Starting phenix.real_space_refine on Tue Mar 19 08:40:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6a_28878/03_2024/8f6a_28878.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6a_28878/03_2024/8f6a_28878.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6a_28878/03_2024/8f6a_28878.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6a_28878/03_2024/8f6a_28878.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6a_28878/03_2024/8f6a_28878.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6a_28878/03_2024/8f6a_28878.pdb" } resolution = 2.06 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= 0.001 sd= 0.011 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: 5 Type Number sf(0) Gaussians S 196 5.16 5 C 29120 2.51 5 N 7770 2.21 5 O 8862 1.98 5 H 47110 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H GLU 17": "OE1" <-> "OE2" Residue "H GLU 23": "OE1" <-> "OE2" Residue "H GLU 62": "OE1" <-> "OE2" Residue "H GLU 64": "OE1" <-> "OE2" Residue "H GLU 77": "OE1" <-> "OE2" Residue "H GLU 139": "OE1" <-> "OE2" Residue "H GLU 150": "OE1" <-> "OE2" Residue "A PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 179": "OE1" <-> "OE2" Residue "A GLU 211": "OE1" <-> "OE2" Residue "I GLU 17": "OE1" <-> "OE2" Residue "I GLU 23": "OE1" <-> "OE2" Residue "I GLU 62": "OE1" <-> "OE2" Residue "I GLU 64": "OE1" <-> "OE2" Residue "I GLU 77": "OE1" <-> "OE2" Residue "I GLU 139": "OE1" <-> "OE2" Residue "I GLU 150": "OE1" <-> "OE2" Residue "J GLU 17": "OE1" <-> "OE2" Residue "J GLU 23": "OE1" <-> "OE2" Residue "J GLU 62": "OE1" <-> "OE2" Residue "J GLU 64": "OE1" <-> "OE2" Residue "J GLU 77": "OE1" <-> "OE2" Residue "J GLU 139": "OE1" <-> "OE2" Residue "J GLU 150": "OE1" <-> "OE2" Residue "K GLU 17": "OE1" <-> "OE2" Residue "K GLU 23": "OE1" <-> "OE2" Residue "K GLU 62": "OE1" <-> "OE2" Residue "K GLU 64": "OE1" <-> "OE2" Residue "K GLU 77": "OE1" <-> "OE2" Residue "K GLU 139": "OE1" <-> "OE2" Residue "K GLU 150": "OE1" <-> "OE2" Residue "L GLU 17": "OE1" <-> "OE2" Residue "L GLU 23": "OE1" <-> "OE2" Residue "L GLU 62": "OE1" <-> "OE2" Residue "L GLU 64": "OE1" <-> "OE2" Residue "L GLU 77": "OE1" <-> "OE2" Residue "L GLU 139": "OE1" <-> "OE2" Residue "L GLU 150": "OE1" <-> "OE2" Residue "M GLU 17": "OE1" <-> "OE2" Residue "M GLU 23": "OE1" <-> "OE2" Residue "M GLU 62": "OE1" <-> "OE2" Residue "M GLU 64": "OE1" <-> "OE2" Residue "M GLU 77": "OE1" <-> "OE2" Residue "M GLU 139": "OE1" <-> "OE2" Residue "M GLU 150": "OE1" <-> "OE2" Residue "N GLU 17": "OE1" <-> "OE2" Residue "N GLU 23": "OE1" <-> "OE2" Residue "N GLU 62": "OE1" <-> "OE2" Residue "N GLU 64": "OE1" <-> "OE2" Residue "N GLU 77": "OE1" <-> "OE2" Residue "N GLU 139": "OE1" <-> "OE2" Residue "N GLU 150": "OE1" <-> "OE2" Residue "V GLU 17": "OE1" <-> "OE2" Residue "V GLU 23": "OE1" <-> "OE2" Residue "V GLU 62": "OE1" <-> "OE2" Residue "V GLU 64": "OE1" <-> "OE2" Residue "V GLU 77": "OE1" <-> "OE2" Residue "V GLU 139": "OE1" <-> "OE2" Residue "V GLU 150": "OE1" <-> "OE2" Residue "W GLU 17": "OE1" <-> "OE2" Residue "W GLU 23": "OE1" <-> "OE2" Residue "W GLU 62": "OE1" <-> "OE2" Residue "W GLU 64": "OE1" <-> "OE2" Residue "W GLU 77": "OE1" <-> "OE2" Residue "W GLU 139": "OE1" <-> "OE2" Residue "W GLU 150": "OE1" <-> "OE2" Residue "X GLU 17": "OE1" <-> "OE2" Residue "X GLU 23": "OE1" <-> "OE2" Residue "X GLU 62": "OE1" <-> "OE2" Residue "X GLU 64": "OE1" <-> "OE2" Residue "X GLU 77": "OE1" <-> "OE2" Residue "X GLU 139": "OE1" <-> "OE2" Residue "X GLU 150": "OE1" <-> "OE2" Residue "Y GLU 17": "OE1" <-> "OE2" Residue "Y GLU 23": "OE1" <-> "OE2" Residue "Y GLU 62": "OE1" <-> "OE2" Residue "Y GLU 64": "OE1" <-> "OE2" Residue "Y GLU 77": "OE1" <-> "OE2" Residue "Y GLU 139": "OE1" <-> "OE2" Residue "Y GLU 150": "OE1" <-> "OE2" Residue "Z GLU 17": "OE1" <-> "OE2" Residue "Z GLU 23": "OE1" <-> "OE2" Residue "Z GLU 62": "OE1" <-> "OE2" Residue "Z GLU 64": "OE1" <-> "OE2" Residue "Z GLU 77": "OE1" <-> "OE2" Residue "Z GLU 139": "OE1" <-> "OE2" Residue "Z GLU 150": "OE1" <-> "OE2" Residue "a GLU 17": "OE1" <-> "OE2" Residue "a GLU 23": "OE1" <-> "OE2" Residue "a GLU 62": "OE1" <-> "OE2" Residue "a GLU 64": "OE1" <-> "OE2" Residue "a GLU 77": "OE1" <-> "OE2" Residue "a GLU 139": "OE1" <-> "OE2" Residue "a GLU 150": "OE1" <-> "OE2" Residue "b GLU 17": "OE1" <-> "OE2" Residue "b GLU 23": "OE1" <-> "OE2" Residue "b GLU 62": "OE1" <-> "OE2" Residue "b GLU 64": "OE1" <-> "OE2" Residue "b GLU 77": "OE1" <-> "OE2" Residue "b GLU 139": "OE1" <-> "OE2" Residue "b GLU 150": "OE1" <-> "OE2" Residue "P PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P GLU 179": "OE1" <-> "OE2" Residue "P GLU 211": "OE1" <-> "OE2" Residue "B PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 