through 57 removed outlier: 6.471A pdb=" N VAL O 60 " --> pdb=" O LEU O 56 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU O 138 " --> pdb=" O GLU O 150 " (cutoff:3.500A) 3023 hydrogen bonds defined for protein. 8631 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 20.35 Time building geometry restraints manager: 18.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 12568 1.33 - 1.45: 7877 1.45 - 1.57: 26411 1.57 - 1.69: 0 1.69 - 1.81: 210 Bond restraints: 47066 Sorted by residual: bond pdb=" N THR X 341 " pdb=" CA THR X 341 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.27e-02 6.20e+03 8.49e+00 bond pdb=" N THR R 341 " pdb=" CA THR R 341 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.25e-02 6.40e+03 8.30e+00 bond pdb=" N ILE Q 336 " pdb=" CA ILE Q 336 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.22e-02 6.72e+03 8.20e+00 bond pdb=" N THR Y 341 " pdb=" CA THR Y 341 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.26e-02 6.30e+03 8.17e+00 bond pdb=" N THR S 341 " pdb=" CA THR S 341 " ideal model delta sigma weight residual 1.454 1.491 -0.036 1.27e-02 6.20e+03 8.11e+00 ... (remaining 47061 not shown) Histogram of bond angle deviations from ideal: 98.16 - 105.32: 737 105.32 - 112.49: 23678 112.49 - 119.65: 15899 119.65 - 126.81: 23102 126.81 - 133.98: 288 Bond angle restraints: 63704 Sorted by residual: angle pdb=" N ARG O 16 " pdb=" CA ARG O 16 " pdb=" C ARG O 16 " ideal model delta sigma weight residual 112.90 107.75 5.15 1.31e+00 5.83e-01 1.55e+01 angle pdb=" O TYR E 89 " pdb=" C TYR E 89 " pdb=" N ASP E 90 " ideal model delta sigma weight residual 120.71 124.20 -3.49 9.00e-01 1.23e+00 1.50e+01 angle pdb=" CA PRO R 414 " pdb=" N PRO R 414 " pdb=" CD PRO R 414 " ideal model delta sigma weight residual 112.00 106.72 5.28 1.40e+00 5.10e-01 1.42e+01 angle pdb=" CA TYR E 89 " pdb=" C TYR E 89 " pdb=" N ASP E 90 " ideal model delta sigma weight residual 119.56 117.42 2.14 5.80e-01 2.97e+00 1.36e+01 angle pdb=" N GLY O 66 " pdb=" CA GLY O 66 " pdb=" C GLY O 66 " ideal model delta sigma weight residual 110.29 114.49 -4.20 1.28e+00 6.10e-01 1.08e+01 ... (remaining 63699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.10: 26209 18.10 - 36.19: 1669 36.19 - 54.29: 349 54.29 - 72.39: 60 72.39 - 90.48: 48 Dihedral angle restraints: 28335 sinusoidal: 10807 harmonic: 17528 Sorted by residual: dihedral pdb=" CA VAL G 212 " pdb=" C VAL G 212 " pdb=" N LEU G 213 " pdb=" CA LEU G 213 " ideal model delta harmonic sigma weight residual 180.00 159.59 20.41 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA VAL H 212 " pdb=" C VAL H 212 " pdb=" N LEU H 213 " pdb=" CA LEU H 213 " ideal model delta harmonic sigma weight residual 180.00 159.73 20.27 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA VAL K 212 " pdb=" C VAL K 212 " pdb=" N LEU K 213 " pdb=" CA LEU K 213 " ideal model delta harmonic sigma weight residual 180.00 159.90 20.10 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 28332 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 5570 0.048 - 0.095: 1281 0.095 - 0.143: 387 0.143 - 0.191: 6 0.191 - 0.239: 7 Chirality restraints: 7251 Sorted by residual: chirality pdb=" CA ILE Z 336 " pdb=" N ILE Z 336 " pdb=" C ILE Z 336 " pdb=" CB ILE Z 336 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA ILE Q 336 " pdb=" N ILE Q 336 " pdb=" C ILE Q 336 " pdb=" CB ILE Q 336 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA ILE b 336 " pdb=" N ILE b 336 " pdb=" C ILE b 336 " pdb=" CB ILE b 336 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 7248 not shown) Planarity restraints: 8400 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP R 413 " 0.086 5.00e-02 4.00e+02 1.28e-01 2.64e+01 pdb=" N PRO R 414 " -0.222 5.00e-02 4.00e+02 pdb=" CA PRO R 414 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO R 414 " 0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG I 135 " -0.036 5.00e-02 4.00e+02 5.44e-02 4.74e+00 pdb=" N PRO I 136 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO I 136 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO I 136 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG H 135 " -0.034 5.00e-02 4.00e+02 5.26e-02 4.42e+00 pdb=" N PRO H 136 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO H 136 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO H 136 " -0.029 5.00e-02 4.00e+02 ... (remaining 8397 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3898 2.74 - 3.28: 43587 3.28 - 3.82: 76895 3.82 - 4.36: 89776 4.36 - 4.90: 163022 Nonbonded interactions: 377178 Sorted by model distance: nonbonded pdb=" OD1 ASP V 338 " pdb=" OG1 THR V 341 " model vdw 2.204 2.440 nonbonded pdb=" OD1 ASP W 338 " pdb=" OG1 THR W 341 " model vdw 2.223 2.440 nonbonded pdb=" OG SER Z 422 " pdb=" OE2 GLU Z 432 " model vdw 2.234 2.440 nonbonded pdb=" O ILE E 147 " pdb=" NE2 GLN e 172 " model vdw 2.235 2.520 nonbonded pdb=" OG SER E 29 " pdb=" O GLY E 157 " model vdw 2.245 2.440 ... (remaining 377173 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: 3.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 13.540 Check model and map are aligned: 0.660 Set scattering table: 0.430 Process input model: 117.490 Find NCS groups from input model: 3.730 Set up NCS constraints: 0.410 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 142.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 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 : 0.003 0.059 47066 Z= 0.231 Angle : 0.572 9.118 63704 Z= 0.341 Chirality : 0.044 0.239 7251 Planarity : 0.004 0.128 8400 Dihedral : 13.295 90.483 17177 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % 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: 2.14 (0.11), residues: 6048 helix: 2.83 (0.10), residues: 2548 sheet: 0.83 (0.13), residues: 1484 loop : 0.06 (0.14), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP T 429 HIS 0.005 0.001 HIS b 365 PHE 0.029 0.002 PHE J 71 TYR 0.021 0.001 TYR M 118 ARG 0.011 0.000 ARG G 21 *********************** 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 685 residues out of total 4641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 685 time to evaluate : 4.974 Fit side-chains REVERT: A 17 SER cc_start: 0.8551 (m) cc_final: 0.8296 (m) REVERT: A 80 GLN cc_start: 0.8468 (mt0) cc_final: 0.8020 (mt0) REVERT: C 14 ARG cc_start: 0.6982 (mtp-110) cc_final: 0.6700 (mtm-85) REVERT: D 174 ASN cc_start: 0.7227 (m-40) cc_final: 