179": "OE1" <-> "OE2" Residue "B GLU 211": "OE1" <-> "OE2" Residue "C PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 179": "OE1" <-> "OE2" Residue "C GLU 211": "OE1" <-> "OE2" Residue "D PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 179": "OE1" <-> "OE2" Residue "D GLU 211": "OE1" <-> "OE2" Residue "E PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 179": "OE1" <-> "OE2" Residue "E GLU 211": "OE1" <-> "OE2" Residue "F PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 179": "OE1" <-> "OE2" Residue "F GLU 211": "OE1" <-> "OE2" Residue "G PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 179": "OE1" <-> "OE2" Residue "G GLU 211": "OE1" <-> "OE2" Residue "O PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O GLU 179": "OE1" <-> "OE2" Residue "O GLU 211": "OE1" <-> "OE2" Residue "Q PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q GLU 179": "OE1" <-> "OE2" Residue "Q GLU 211": "OE1" <-> "OE2" Residue "R PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R GLU 179": "OE1" <-> "OE2" Residue "R GLU 211": "OE1" <-> "OE2" Residue "S PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S GLU 179": "OE1" <-> "OE2" Residue "S GLU 211": "OE1" <-> "OE2" Residue "T PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T GLU 179": "OE1" <-> "OE2" Residue "T GLU 211": "OE1" <-> "OE2" Residue "U PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U GLU 179": "OE1" <-> "OE2" Residue "U GLU 211": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 93058 Number of models: 1 Model: "" Number of chains: 28 Chain: "H" Number of atoms: 3145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 3145 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "A" Number of atoms: 3502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 3502 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 216} Chain: "I" Number of atoms: 3145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 3145 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "J" Number of atoms: 3145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 3145 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "K" Number of atoms: 3145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 3145 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "L" Number of atoms: 3145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 3145 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "M" Number of atoms: 3145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 3145 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "N" Number of atoms: 3145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 3145 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "V" Number of atoms: 3145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 3145 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "W" Number of atoms: 3145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 3145 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "X" Number of atoms: 3145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 3145 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "Y" Number of atoms: 3145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 3145 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "Z" Number of atoms: 3145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 3145 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "a" Number of atoms: 3145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 3145 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "b" Number of atoms: 3145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 3145 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "P" Number of atoms: 3502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 3502 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 216} Chain: "B" Number of atoms: 3502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 3502 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 216} Chain: "C" Number of atoms: 3502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 3502 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 216} Chain: "D" Number of atoms: 3502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 3502 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 216} Chain: "E" Number of atoms: 3502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 3502 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 216} Chain: "F" Number of atoms: 3502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 3502 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 216} Chain: "G" Number of atoms: 3502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 3502 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 216} Chain: "O" Number of atoms: 3502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 3502 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 216} Chain: "Q" Number of atoms: 3502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 3502 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 216} Chain: "R" Number of atoms: 3502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 3502 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 216} Chain: "S" Number of atoms: 3502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 3502 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 216} Chain: "T" Number of atoms: 3502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 3502 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 216} Chain: "U" Number of atoms: 3502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 3502 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 216} Time building chain proxies: 29.47, per 1000 atoms: 0.32 Number of scatterers: 93058 At special positions: 0 Unit cell: (134.46, 131.76, 173.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 196 16.00 O 8862 8.00 N 7770 7.00 C 29120 6.00 H 47110 1.00 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: 58.30 Conformation dependent library (CDL) restraints added in 7.6 seconds 11788 Ramachandran restraints generated. 5894 Oldfield, 0 Emsley, 5894 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10948 Finding SS restraints... Secondary structure from input PDB file: 154 helices and 70 sheets defined 40.9% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.52 Creating SS restraints... Processing helix chain 'H' and resid 48 through 71 Processing helix chain 'H' and resid 75 through 90 removed outlier: 3.754A pdb=" N VAL H 90 " --> pdb=" O MET H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 142 Processing helix chain 'H' and resid 147 through 166 removed outlier: 3.549A pdb=" N ARG H 165 " --> pdb=" O ALA H 161 " (cutoff:3.500A) Processing helix chain 'H' and resid 188 through 199 Processing helix chain 'A' and resid 21 through 33 removed outlier: 3.571A pdb=" N LYS A 33 " --> pdb=" O GLU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 104 Processing helix chain 'A' and resid 108 through 123 removed outlier: 4.023A pdb=" N LEU A 112 " --> pdb=" O ASN A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 180 Processing helix chain 'A' and resid 185 through 200 removed outlier: 3.570A pdb=" N SER A 200 " --> pdb=" O ALA A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 231 Processing helix chain 'I' and resid 48 through 71 Processing helix chain 'I' and resid 75 through 90 removed outlier: 3.754A pdb=" N VAL I 90 " --> pdb=" O MET I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 130 through 142 Processing helix chain 'I' and resid 147 through 166 removed outlier: 3.549A pdb=" N ARG I 165 " --> pdb=" O ALA I 161 " (cutoff:3.500A) Processing helix chain 'I' and resid 188 through 199 Processing helix chain 'J' and resid 48 through 71 Processing helix chain 'J' and resid 75 through 90 removed outlier: 3.753A pdb=" N VAL J 90 " --> pdb=" O MET J 86 " (cutoff:3.500A) Processing helix chain 'J' and resid 130 through 142 Processing helix chain 'J' and resid 147 through 166 removed outlier: 3.549A pdb=" N ARG J 165 " --> pdb=" O ALA J 161 " (cutoff:3.500A) Processing helix chain 'J' and resid 188 through 199 Processing helix chain 'K' and resid 48 through 71 Processing helix chain 'K' and resid 75 through 90 removed outlier: 3.754A pdb=" N VAL K 90 " --> pdb=" O MET K 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 130 through 142 Processing helix chain 'K' and resid 147 through 166 removed outlier: 3.549A pdb=" N ARG K 165 " --> pdb=" O ALA K 161 " (cutoff:3.500A) Processing helix chain 'K' and resid 188 through 199 Processing helix chain 'L' and resid 48 through 71 Processing helix chain 'L' and resid 75 through 90 removed outlier: 3.754A pdb=" N VAL L 90 " --> pdb=" O MET L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 142 Processing helix chain 'L' and resid 147 through 166 removed outlier: 3.548A pdb=" N ARG L 165 " --> pdb=" O ALA L 161 " (cutoff:3.500A) Processing helix chain 'L' and resid 188 through 199 Processing helix chain 'M' and resid 48 through 71 Processing helix chain 'M' and resid 75 through 90 removed outlier: 3.754A pdb=" N VAL M 90 " --> pdb=" O MET M 86 " (cutoff:3.500A) Processing helix chain 'M' and resid 130 through 142 Processing helix chain 'M' and resid 147 through 166 removed outlier: 3.549A pdb=" N ARG M 165 " --> pdb=" O ALA M 161 " (cutoff:3.500A) Processing helix chain 'M' and resid 188 through 199 Processing helix chain 'N' and resid 48 through 71 Processing