0.6593 (t0) REVERT: E 106 THR cc_start: 0.8420 (t) cc_final: 0.7967 (p) REVERT: G 29 SER cc_start: 0.7815 (m) cc_final: 0.7549 (m) REVERT: G 109 THR cc_start: 0.7922 (m) cc_final: 0.7722 (m) REVERT: J 80 GLN cc_start: 0.8129 (tm-30) cc_final: 0.7670 (tp40) REVERT: J 156 MET cc_start: 0.8899 (mtm) cc_final: 0.8603 (mtm) REVERT: K 93 ASP cc_start: 0.8967 (m-30) cc_final: 0.8623 (m-30) REVERT: L 29 SER cc_start: 0.9334 (m) cc_final: 0.9126 (m) REVERT: L 47 SER cc_start: 0.8588 (m) cc_final: 0.8379 (m) REVERT: M 22 LYS cc_start: 0.7937 (mtmt) cc_final: 0.7606 (mtmt) REVERT: R 503 VAL cc_start: 0.8826 (m) cc_final: 0.8527 (p) REVERT: V 354 GLU cc_start: 0.7587 (tt0) cc_final: 0.7265 (tt0) REVERT: X 444 LEU cc_start: 0.8677 (mp) cc_final: 0.8476 (mp) REVERT: Y 458 THR cc_start: 0.8330 (p) cc_final: 0.8053 (p) REVERT: O 93 ASP cc_start: 0.9004 (m-30) cc_final: 0.8785 (m-30) outliers start: 0 outliers final: 0 residues processed: 685 average time/residue: 0.6058 time to fit residues: 682.0335 Evaluate side-chains 585 residues out of total 4641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 585 time to evaluate : 5.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 508 optimal weight: 0.0170 chunk 456 optimal weight: 0.9990 chunk 253 optimal weight: 0.9980 chunk 155 optimal weight: 0.0670 chunk 307 optimal weight: 2.9990 chunk 243 optimal weight: 4.9990 chunk 471 optimal weight: 0.9980 chunk 182 optimal weight: 0.9980 chunk 286 optimal weight: 4.9990 chunk 351 optimal weight: 1.9990 chunk 546 optimal weight: 0.0050 overall best weight: 0.4170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 216 ASN G 80 GLN ** J 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 105 GLN L 80 GLN M 45 ASN M 80 GLN N 45 ASN P 322 GLN R 322 GLN ** d 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 172 GLN ** h 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 174 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.0709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 47066 Z= 0.128 Angle : 0.447 7.343 63704 Z= 0.240 Chirality : 0.042 0.172 7251 Planarity : 0.003 0.047 8400 Dihedral : 3.526 23.628 6853 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.71 % Allowed : 5.30 % Favored : 93.99 % 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: 2.40 (0.11), residues: 6048 helix: 3.07 (0.10), residues: 2576 sheet: 0.95 (0.14), residues: 1484 loop : 0.12 (0.14), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP T 429 HIS 0.004 0.001 HIS Z 365 PHE 0.037 0.002 PHE N 71 TYR 0.009 0.001 TYR b 359 ARG 0.006 0.000 ARG F 21 *********************** 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 644 residues out of total 4641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 611 time to evaluate : 5.445 Fit side-chains revert: symmetry clash REVERT: A 17 SER cc_start: 0.8573 (m) cc_final: 0.8326 (m) REVERT: D 174 ASN cc_start: 0.7202 (m-40) cc_final: 0.6989 (m110) REVERT: E 105 GLN cc_start: 0.7377 (tp40) cc_final: 0.7085 (tp40) REVERT: G 29 SER cc_start: 0.7744 (m) cc_final: 0.7506 (m) REVERT: G 109 THR cc_start: 0.7981 (m) cc_final: 0.7696 (m) REVERT: H 143 TYR cc_start: 0.7489 (p90) cc_final: 0.7257 (p90) REVERT: I 133 THR cc_start: 0.8216 (t) cc_final: 0.8005 (m) REVERT: L 156 MET cc_start: 0.8704 (mtm) cc_final: 0.8295 (mtm) REVERT: P 333 LYS cc_start: 0.8968 (mttt) cc_final: 0.8671 (mtmt) REVERT: Q 314 MET cc_start: 0.8719 (ttt) cc_final: 0.8514 (ttt) REVERT: R 503 VAL cc_start: 0.8786 (m) cc_final: 0.8538 (p) REVERT: V 401 LEU cc_start: 0.7957 (mt) cc_final: 0.7675 (mp) REVERT: X 469 GLU cc_start: 0.7689 (tt0) cc_final: 0.7476 (tt0) REVERT: Y 314 MET cc_start: 0.8849 (ttt) cc_final: 0.8612 (ttt) outliers start: 33 outliers final: 20 residues processed: 624 average time/residue: 0.5831 time to fit residues: 597.4110 Evaluate side-chains 588 residues out of total 4641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 568 time to evaluate : 5.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain H residue 147 ILE Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain M residue 203 LEU Chi-restraints excluded: chain N residue 160 THR Chi-restraints excluded: chain P residue 413 ASP Chi-restraints excluded: chain R residue 401 LEU Chi-restraints excluded: chain V residue 301 THR Chi-restraints excluded: chain X residue 395 MET Chi-restraints excluded: chain X residue 500 ASP Chi-restraints excluded: chain Y residue 401 LEU Chi-restraints excluded: chain Z residue 504 ASP Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain b residue 301 THR Chi-restraints excluded: chain b residue 330 ASP Chi-restraints excluded: chain c residue 388 ARG 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: 5.9990 chunk 454 optimal weight: 0.9980 chunk 372 optimal weight: 9.9990 chunk 150 optimal weight: 0.6980 chunk 547 optimal weight: 1.9990 chunk 591 optimal weight: 0.7980 chunk 487 optimal weight: 0.7980 chunk 543 optimal weight: 2.9990 chunk 186 optimal weight: 8.9990 chunk 439 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 114 GLN F 216 ASN G 80 GLN ** J 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 105 GLN M 45 ASN M 165 ASN P 322 GLN S 390 ASN ** d 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 174 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.0879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 47066 Z= 0.175 Angle : 0.454 7.358 63704 Z= 0.241 Chirality : 0.042 0.174 7251 Planarity : 0.003 0.044 8400 Dihedral : 3.512 23.752 6853 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.06 % Allowed : 7.35 % Favored : 91.59 % 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: 2.39 (0.11), residues: 6048 helix: 3.09 (0.10), residues: 2576 sheet: 0.87 (0.13), residues: 1526 loop : 0.12 (0.14), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP T 429 HIS 0.004 0.001 HIS S 365 PHE 0.034 0.002 PHE N 71 TYR 0.012 0.001 TYR M 87 ARG 0.007 0.000 ARG G 21 *********************** 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 626 residues out of total 4641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 577 time to evaluate : 4.775 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 SER cc_start: 0.8586 (m) cc_final: 0.8344 (m) REVERT: D 174 ASN cc_start: 0.7184 (m-40) cc_final: 0.6982 (m110) REVERT: E 105 GLN cc_start: 0.7442 (tp40) cc_final: 0.7113 (tp40) REVERT: F 118 TYR cc_start: 0.8728 (m-10) cc_final: 