helix chain 'N' and resid 75 through 90 removed outlier: 3.754A pdb=" N VAL N 90 " --> pdb=" O MET N 86 " (cutoff:3.500A) Processing helix chain 'N' and resid 130 through 142 Processing helix chain 'N' and resid 147 through 166 removed outlier: 3.549A pdb=" N ARG N 165 " --> pdb=" O ALA N 161 " (cutoff:3.500A) Processing helix chain 'N' and resid 188 through 199 Processing helix chain 'V' and resid 48 through 71 Processing helix chain 'V' and resid 75 through 90 removed outlier: 3.753A pdb=" N VAL V 90 " --> pdb=" O MET V 86 " (cutoff:3.500A) Processing helix chain 'V' and resid 130 through 142 Processing helix chain 'V' and resid 147 through 166 removed outlier: 3.549A pdb=" N ARG V 165 " --> pdb=" O ALA V 161 " (cutoff:3.500A) Processing helix chain 'V' and resid 188 through 199 Processing helix chain 'W' and resid 48 through 71 Processing helix chain 'W' and resid 75 through 90 removed outlier: 3.753A pdb=" N VAL W 90 " --> pdb=" O MET W 86 " (cutoff:3.500A) Processing helix chain 'W' and resid 130 through 142 Processing helix chain 'W' and resid 147 through 166 removed outlier: 3.549A pdb=" N ARG W 165 " --> pdb=" O ALA W 161 " (cutoff:3.500A) Processing helix chain 'W' and resid 188 through 199 Processing helix chain 'X' and resid 48 through 71 Processing helix chain 'X' and resid 75 through 90 removed outlier: 3.754A pdb=" N VAL X 90 " --> pdb=" O MET X 86 " (cutoff:3.500A) Processing helix chain 'X' and resid 130 through 142 Processing helix chain 'X' and resid 147 through 166 removed outlier: 3.549A pdb=" N ARG X 165 " --> pdb=" O ALA X 161 " (cutoff:3.500A) Processing helix chain 'X' and resid 188 through 199 Processing helix chain 'Y' and resid 48 through 71 Processing helix chain 'Y' and resid 75 through 90 removed outlier: 3.753A pdb=" N VAL Y 90 " --> pdb=" O MET Y 86 " (cutoff:3.500A) Processing helix chain 'Y' and resid 130 through 142 Processing helix chain 'Y' and resid 147 through 166 removed outlier: 3.549A pdb=" N ARG Y 165 " --> pdb=" O ALA Y 161 " (cutoff:3.500A) Processing helix chain 'Y' and resid 188 through 199 Processing helix chain 'Z' and resid 48 through 71 Processing helix chain 'Z' and resid 75 through 90 removed outlier: 3.754A pdb=" N VAL Z 90 " --> pdb=" O MET Z 86 " (cutoff:3.500A) Processing helix chain 'Z' and resid 130 through 142 Processing helix chain 'Z' and resid 147 through 166 removed outlier: 3.549A pdb=" N ARG Z 165 " --> pdb=" O ALA Z 161 " (cutoff:3.500A) Processing helix chain 'Z' and resid 188 through 199 Processing helix chain 'a' and resid 48 through 71 Processing helix chain 'a' and resid 75 through 90 removed outlier: 3.754A pdb=" N VAL a 90 " --> pdb=" O MET a 86 " (cutoff:3.500A) Processing helix chain 'a' and resid 130 through 142 Processing helix chain 'a' and resid 147 through 166 removed outlier: 3.549A pdb=" N ARG a 165 " --> pdb=" O ALA a 161 " (cutoff:3.500A) Processing helix chain 'a' and resid 188 through 199 Processing helix chain 'b' and resid 48 through 71 Processing helix chain 'b' and resid 75 through 90 removed outlier: 3.754A pdb=" N VAL b 90 " --> pdb=" O MET b 86 " (cutoff:3.500A) Processing helix chain 'b' and resid 130 through 142 Processing helix chain 'b' and resid 147 through 166 removed outlier: 3.549A pdb=" N ARG b 165 " --> pdb=" O ALA b 161 " (cutoff:3.500A) Processing helix chain 'b' and resid 188 through 199 Processing helix chain 'P' and resid 21 through 33 removed outlier: 3.571A pdb=" N LYS P 33 " --> pdb=" O GLU P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 81 through 104 Processing helix chain 'P' and resid 108 through 123 removed outlier: 4.023A pdb=" N LEU P 112 " --> pdb=" O ASN P 108 " (cutoff:3.500A) Processing helix chain 'P' and resid 168 through 180 Processing helix chain 'P' and resid 185 through 200 removed outlier: 3.570A pdb=" N SER P 200 " --> pdb=" O ALA P 196 " (cutoff:3.500A) Processing helix chain 'P' and resid 225 through 231 Processing helix chain 'B' and resid 21 through 33 removed outlier: 3.571A pdb=" N LYS B 33 " --> pdb=" O GLU B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 104 Processing helix chain 'B' and resid 108 through 123 removed outlier: 4.023A pdb=" N LEU B 112 " --> pdb=" O ASN B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 180 Processing helix chain 'B' and resid 185 through 200 removed outlier: 3.569A pdb=" N SER B 200 " --> pdb=" O ALA B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 231 Processing helix chain 'C' and resid 21 through 33 removed outlier: 3.571A pdb=" N LYS C 33 " --> pdb=" O GLU C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 104 Processing helix chain 'C' and resid 108 through 123 removed outlier: 4.024A pdb=" N LEU C 112 " --> pdb=" O ASN C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 180 Processing helix chain 'C' and resid 185 through 200 removed outlier: 3.570A pdb=" N SER C 200 " --> pdb=" O ALA C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 231 Processing helix chain 'D' and resid 21 through 33 removed outlier: 3.571A pdb=" N LYS D 33 " --> pdb=" O GLU D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 104 Processing helix chain 'D' and resid 108 through 123 removed outlier: 4.023A pdb=" N LEU D 112 " --> pdb=" O ASN D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 180 Processing helix chain 'D' and resid 185 through 200 removed outlier: 3.569A pdb=" N SER D 200 " --> pdb=" O ALA D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 231 Processing helix chain 'E' and resid 21 through 33 removed outlier: 3.571A pdb=" N LYS E 33 " --> pdb=" O GLU E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 104 Processing helix chain 'E' and resid 108 through 123 removed outlier: 4.023A pdb=" N LEU E 112 " --> pdb=" O ASN E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 180 Processing helix chain 'E' and resid 185 through 200 removed outlier: 3.570A pdb=" N SER E 200 " --> pdb=" O ALA E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 231 Processing helix chain 'F' and resid 21 through 33 removed outlier: 3.572A pdb=" N LYS F 33 " --> pdb=" O GLU F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 104 Processing helix chain 'F' and resid 108 through 123 removed outlier: 4.024A pdb=" N LEU F 112 " --> pdb=" O ASN F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 180 Processing helix chain 'F' and resid 185 through 200 removed outlier: 3.569A pdb=" N SER F 200 " --> pdb=" O ALA F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 231 Processing helix chain 'G' and resid 21 through 33 removed outlier: 3.570A pdb=" N LYS G 33 " --> pdb=" O GLU G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 104 Processing helix chain 'G' and resid 108 through 123 removed outlier: 4.023A pdb=" N LEU G 112 " --> pdb=" O ASN G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 180 Processing helix chain 'G' and resid 185 through 200 removed outlier: 3.570A pdb=" N SER G 200 " --> pdb=" O ALA G 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 231 Processing helix chain 'O' and resid 21 through 33 removed outlier: 3.571A pdb=" N LYS O 33 " --> pdb=" O GLU O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 81 through 104 Processing helix chain 'O' and resid 108 through 123 removed outlier: 4.023A pdb=" N LEU O 112 " --> pdb=" O ASN O 108 " (cutoff:3.500A) Processing helix chain 'O' and resid 168 through 180 Processing helix chain 'O' and resid 185 through 200 removed outlier: 3.570A pdb=" N SER O 200 " --> pdb=" O ALA O 196 " (cutoff:3.500A) Processing helix chain 'O' and resid 225 through 231 Processing helix chain 'Q' and resid 21 through 33 removed outlier: 3.571A pdb=" N LYS Q 33 " --> pdb=" O GLU Q 29 " (cutoff:3.500A) Processing helix chain 'Q' and resid 81 through 104 Processing helix chain 'Q' and resid 108 through 123 removed outlier: 4.023A pdb=" N LEU Q 112 " --> pdb=" O ASN Q 108 " (cutoff:3.500A) Processing helix chain 'Q' and resid 168 through 180 Processing helix chain 'Q' and resid 185 through 200 removed outlier: 3.569A pdb=" N SER Q 200 " --> pdb=" O ALA Q 196 " (cutoff:3.500A) Processing helix chain 'Q' and resid 225 through 231 Processing helix chain 'R' and resid 21 through 33 removed outlier: 3.571A pdb=" N LYS R 33 " --> pdb=" O GLU R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 104 Processing helix chain 'R' and resid 108 through 123 removed outlier: 4.024A pdb=" N LEU R 112 " --> pdb=" O ASN R 108 " (cutoff:3.500A) Processing helix chain 'R' and resid 168 through 180 Processing helix chain 'R' and resid 185 through 200 removed outlier: 3.570A pdb=" N SER R 200 " --> pdb=" O ALA R 196 " (cutoff:3.500A) Processing helix chain 'R' and resid 225 through 231 Processing helix chain 'S' and resid 21 through 33 removed outlier: 3.571A pdb=" N LYS S 33 " --> pdb=" O GLU S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 81 through 104 Processing helix chain 'S' and resid 108 through 123 removed outlier: 4.023A pdb=" N LEU S 112 " --> pdb=" O ASN S 108 " (cutoff:3.500A) Processing helix chain 'S' and resid 168 through 180 Processing helix chain 'S' and resid 185 through 200 removed outlier: 3.569A pdb=" N SER S 200 " --> pdb=" O ALA S 196 " (cutoff:3.500A) Processing helix chain 'S' and resid 225 through 231 Processing helix chain 'T' and resid 21 through 33 removed outlier: 3.572A pdb=" N LYS T 33 " --> pdb=" O GLU T 29 " (cutoff:3.500A) Processing helix