0.8519 (m-10) REVERT: G 29 SER cc_start: 0.7841 (m) cc_final: 0.7584 (m) REVERT: G 109 THR cc_start: 0.8006 (m) cc_final: 0.7722 (m) REVERT: H 225 ILE cc_start: 0.8227 (mt) cc_final: 0.7772 (tp) REVERT: I 209 GLU cc_start: 0.6951 (tt0) cc_final: 0.6689 (tt0) REVERT: L 156 MET cc_start: 0.8774 (mtm) cc_final: 0.8425 (mtm) REVERT: M 22 LYS cc_start: 0.7850 (mtmt) cc_final: 0.7453 (mtmt) REVERT: N 167 LEU cc_start: 0.7892 (mt) cc_final: 0.7685 (mt) REVERT: Q 314 MET cc_start: 0.8831 (ttt) cc_final: 0.8604 (ttt) REVERT: R 503 VAL cc_start: 0.8807 (m) cc_final: 0.8540 (p) REVERT: S 395 MET cc_start: 0.6917 (mmm) cc_final: 0.6306 (mmt) REVERT: Y 314 MET cc_start: 0.8824 (ttt) cc_final: 0.8604 (ttt) REVERT: Z 364 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7459 (tp30) REVERT: a 509 ARG cc_start: 0.7807 (ttt180) cc_final: 0.7591 (ttt180) outliers start: 49 outliers final: 40 residues processed: 596 average time/residue: 0.5905 time to fit residues: 583.9042 Evaluate side-chains 599 residues out of total 4641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 558 time to evaluate : 4.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain H residue 147 ILE Chi-restraints excluded: chain I residue 73 ASN Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain M residue 163 ILE Chi-restraints excluded: chain M residue 203 LEU Chi-restraints excluded: chain N residue 160 THR Chi-restraints excluded: chain N residue 178 THR Chi-restraints excluded: chain P residue 325 MET Chi-restraints excluded: chain P residue 413 ASP Chi-restraints excluded: chain Q residue 338 ASP Chi-restraints excluded: chain R residue 401 LEU Chi-restraints excluded: chain S residue 399 LEU Chi-restraints excluded: chain T residue 395 MET Chi-restraints excluded: chain U residue 338 ASP Chi-restraints excluded: chain U residue 341 THR Chi-restraints excluded: chain V residue 301 THR Chi-restraints excluded: chain X residue 341 THR Chi-restraints excluded: chain X residue 444 LEU Chi-restraints excluded: chain X residue 500 ASP Chi-restraints excluded: chain X residue 503 VAL Chi-restraints excluded: chain Y residue 401 LEU Chi-restraints excluded: chain Z residue 364 GLU Chi-restraints excluded: chain Z residue 401 LEU Chi-restraints excluded: chain Z residue 504 ASP Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain b residue 301 THR Chi-restraints excluded: chain b residue 330 ASP Chi-restraints excluded: chain b residue 447 LYS Chi-restraints excluded: chain c residue 325 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 541 optimal weight: 4.9990 chunk 411 optimal weight: 3.9990 chunk 284 optimal weight: 0.0970 chunk 60 optimal weight: 9.9990 chunk 261 optimal weight: 2.9990 chunk 367 optimal weight: 1.9990 chunk 549 optimal weight: 0.6980 chunk 581 optimal weight: 0.7980 chunk 287 optimal weight: 1.9990 chunk 520 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 216 ASN G 80 GLN J 105 GLN K 73 ASN K 105 GLN M 45 ASN N 45 ASN P 322 GLN ** d 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 174 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 47066 Z= 0.218 Angle : 0.469 7.742 63704 Z= 0.250 Chirality : 0.043 0.176 7251 Planarity : 0.003 0.044 8400 Dihedral : 3.598 25.256 6853 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.31 % Allowed : 8.36 % Favored : 90.32 % 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: 2576 sheet: 0.99 (0.14), residues: 1484 loop : -0.00 (0.14), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP T 429 HIS 0.004 0.001 HIS S 365 PHE 0.034 0.002 PHE I 71 TYR 0.012 0.001 TYR N 87 ARG 0.007 0.000 ARG G 21 *********************** 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 637 residues out of total 4641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 576 time to evaluate : 5.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 SER cc_start: 0.8596 (m) cc_final: 0.8351 (m) REVERT: A 156 MET cc_start: 0.8824 (mtm) cc_final: 0.8211 (mtt) REVERT: D 134 LYS cc_start: 0.7797 (ttpt) cc_final: 0.7589 (ttpt) REVERT: E 105 GLN cc_start: 0.7471 (tp40) cc_final: 0.7108 (tp40) REVERT: E 140 ARG cc_start: 0.7046 (OUTLIER) cc_final: 0.6599 (ttm-80) REVERT: G 29 SER cc_start: 0.7858 (m) cc_final: 0.7628 (m) REVERT: G 109 THR cc_start: 0.8006 (m) cc_final: 0.7748 (m) REVERT: H 73 ASN cc_start: 0.7628 (t0) cc_final: 0.7255 (m-40) REVERT: H 225 ILE cc_start: 0.8309 (mt) cc_final: 0.7850 (tp) REVERT: L 156 MET cc_start: 0.8769 (mtm) cc_final: 0.8409 (mtm) REVERT: M 22 LYS cc_start: 0.7853 (mtmt) cc_final: 0.7397 (mtmt) REVERT: N 24 ILE cc_start: 0.8660 (mm) cc_final: 0.8208 (mt) REVERT: a 324 ASN cc_start: 0.7845 (m-40) cc_final: 0.7610 (m-40) REVERT: a 509 ARG cc_start: 0.7827 (ttt180) cc_final: 0.7618 (ttt180) REVERT: O 114 GLN cc_start: 0.8237 (mt0) cc_final: 0.7841 (mt0) outliers start: 61 outliers final: 51 residues processed: 602 average time/residue: 0.6114 time to fit residues: 611.2783 Evaluate side-chains 612 residues out of total 4641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 560 time to evaluate : 4.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 140 ARG Chi-restraints excluded: chain E residue 169 GLU Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 147 ILE Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain K residue 73 ASN Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 163 ILE Chi-restraints excluded: chain M residue 163 ILE Chi-restraints excluded: chain M residue 203 LEU Chi-restraints excluded: chain N residue 160 THR Chi-restraints excluded: chain N residue 178 THR Chi-restraints excluded: chain P residue 325 MET Chi-restraints excluded: chain P residue 341 THR Chi-restraints excluded: chain P residue 413 ASP Chi-restraints excluded: chain Q residue 338 ASP Chi-restraints excluded: chain R residue 401 LEU Chi-restraints excluded: chain S residue 399 LEU Chi-restraints excluded: chain T residue 395 MET Chi-restraints excluded: chain U residue 341 THR Chi-restraints excluded: chain U residue 401 LEU Chi-restraints excluded: chain V residue 301 THR Chi-restraints excluded: chain V residue 322 GLN Chi-restraints excluded: chain W residue 395 MET Chi-restraints excluded: chain W residue 401 LEU Chi-restraints excluded: chain X residue 341 THR Chi-restraints excluded: chain X residue 444 LEU Chi-restraints excluded: chain X residue 500 ASP Chi-restraints excluded: chain X residue 503 VAL Chi-restraints excluded: chain Y residue 401 LEU Chi-restraints excluded: chain Z residue 364 GLU Chi-restraints excluded: chain Z residue 401 LEU Chi-restraints excluded: chain Z residue 504 ASP Chi-restraints excluded: chain a residue 391 LEU Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain b residue 301 THR Chi-restraints excluded: chain b residue 330 ASP Chi-restraints excluded: chain b residue 447 LYS Chi-restraints excluded: chain c residue 325 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 484 optimal weight: 2.9990 chunk 330 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 433 optimal weight: 2.9990 chunk 240 optimal weight: 2.9990 chunk 496 optimal weight: 1.9990 chunk 402 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 297 optimal weight: 2.9990 chunk 522 optimal weight: 0.0980 chunk 146 optimal weight: 6.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 216 ASN G 80 GLN J 105 GLN K 80 GLN K 105 GLN M 45 ASN M 165 ASN P 322 GLN S 390 ASN W 437 GLN Y 390 ASN ** d 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 174 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 47066 Z= 0.323 Angle : 0.524 9.008 63704 Z= 0.277 Chirality : 0.044 0.190 7251 Planarity : 0.004 0.045 8400 Dihedral : 3.847 28.817 6853 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.51 % Allowed : 9.42 % Favored : 89.07 % 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: 2.80 (0.10), residues: 2590 sheet: 0.87 (0.13), residues: 1484 loop : -0.19 (0.14), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP b 429 HIS 0.005 0.001 HIS V 365 PHE 0.035 0.003 PHE J 71 TYR 0.013 0.001 TYR J 87 ARG 0.008 0.000 ARG K 75 *********************** 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 641 residues out of total 4641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 571 time to evaluate : 5.469 Fit side-chains revert: symmetry clash REVERT: A 17 SER cc_start: 0.8624 (m) cc_final: 0.8395 (m) REVERT: E 140 ARG cc_start: 0.6998 (OUTLIER) cc_final: 0.6565 (ttm-80) REVERT: G 109 THR cc_start: 0.8072 (m) cc_final: 0.7824 (m) REVERT: G 143 TYR cc_start: 0.6943 (p90) cc_final: 0.6472 (p90) REVERT: H 73 ASN cc_start: 0.7817 (t0) cc_final: 0.7387 (m-40) REVERT: H 156 MET cc_start: 0.8127 (mtm) cc_final: 0.7450 (mtm) REVERT: H 225 ILE cc_start: 0.8317 (mt) cc_final: 0.7886 (tp) REVERT: J 233 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7723 (tp) REVERT: K 80 GLN cc_start: 0.8197 (mt0) cc_final: 0.7678 (tt0) REVERT: L 24 ILE cc_start: 0.8638 (mt) cc_final: 0.8427 (mp) REVERT: L 156 MET cc_start: 0.8835 (mtm) cc_final: 0.8474 (mtm) REVERT: N 24 ILE cc_start: 0.8639 (mm) cc_final: 0.8260 (mt) REVERT: S 395 MET cc_start: 0.7007 (mmm) cc_final: 0.6497 (mmt) REVERT: X 345 ILE cc_start: 0.9169 (OUTLIER) cc_final: 0.8958 (mm) REVERT: a 324 ASN cc_start: 0.7902 (m-40) cc_final: 0.7652 (m-40) REVERT: c 430 ASN cc_start: 0.7811 (t0) cc_final: 0.7585 (t0) REVERT: O 114 GLN cc_start: 0.8374 (mt0) cc_final: 0.7993 (mt0) REVERT: O 183 ILE cc_start: 0.7701 (mt) cc_final: 0.7487 (mt) outliers start: 70 outliers final: 59 residues processed: 600 average time/residue: 0.5840 time to fit residues: 575.8699 Evaluate side-chains 612 residues out of total 4641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 550 time to evaluate : 5.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 140 ARG Chi-restraints excluded: chain E residue 169 GLU Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 147 ILE Chi-restraints excluded: chain I residue 73 ASN Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain J residue 29 SER Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 163 ILE Chi-restraints excluded: chain L residue 170 SER Chi-restraints excluded: chain M residue 163 ILE Chi-restraints excluded: chain M residue 203 LEU Chi-restraints excluded: chain N residue 160 THR Chi-restraints excluded: chain N residue 178 THR Chi-restraints excluded: chain N residue 205 VAL Chi-restraints excluded: chain P residue 325 MET Chi-restraints excluded: chain P residue 413 ASP Chi-restraints excluded: chain R residue 399 LEU Chi-restraints excluded: chain R residue 401 LEU Chi-restraints excluded: chain S residue 399 LEU Chi-restraints excluded: chain T residue 313 VAL Chi-restraints excluded: chain T residue 395 MET Chi-restraints excluded: chain T residue 401 LEU Chi-restraints excluded: chain U residue 401 LEU Chi-restraints excluded: chain V residue 301 THR Chi-restraints excluded: chain V residue 322 GLN Chi-restraints excluded: chain W residue 401 LEU Chi-restraints excluded: chain X residue 341 THR Chi-restraints excluded: chain X residue 345 ILE Chi-restraints excluded: chain X residue 395 MET Chi-restraints excluded: chain X residue 444 LEU Chi-restraints excluded: chain X residue 500 ASP Chi-restraints excluded: chain X residue 503 VAL Chi-restraints excluded: chain Y residue 401 LEU Chi-restraints excluded: chain Y residue 458 THR Chi-restraints excluded: chain Z residue 364 GLU Chi-restraints excluded: chain Z residue 401 LEU Chi-restraints excluded: chain Z residue 504 ASP Chi-restraints excluded: chain a residue 391 LEU Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain b residue 301 THR Chi-restraints excluded: chain b residue 330 ASP Chi-restraints excluded: chain b residue 401 LEU Chi-restraints excluded: chain b residue 447 LYS Chi-restraints excluded: chain b residue 458 THR Chi-restraints excluded: chain c residue 325 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 195 optimal weight: 0.8980 chunk 524 optimal weight: 0.0980 chunk 115 optimal weight: 6.9990 chunk 341 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 582 optimal weight: 7.9990 chunk 483 optimal weight: 0.8980 chunk 269 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 192 optimal weight: 3.9990 chunk 305 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 80 GLN G 165 ASN K 73 ASN K 105 GLN K 231 GLN L 80 GLN M 165 ASN P 322 GLN ** d 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 174 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 47066 Z= 0.167 Angle : 0.450 7.134 63704 Z= 0.241 Chirality : 0.042 0.171 7251 Planarity : 0.003 0.044 8400 Dihedral : 3.627 26.542 6853 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.40 % Allowed : 10.17 % Favored : 88.43 % 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: 2.25 (0.11), residues: 6048 helix: 3.01 (0.10), residues: 2590 sheet: 