chain 'T' and resid 81 through 104 Processing helix chain 'T' and resid 108 through 123 removed outlier: 4.023A pdb=" N LEU T 112 " --> pdb=" O ASN T 108 " (cutoff:3.500A) Processing helix chain 'T' and resid 168 through 180 Processing helix chain 'T' and resid 185 through 200 removed outlier: 3.570A pdb=" N SER T 200 " --> pdb=" O ALA T 196 " (cutoff:3.500A) Processing helix chain 'T' and resid 225 through 231 Processing helix chain 'U' and resid 21 through 33 removed outlier: 3.570A pdb=" N LYS U 33 " --> pdb=" O GLU U 29 " (cutoff:3.500A) Processing helix chain 'U' and resid 81 through 104 Processing helix chain 'U' and resid 108 through 123 removed outlier: 4.024A pdb=" N LEU U 112 " --> pdb=" O ASN U 108 " (cutoff:3.500A) Processing helix chain 'U' and resid 168 through 180 Processing helix chain 'U' and resid 185 through 200 removed outlier: 3.570A pdb=" N SER U 200 " --> pdb=" O ALA U 196 " (cutoff:3.500A) Processing helix chain 'U' and resid 225 through 231 Processing sheet with id=AA1, first strand: chain 'H' and resid 124 through 127 removed outlier: 3.728A pdb=" N ALA H 11 " --> pdb=" O LEU H 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 20 through 22 removed outlier: 3.528A pdb=" N HIS H 28 " --> pdb=" O VAL H 20 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N MET H 22 " --> pdb=" O ILE H 26 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ILE H 26 " --> pdb=" O MET H 22 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 34 through 38 removed outlier: 6.431A pdb=" N THR H 41 " --> pdb=" O ILE H 37 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 162 through 165 Processing sheet with id=AA5, first strand: chain 'A' and resid 68 through 69 removed outlier: 3.539A pdb=" N ASN A 158 " --> pdb=" O ASP A 150 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 124 through 127 removed outlier: 3.728A pdb=" N ALA I 11 " --> pdb=" O LEU I 8 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 20 through 22 removed outlier: 3.527A pdb=" N HIS I 28 " --> pdb=" O VAL I 20 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N MET I 22 " --> pdb=" O ILE I 26 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ILE I 26 " --> pdb=" O MET I 22 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 34 through 38 removed outlier: 6.431A pdb=" N THR I 41 " --> pdb=" O ILE I 37 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 124 through 127 removed outlier: 3.727A pdb=" N ALA J 11 " --> pdb=" O LEU J 8 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 20 through 22 removed outlier: 3.528A pdb=" N HIS J 28 " --> pdb=" O VAL J 20 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N MET J 22 " --> pdb=" O ILE J 26 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ILE J 26 " --> pdb=" O MET J 22 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 34 through 38 removed outlier: 6.430A pdb=" N THR J 41 " --> pdb=" O ILE J 37 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 124 through 127 removed outlier: 3.729A pdb=" N ALA K 11 " --> pdb=" O LEU K 8 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 20 through 22 removed outlier: 3.527A pdb=" N HIS K 28 " --> pdb=" O VAL K 20 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N MET K 22 " --> pdb=" O ILE K 26 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ILE K 26 " --> pdb=" O MET K 22 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 34 through 38 removed outlier: 6.430A pdb=" N THR K 41 " --> pdb=" O ILE K 37 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 124 through 127 removed outlier: 3.728A pdb=" N ALA L 11 " --> pdb=" O LEU L 8 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 20 through 22 removed outlier: 3.527A pdb=" N HIS L 28 " --> pdb=" O VAL L 20 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N MET L 22 " --> pdb=" O ILE L 26 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ILE L 26 " --> pdb=" O MET L 22 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 34 through 38 removed outlier: 6.430A pdb=" N THR L 41 " --> pdb=" O ILE L 37 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 124 through 127 removed outlier: 3.728A pdb=" N ALA M 11 " --> pdb=" O LEU M 8 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'M' and resid 20 through 22 removed outlier: 3.528A pdb=" N HIS M 28 " --> pdb=" O VAL M 20 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N MET M 22 " --> pdb=" O ILE M 26 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ILE M 26 " --> pdb=" O MET M 22 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'M' and resid 34 through 38 removed outlier: 6.431A pdb=" N THR M 41 " --> pdb=" O ILE M 37 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'N' and