0.83 (0.13), residues: 1526 loop : -0.07 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP T 429 HIS 0.003 0.001 HIS S 365 PHE 0.031 0.002 PHE I 71 TYR 0.010 0.001 TYR W 359 ARG 0.011 0.000 ARG J 26 *********************** 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 635 residues out of total 4641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 570 time to evaluate : 5.237 Fit side-chains revert: symmetry clash REVERT: A 17 SER cc_start: 0.8614 (m) cc_final: 0.8381 (m) REVERT: A 51 GLN cc_start: 0.8460 (mm-40) cc_final: 0.8071 (mm-40) REVERT: E 105 GLN cc_start: 0.7487 (tp40) cc_final: 0.7115 (tp40) REVERT: E 140 ARG cc_start: 0.6969 (OUTLIER) cc_final: 0.6506 (ttm170) REVERT: G 109 THR cc_start: 0.7991 (m) cc_final: 0.7730 (m) REVERT: G 143 TYR cc_start: 0.6840 (p90) cc_final: 0.6435 (p90) REVERT: H 73 ASN cc_start: 0.7620 (t0) cc_final: 0.7268 (m-40) REVERT: H 156 MET cc_start: 0.8119 (mtm) cc_final: 0.7381 (mtm) REVERT: H 225 ILE cc_start: 0.8313 (mt) cc_final: 0.7866 (tp) REVERT: J 233 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7770 (tp) REVERT: L 156 MET cc_start: 0.8806 (mtm) cc_final: 0.8452 (mtm) REVERT: M 22 LYS cc_start: 0.7914 (mtmt) cc_final: 0.7562 (mtmt) REVERT: N 24 ILE cc_start: 0.8594 (mm) cc_final: 0.8189 (mt) REVERT: S 395 MET cc_start: 0.6901 (mmm) cc_final: 0.6289 (mmt) REVERT: X 322 GLN cc_start: 0.7983 (OUTLIER) cc_final: 0.7760 (pm20) REVERT: X 345 ILE cc_start: 0.9136 (OUTLIER) cc_final: 0.8923 (mm) REVERT: Z 364 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7589 (tp30) REVERT: a 324 ASN cc_start: 0.7832 (m-40) cc_final: 0.7590 (m-40) REVERT: O 114 GLN cc_start: 0.8321 (mt0) cc_final: 0.7944 (mt0) REVERT: O 183 ILE cc_start: 0.7791 (mt) cc_final: 0.7570 (mt) outliers start: 65 outliers final: 50 residues processed: 599 average time/residue: 0.5811 time to fit residues: 574.3403 Evaluate side-chains 610 residues out of total 4641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 555 time to evaluate : 5.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 140 ARG Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain H residue 147 ILE Chi-restraints excluded: chain I residue 73 ASN Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain L residue 17 SER Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 163 ILE Chi-restraints excluded: chain M residue 147 ILE Chi-restraints excluded: chain M residue 163 ILE Chi-restraints excluded: chain M residue 203 LEU Chi-restraints excluded: chain N residue 160 THR Chi-restraints excluded: chain N residue 178 THR Chi-restraints excluded: chain N residue 205 VAL Chi-restraints excluded: chain P residue 325 MET Chi-restraints excluded: chain P residue 413 ASP Chi-restraints excluded: chain R residue 401 LEU Chi-restraints excluded: chain S residue 399 LEU Chi-restraints excluded: chain S residue 401 LEU Chi-restraints excluded: chain T residue 395 MET Chi-restraints excluded: chain U residue 341 THR Chi-restraints excluded: chain U residue 401 LEU Chi-restraints excluded: chain V residue 301 THR Chi-restraints excluded: chain V residue 322 GLN Chi-restraints excluded: chain V residue 330 ASP Chi-restraints excluded: chain V residue 399 LEU Chi-restraints excluded: chain W residue 401 LEU Chi-restraints excluded: chain X residue 322 GLN Chi-restraints excluded: chain X residue 341 THR Chi-restraints excluded: chain X residue 345 ILE Chi-restraints excluded: chain X residue 395 MET Chi-restraints excluded: chain X residue 444 LEU Chi-restraints excluded: chain X residue 500 ASP Chi-restraints excluded: chain Y residue 401 LEU Chi-restraints excluded: chain Z residue 364 GLU Chi-restraints excluded: chain Z residue 401 LEU Chi-restraints excluded: chain Z residue 504 ASP Chi-restraints excluded: chain a residue 391 LEU Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain b residue 301 THR Chi-restraints excluded: chain b residue 330 ASP Chi-restraints excluded: chain b residue 447 LYS Chi-restraints excluded: chain b residue 458 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 561 optimal weight: 4.9990 chunk 65 optimal weight: 9.9990 chunk 331 optimal weight: 0.9980 chunk 425 optimal weight: 4.9990 chunk 329 optimal weight: 2.9990 chunk 490 optimal weight: 2.9990 chunk 325 optimal weight: 0.8980 chunk 580 optimal weight: 0.5980 chunk 363 optimal weight: 0.8980 chunk 353 optimal weight: 0.9990 chunk 267 optimal weight: 0.0370 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 80 GLN K 105 GLN M 165 ASN P 322 GLN S 390 ASN ** d 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 174 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 47066 Z= 0.157 Angle : 0.440 6.801 63704 Z= 0.235 Chirality : 0.042 0.170 7251 Planarity : 0.003 0.050 8400 Dihedral : 3.513 22.925 6853 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.40 % Allowed : 10.58 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.11), residues: 6048 helix: 3.09 (0.10), residues: 2590 sheet: 0.89 (0.13), residues: 1526 loop : -0.02 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP T 429 HIS 0.003 0.001 HIS S 365 PHE 0.031 0.002 PHE I 71 TYR 0.010 0.001 TYR W 359 ARG 0.012 0.000 ARG J 26 *********************** 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 639 residues out of total 4641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 574 time to evaluate : 4.674 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 SER cc_start: 0.8617 (m) cc_final: 0.8368 (m) REVERT: A 51 GLN cc_start: 0.8463 (mm-40) cc_final: 0.8127 (mm-40) REVERT: E 105 GLN cc_start: 0.7472 (tp40) cc_final: 0.7074 (tp40) REVERT: E 140 ARG cc_start: 0.6899 (OUTLIER) cc_final: 0.6456 (ttm170) REVERT: E 156 MET cc_start: 0.8373 (mtm) cc_final: 0.8090 (mtm) REVERT: G 109 THR cc_start: 0.7944 (m) cc_final: 0.7687 (m) REVERT: G 143 TYR cc_start: 0.6853 (p90) cc_final: 0.6527 (p90) REVERT: H 83 ASP cc_start: 0.8750 (m-30) cc_final: 0.7960 (m-30) REVERT: I 135 ARG cc_start: 0.7469 (ptm160) cc_final: 0.7159 (mmm-85) REVERT: J 233 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7772 (tp) REVERT: L 156 MET cc_start: 0.8776 (mtm) cc_final: 0.8424 (mtm) REVERT: M 22 LYS cc_start: 0.7954 (mtmt) cc_final: 0.7579 (mtmt) REVERT: N 24 ILE cc_start: 0.8580 (mm) cc_final: 0.8159 (mt) REVERT: X 322 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7743 (pm20) REVERT: X 345 ILE cc_start: 0.9125 (OUTLIER) cc_final: 0.8919 (mm) REVERT: Z 364 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7595 (tp30) REVERT: a 324 ASN cc_start: 0.7845 (m-40) cc_final: 0.7616 (m-40) outliers start: 65 outliers final: 49 residues processed: 600 average time/residue: 0.5817 time to fit residues: 572.7320 Evaluate side-chains 613 residues out of total 4641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 559 time to evaluate : 4.