resid 124 through 127 removed outlier: 3.728A pdb=" N ALA N 11 " --> pdb=" O LEU N 8 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 20 through 22 removed outlier: 3.527A pdb=" N HIS N 28 " --> pdb=" O VAL N 20 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N MET N 22 " --> pdb=" O ILE N 26 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ILE N 26 " --> pdb=" O MET N 22 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'N' and resid 34 through 38 removed outlier: 6.430A pdb=" N THR N 41 " --> pdb=" O ILE N 37 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'V' and resid 124 through 127 removed outlier: 3.728A pdb=" N ALA V 11 " --> pdb=" O LEU V 8 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'V' and resid 20 through 22 removed outlier: 3.528A pdb=" N HIS V 28 " --> pdb=" O VAL V 20 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N MET V 22 " --> pdb=" O ILE V 26 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ILE V 26 " --> pdb=" O MET V 22 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'V' and resid 34 through 38 removed outlier: 6.431A pdb=" N THR V 41 " --> pdb=" O ILE V 37 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'W' and resid 124 through 127 removed outlier: 3.727A pdb=" N ALA W 11 " --> pdb=" O LEU W 8 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'W' and resid 20 through 22 removed outlier: 3.527A pdb=" N HIS W 28 " --> pdb=" O VAL W 20 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N MET W 22 " --> pdb=" O ILE W 26 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ILE W 26 " --> pdb=" O MET W 22 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'W' and resid 34 through 38 removed outlier: 6.430A pdb=" N THR W 41 " --> pdb=" O ILE W 37 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'X' and resid 124 through 127 removed outlier: 3.727A pdb=" N ALA X 11 " --> pdb=" O LEU X 8 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'X' and resid 20 through 22 removed outlier: 3.528A pdb=" N HIS X 28 " --> pdb=" O VAL X 20 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N MET X 22 " --> pdb=" O ILE X 26 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ILE X 26 " --> pdb=" O MET X 22 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'X' and resid 34 through 38 removed outlier: 6.430A pdb=" N THR X 41 " --> pdb=" O ILE X 37 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Y' and resid 124 through 127 removed outlier: 3.727A pdb=" N ALA Y 11 " --> pdb=" O LEU Y 8 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Y' and resid 20 through 22 removed outlier: 3.528A pdb=" N HIS Y 28 " --> pdb=" O VAL Y 20 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N MET Y 22 " --> pdb=" O ILE Y 26 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ILE Y 26 " --> pdb=" O MET Y 22 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Y' and resid 34 through 38 removed outlier: 6.431A pdb=" N THR Y 41 " --> pdb=" O ILE Y 37 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Z' and resid 124 through 127 removed outlier: 3.728A pdb=" N ALA Z 11 " --> pdb=" O LEU Z 8 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Z' and resid 20 through 22 removed outlier: 3.528A pdb=" N HIS Z 28 " --> pdb=" O VAL Z 20 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N MET Z 22 " --> pdb=" O ILE Z 26 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ILE Z 26 " --> pdb=" O MET Z 22 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'Z' and resid 34 through 38 removed outlier: 6.430A pdb=" N THR Z 41 " --> pdb=" O ILE Z 37 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'a' and resid 124 through 127 removed outlier: 3.727A pdb=" N ALA a 11 " --> pdb=" O LEU a 8 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'a' and resid 20 through 22 removed outlier: 3.527A pdb=" N HIS a 28 " --> pdb=" O VAL a 20 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N MET a 22 " --> pdb=" O ILE a 26 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ILE a 26 " --> pdb=" O MET a 22 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'a' and resid 34 through 38 removed outlier: 6.431A pdb=" N THR a 41 " --> pdb=" O ILE a 37 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'b' and resid 124 through 127 removed outlier: 3.728A pdb=" N ALA b 11 " --> pdb=" O LEU b 8 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'b' and resid 20 through 22 removed outlier: 3.527A pdb=" N HIS b 28 " --> pdb=" O VAL b 20 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N MET b 22 " --> pdb=" O ILE b 26 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ILE b 26 " --> pdb=" O MET b 22 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'b' and