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 140 ARG Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain H residue 147 ILE Chi-restraints excluded: chain I residue 73 ASN Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain L residue 17 SER Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 163 ILE Chi-restraints excluded: chain M residue 147 ILE Chi-restraints excluded: chain M residue 203 LEU Chi-restraints excluded: chain N residue 160 THR Chi-restraints excluded: chain N residue 178 THR Chi-restraints excluded: chain N residue 205 VAL Chi-restraints excluded: chain P residue 325 MET Chi-restraints excluded: chain P residue 413 ASP Chi-restraints excluded: chain S residue 399 LEU Chi-restraints excluded: chain S residue 401 LEU Chi-restraints excluded: chain T residue 313 VAL Chi-restraints excluded: chain T residue 401 LEU Chi-restraints excluded: chain U residue 338 ASP Chi-restraints excluded: chain U residue 341 THR Chi-restraints excluded: chain U residue 401 LEU Chi-restraints excluded: chain V residue 301 THR Chi-restraints excluded: chain V residue 322 GLN Chi-restraints excluded: chain V residue 330 ASP Chi-restraints excluded: chain W residue 401 LEU Chi-restraints excluded: chain X residue 322 GLN Chi-restraints excluded: chain X residue 341 THR Chi-restraints excluded: chain X residue 345 ILE Chi-restraints excluded: chain X residue 395 MET Chi-restraints excluded: chain X residue 444 LEU Chi-restraints excluded: chain X residue 500 ASP Chi-restraints excluded: chain X residue 503 VAL Chi-restraints excluded: chain Y residue 401 LEU Chi-restraints excluded: chain Z residue 364 GLU Chi-restraints excluded: chain Z residue 401 LEU Chi-restraints excluded: chain Z residue 504 ASP Chi-restraints excluded: chain a residue 391 LEU Chi-restraints excluded: chain b residue 301 THR Chi-restraints excluded: chain b residue 330 ASP Chi-restraints excluded: chain b residue 447 LYS Chi-restraints excluded: chain b residue 458 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 358 optimal weight: 3.9990 chunk 231 optimal weight: 1.9990 chunk 346 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 chunk 112 optimal weight: 3.9990 chunk 368 optimal weight: 0.8980 chunk 395 optimal weight: 0.1980 chunk 286 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 456 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 80 GLN K 105 GLN P 322 GLN S 390 ASN ** h 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 174 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 47066 Z= 0.202 Angle : 0.465 11.483 63704 Z= 0.246 Chirality : 0.042 0.175 7251 Planarity : 0.003 0.052 8400 Dihedral : 3.572 22.122 6853 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.38 % Allowed : 11.16 % Favored : 87.46 % 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: 3.04 (0.10), residues: 2590 sheet: 0.87 (0.13), residues: 1526 loop : -0.05 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP T 429 HIS 0.004 0.001 HIS S 365 PHE 0.032 0.002 PHE I 71 TYR 0.009 0.001 TYR J 87 ARG 0.013 0.000 ARG J 26 *********************** 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 626 residues out of total 4641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 562 time to evaluate : 5.722 Fit side-chains revert: symmetry clash REVERT: A 17 SER cc_start: 0.8624 (m) cc_final: 0.8370 (m) REVERT: A 51 GLN cc_start: 0.8473 (mm-40) cc_final: 0.8138 (mm-40) REVERT: E 105 GLN cc_start: 0.7490 (tp40) cc_final: 0.7089 (tp40) REVERT: E 140 ARG cc_start: 0.6986 (OUTLIER) cc_final: 0.6484 (ttm170) REVERT: G 109 THR cc_start: 0.7972 (m) cc_final: 0.7702 (m) REVERT: G 143 TYR cc_start: 0.6924 (p90) cc_final: 0.6601 (p90) REVERT: H 73 ASN cc_start: 0.7629 (t0) cc_final: 0.7262 (m-40) REVERT: H 156 MET cc_start: 0.8119 (mtm) cc_final: 0.7315 (mtm) REVERT: I 135 ARG cc_start: 0.7469 (ptm160) cc_final: 0.7159 (mmm-85) REVERT: J 233 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7709 (tp) REVERT: L 156 MET cc_start: 0.8822 (mtm) cc_final: 0.8463 (mtm) REVERT: M 22 LYS cc_start: 0.8068 (mtmt) cc_final: 0.7673 (mtmt) REVERT: N 24 ILE cc_start: 0.8604 (mm) cc_final: 0.8208 (mt) REVERT: S 395 MET cc_start: 0.6929 (mmm) cc_final: 0.6476 (mmt) REVERT: X 322 GLN cc_start: 0.7966 (OUTLIER) cc_final: 0.7746 (pm20) REVERT: X 345 ILE cc_start: 0.9152 (OUTLIER) cc_final: 0.8937 (mm) REVERT: Z 364 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7603 (tp30) REVERT: a 324 ASN cc_start: 0.7862 (m-40) cc_final: 0.7635 (m-40) REVERT: a 390 ASN cc_start: 0.8763 (t0) cc_final: 0.8424 (t0) REVERT: O 114 GLN cc_start: 0.8239 (mt0) cc_final: 0.7857 (mt0) REVERT: O 183 ILE cc_start: 0.7764 (mt) cc_final: 0.7520 (mt) outliers start: 64 outliers final: 54 residues processed: 588 average time/residue: 0.5889 time to fit residues: 571.4953 Evaluate side-chains 615 residues out of total 4641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 556 time to evaluate : 5.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 140 ARG Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain H residue 147 ILE Chi-restraints excluded: chain I residue 73 ASN Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain L residue 17 SER Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 163 ILE Chi-restraints excluded: chain L residue 170 SER Chi-restraints excluded: chain M residue 147 ILE Chi-restraints excluded: chain M residue 163 ILE Chi-restraints excluded: chain M residue 203 LEU Chi-restraints excluded: chain N residue 160 THR Chi-restraints excluded: chain N residue 178 THR Chi-restraints excluded: chain P residue 325 MET Chi-restraints excluded: chain P residue 413 ASP Chi-restraints excluded: chain R residue 401 LEU Chi-restraints excluded: chain S residue 399 LEU Chi-restraints excluded: chain S residue 401 LEU Chi-restraints excluded: chain T residue 313 VAL Chi-restraints excluded: chain T residue 395 MET Chi-restraints excluded: chain T residue 401 LEU Chi-restraints excluded: chain U residue 341 THR Chi-restraints excluded: chain U residue 401 LEU Chi-restraints excluded: chain V residue 301 THR Chi-restraints excluded: chain V residue 322 GLN Chi-restraints excluded: chain V residue 330 ASP Chi-restraints excluded: chain W residue 401 LEU Chi-restraints excluded: chain X residue 322 GLN Chi-restraints excluded: chain X residue 341 THR Chi-restraints excluded: chain X residue 345 ILE Chi-restraints excluded: chain X residue 395 MET Chi-restraints excluded: chain X residue 444 LEU Chi-restraints excluded: chain X residue 500 ASP Chi-restraints excluded: chain X residue 503 VAL Chi-restraints excluded: chain Y residue 401 LEU Chi-restraints excluded: chain Z residue 364 GLU Chi-restraints excluded: chain Z residue 401 LEU Chi-restraints excluded: chain Z residue 504 ASP Chi-restraints excluded: chain a residue 391 LEU Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain b residue 301 THR Chi-restraints excluded: chain b residue 330 ASP Chi-restraints excluded: chain b residue 401 LEU Chi-restraints excluded: chain b residue 447 LYS Chi-restraints excluded: chain b residue 458 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 527 optimal weight: 0.9980 chunk 555 optimal weight: 4.9990 chunk 507 optimal weight: 0.0170 chunk 540 optimal weight: 0.9980 chunk 325 optimal weight: 0.6980 chunk 235 optimal weight: 4.9990 chunk 424 optimal weight: 3.9990 chunk 165 optimal weight: 6.9990 chunk 488 optimal weight: 0.5980 chunk 511 optimal weight: 0.9990 chunk 538 optimal weight: 2.9990 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 80 GLN G 174 ASN J 105 GLN K 73 ASN K 105 GLN M 165 ASN P 322 GLN ** h 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 174 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 47066 Z= 0.153 Angle : 0.444 10.738 63704 Z= 0.236 Chirality : 0.042 0.168 7251 Planarity : 0.003 0.057 8400 Dihedral : 3.474 21.382 6853 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.27 % Allowed : 11.31 % Favored : 87.41 % 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: 3.15 (0.10), residues: 2590 sheet: 0.92 (0.14), residues: 1526 loop : 0.01 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP T 429 HIS 0.003 0.001 HIS S 365 PHE 0.031 0.002 PHE I 71 TYR 0.009 0.001 TYR W 359 ARG 0.013 0.000 ARG J 26 *********************** 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 628 residues out of total 4641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 569 time to evaluate : 5.030 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 SER cc_start: 0.8625 (m) cc_final: 0.8373 (m) REVERT: A 51 GLN cc_start: 0.8451 (mm-40) cc_final: 0.8135 (mm-40) REVERT: E 105 GLN cc_start: 0.7463 (tp40) cc_final: 0.7038 (tp40) REVERT: E 140 ARG cc_start: 0.6941 (OUTLIER) cc_final: 0.6456 (ttm170) REVERT: E 156 MET cc_start: 0.8358 (mtm) cc_final: 0.7908 (mtm) REVERT: F 135 ARG cc_start: 0.7552 (ttm-80) cc_final: 0.7290 (ttp-170) REVERT: G 109 THR cc_start: 0.7979 (m) cc_final: 0.7701 (m) REVERT: G 143 TYR cc_start: 0.6919 (p90) cc_final: 0.6463 (p90) REVERT: H 83 ASP cc_start: 0.8733 (m-30) cc_final: 0.7968 (m-30) REVERT: I 135 ARG cc_start: 0.7465 (ptm160) cc_final: 0.7167 (mmm-85) REVERT: J 233 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7765 (tp) REVERT: L 156 MET cc_start: 0.8805 (mtm) cc_final: 0.8460 (mtm) REVERT: M 22 LYS cc_start: 0.8137 (mtmt) cc_final: 0.7759 (mtmt) REVERT: N 24 ILE cc_start: 0.8579 (mm) cc_final: 0.8178 (mt) REVERT: S 395 MET cc_start: 0.6913 (mmm) cc_final: 0.6453 (mmt) REVERT: X 322 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.7762 (pm20) REVERT: X 345 ILE cc_start: 0.9116 (OUTLIER) cc_final: 0.8906 (mm) REVERT: Y 314 MET cc_start: 0.9016 (ttt) cc_final: 0.8769 (ttt) REVERT: Z 364 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7472 (tp30) REVERT: a 324 ASN cc_start: 0.7795 (m-40) cc_final: 0.7538 (m-40) REVERT: a 390 ASN cc_start: 0.8749 (t0) cc_final: 0.8431 (t0) REVERT: O 183 ILE cc_start: 0.7780 (mt) cc_final: 0.7519 (mt) outliers start: 59 outliers final: 51 residues processed: 591 average time/residue: 0.5854 time to fit residues: 570.6318 Evaluate side-chains 614 residues out of total 4641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 558 time to evaluate : 4.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 140 ARG Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain H residue 147 ILE Chi-restraints excluded: chain I residue 73 ASN Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain K residue 73 ASN Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain L residue 17 SER Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 163 ILE Chi-restraints excluded: chain M residue 147 ILE Chi-restraints excluded: chain M residue 203 LEU Chi-restraints excluded: chain N residue 160 THR Chi-restraints excluded: chain N residue 178 THR Chi-restraints excluded: chain P residue 325 MET Chi-restraints excluded: chain P residue 413 ASP Chi-restraints excluded: chain S residue 399 LEU Chi-restraints excluded: chain T residue 313 VAL Chi-restraints excluded: chain T residue 395 MET Chi-restraints excluded: chain T residue 401 LEU Chi-restraints excluded: chain U residue 338 ASP Chi-restraints excluded: chain U residue 401 LEU Chi-restraints excluded: chain V residue 301 THR Chi-restraints excluded: chain V residue 322 GLN Chi-restraints excluded: chain V residue 330 ASP Chi-restraints excluded: chain W residue 399 LEU Chi-restraints excluded: chain W residue 401 LEU Chi-restraints excluded: chain X residue 322 GLN Chi-restraints excluded: chain X residue 341 THR Chi-restraints excluded: chain X residue 345 ILE Chi-restraints excluded: chain X residue 444 LEU Chi-restraints excluded: chain X residue 500 ASP Chi-restraints excluded: chain X residue 503 VAL Chi-restraints excluded: chain Y residue 401 LEU Chi-restraints excluded: chain Z residue 364 GLU Chi-restraints excluded: chain Z residue 401 LEU Chi-restraints excluded: chain Z residue 504 ASP Chi-restraints excluded: chain a residue 391 LEU Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain b residue 301 THR Chi-restraints excluded: chain b residue 330 ASP Chi-restraints excluded: chain b residue 401 LEU Chi-restraints excluded: chain b residue 447 LYS Chi-restraints excluded: chain b residue 458 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 355 optimal weight: 0.9980 chunk 571 optimal weight: 0.7980 chunk 348 optimal weight: 3.9990 chunk 271 optimal weight: 2.9990 chunk 397 optimal weight: 1.9990 chunk 599 optimal weight: 10.0000 chunk 551 optimal weight: 4.9990 chunk 477 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 368 optimal weight: 0.6980 chunk 292 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 80 GLN J 105 GLN K 105 GLN M 165 ASN P 322 GLN T 324 ASN ** h 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 174 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 47066 Z= 0.187 Angle : 0.461 10.547 63704 Z= 0.244 Chirality : 0.042 0.173 7251 Planarity : 0.003 0.062 8400 Dihedral : 3.518 21.862 6853 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.29 % Allowed : 11.42 % Favored : 87.28 % 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: 3.10 (0.10), residues: 2590 sheet: 0.90 (0.13), residues: 1526 loop : -0.04 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP T 429 HIS 0.004 0.001 HIS S 365 PHE 0.032 0.002 PHE I 71 TYR 0.012 0.001 TYR N 130 ARG 0.014 0.000 ARG J 26 ********************** 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 618 residues out of total 4641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 558 time to evaluate : 5.015 Fit side-chains revert: symmetry clash REVERT: A 17 SER cc_start: 0.8631 (m) cc_final: 0.8371 (m) REVERT: A 51 GLN cc_start: 0.8455 (mm-40) cc_final: 0.8148 (mm-40) REVERT: E 140 ARG cc_start: 0.6946 (OUTLIER) cc_final: 0.6453 (ttm170) REVERT: G 109 THR cc_start: 0.7950 (m) cc_final: 0.7685 (m) REVERT: G 143 TYR cc_start: 0.6941 (p90) cc_final: 0.6498 (p90) REVERT: H 83 ASP cc_start: 0.8738 (m-30) cc_final: 0.7971 (m-30) REVERT: I 135 ARG cc_start: 0.7471 (ptm160) cc_final: 0.7159 (mmm-85) REVERT: J 233 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7704 (tp) REVERT: L 156 MET cc_start: 0.8822 (mtm) cc_final: 0.8477 (mtm) REVERT: M 22 LYS cc_start: 0.8148 (mtmt) cc_final: 0.7765 (mtmt) REVERT: N 24 ILE cc_start: 0.8597 (mm) cc_final: 0.8194 (mt) REVERT: S 395 MET cc_start: 0.6943 (mmm) cc_final: 0.6485 (mmt) REVERT: X 322 GLN cc_start: 0.7944 (OUTLIER) cc_final: 0.7724 (pm20) REVERT: X 345 ILE cc_start: 0.9130 (OUTLIER) cc_final: 0.8918 (mm) REVERT: Y 314 MET cc_start: 0.9017 (ttt) cc_final: 0.8785 (ttt) REVERT: Z 364 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7600 (tp30) REVERT: a 324 ASN cc_start: 0.7808 (m-40) cc_final: 0.7554 (m-40) REVERT: a 390 ASN cc_start: 0.8757 (t0) cc_final: 0.8432 (t0) REVERT: O 114 GLN cc_start: 0.8218 (mt0) cc_final: 0.7836 (mt0) REVERT: O 183 ILE cc_start: 0.7747 (mt) cc_final: 0.7504 (mt) outliers start: 60 outliers final: 52 residues processed: 582 average time/residue: 0.5851 time to fit residues: 559.8810 Evaluate side-chains 608 residues out of total 4641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 551 time to evaluate : 5.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 140 ARG Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain H residue 147 ILE Chi-restraints excluded: chain I residue 73 ASN Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain L residue 17 SER Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 163 ILE Chi-restraints excluded: chain L residue 170 SER Chi-restraints excluded: chain M residue 147 ILE Chi-restraints excluded: chain M residue 203 LEU Chi-restraints excluded: chain N residue 160 THR Chi-restraints excluded: chain N residue 178 THR Chi-restraints excluded: chain P residue 325 MET Chi-restraints excluded: chain P residue 413 ASP Chi-restraints excluded: chain S residue 399 LEU Chi-restraints excluded: chain S residue 401 LEU Chi-restraints excluded: chain T residue 313 VAL Chi-restraints excluded: chain T residue 395 MET Chi-restraints excluded: chain T residue 401 LEU Chi-restraints excluded: chain U residue 401 LEU Chi-restraints excluded: chain V residue 301 THR Chi-restraints excluded: chain V residue 322 GLN Chi-restraints excluded: chain V residue 330 ASP Chi-restraints excluded: chain W residue 399 LEU Chi-restraints excluded: chain W residue 401 LEU Chi-restraints excluded: chain X residue 322 GLN Chi-restraints excluded: chain X residue 341 THR Chi-restraints excluded: chain X residue 345 ILE Chi-restraints excluded: chain X residue 444 LEU Chi-restraints excluded: chain X residue 500 ASP Chi-restraints excluded: chain X residue 503 VAL Chi-restraints excluded: chain Y residue 401 LEU Chi-restraints excluded: chain Z residue 364 GLU Chi-restraints excluded: chain Z residue 401 LEU Chi-restraints excluded: chain Z residue 504 ASP Chi-restraints excluded: chain a residue 391 LEU Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain b residue 301 THR Chi-restraints excluded: chain b residue 330 ASP Chi-restraints excluded: chain b residue 401 LEU Chi-restraints excluded: chain b residue 447 LYS Chi-restraints excluded: chain b residue 458 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 379 optimal weight: 2.9990 chunk 508 optimal weight: 0.5980 chunk 146 optimal weight: 0.7980 chunk 440 optimal weight: 0.8980 chunk 70 optimal weight: 0.5980 chunk 132 optimal weight: 0.9980 chunk 478 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 chunk 491 optimal weight: 2.9990 chunk 60 optimal weight: 9.9990 chunk 88 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 80 GLN J 105 GLN K 73 ASN K 105 GLN M 165 ASN P 322 GLN T 324 ASN ** h 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 174 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.126426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.093711 restraints weight = 53451.053| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 1.63 r_work: 0.2784 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2627 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 47066 Z= 0.170 Angle : 0.453 10.202 63704 Z= 0.239 Chirality : 0.042 0.169 7251 Planarity : 0.003 0.062 8400 Dihedral : 3.487 21.604 6853 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.25 % Allowed : 11.47 % Favored : 87.28 % 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: 2.39 (0.11), residues: 6048 helix: 3.13 (0.10), residues: 2590 sheet: 0.91 (0.13), residues: 1526 loop : -0.02 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP T 429 HIS 0.003 0.001 HIS S 365 PHE 0.031 0.002 PHE I 71 TYR 0.009 0.001 TYR W 359 ARG 0.014 0.000 ARG J 26 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10964.09 seconds wall clock time: 198 minutes 30.17 seconds (11910.17 seconds total)