resid 34 through 38 removed outlier: 6.431A pdb=" N THR b 41 " --> pdb=" O ILE b 37 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'P' and resid 162 through 165 Processing sheet with id=AF1, first strand: chain 'P' and resid 68 through 69 removed outlier: 3.539A pdb=" N ASN P 158 " --> pdb=" O ASP P 150 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 162 through 165 Processing sheet with id=AF3, first strand: chain 'B' and resid 68 through 69 removed outlier: 3.540A pdb=" N ASN B 158 " --> pdb=" O ASP B 150 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 162 through 165 Processing sheet with id=AF5, first strand: chain 'C' and resid 68 through 69 removed outlier: 3.539A pdb=" N ASN C 158 " --> pdb=" O ASP C 150 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 162 through 165 Processing sheet with id=AF7, first strand: chain 'D' and resid 68 through 69 removed outlier: 3.539A pdb=" N ASN D 158 " --> pdb=" O ASP D 150 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 162 through 165 Processing sheet with id=AF9, first strand: chain 'E' and resid 68 through 69 removed outlier: 3.539A pdb=" N ASN E 158 " --> pdb=" O ASP E 150 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 162 through 165 Processing sheet with id=AG2, first strand: chain 'F' and resid 68 through 69 removed outlier: 3.538A pdb=" N ASN F 158 " --> pdb=" O ASP F 150 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'G' and resid 162 through 165 Processing sheet with id=AG4, first strand: chain 'G' and resid 68 through 69 removed outlier: 3.538A pdb=" N ASN G 158 " --> pdb=" O ASP G 150 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'O' and resid 162 through 165 Processing sheet with id=AG6, first strand: chain 'O' and resid 68 through 69 removed outlier: 3.538A pdb=" N ASN O 158 " --> pdb=" O ASP O 150 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Q' and resid 162 through 165 Processing sheet with id=AG8, first strand: chain 'Q' and resid 68 through 69 removed outlier: 3.539A pdb=" N ASN Q 158 " --> pdb=" O ASP Q 150 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'R' and resid 162 through 165 Processing sheet with id=AH1, first strand: chain 'R' and resid 68 through 69 removed outlier: 3.539A pdb=" N ASN R 158 " --> pdb=" O ASP R 150 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'S' and resid 162 through 165 Processing sheet with id=AH3, first strand: chain 'S' and resid 68 through 69 removed outlier: 3.539A pdb=" N ASN S 158 " --> pdb=" O ASP S 150 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'T' and resid 162 through 165 Processing sheet with id=AH5, first strand: chain 'T' and resid 68 through 69 removed outlier: 3.539A pdb=" N ASN T 158 " --> pdb=" O ASP T 150 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'U' and resid 162 through 165 Processing sheet with id=AH7, first strand: chain 'U' and resid 68 through 69 removed outlier: 3.539A pdb=" N ASN U 158 " --> pdb=" O ASP U 150 " (cutoff:3.500A) 2758 hydrogen bonds defined for protein. 7854 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: 35.57 Time building geometry restraints manager: 61.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 47096 1.03 - 1.23: 142 1.23 - 1.42: 18436 1.42 - 1.62: 27594 1.62 - 1.81: 378 Bond restraints: 93646 Sorted by residual: bond pdb=" C ASN O 111 " pdb=" O ASN O 111 " ideal model delta sigma weight residual 1.237 1.198 0.039 1.17e-02 7.31e+03 1.11e+01 bond pdb=" C ASN G 111 " pdb=" O ASN G 111 " ideal model delta sigma weight residual 1.237 1.198 0.039 1.17e-02 7.31e+03 1.11e+01 bond pdb=" C ASN R 111 " pdb=" O ASN R 111 " ideal model delta sigma weight residual 1.237 1.198 0.039 1.17e-02 7.31e+03 1.10e+01 bond pdb=" C ASN U 111 " pdb=" O ASN U 111 " ideal model delta sigma weight residual 1.237 1.198 0.039 1.17e-02 7.31e+03 1.10e+01 bond pdb=" C ASN E 111 " pdb=" O ASN E 111 " ideal model delta sigma weight residual 1.237 1.198 0.039 1.17e-02 7.31e+03 1.09e+01 ... (remaining 93641 not shown) Histogram of bond angle deviations from ideal: 99.76 - 106.10: 1334 106.10 - 112.45: 110451 112.45 - 118.79: 20433 118.79 - 125.13: 37166 125.13 - 131.47: 422 Bond angle restraints: 169806 Sorted by residual: angle pdb=" O GLU L 64 " pdb=" C GLU L 64 " pdb=" N LEU L 65 " ideal model delta sigma weight residual 122.09 125.63 -3.54 1.08e+00 8.57e-01 1.07e+01 angle pdb=" O GLU a 64 " pdb=" C GLU a 64 " pdb=" N LEU a 65 " ideal model delta sigma weight residual 122.09 125.58 -3.49 1.08e+00 8.57e-01 1.05e+01 angle pdb=" O GLU M 64 " pdb=" C GLU M 64 " pdb=" N LEU M 65 " ideal model delta sigma weight residual 122.09 125.58 -3.49 1.08e+00 8.57e-01 1.05e+01 angle pdb=" O GLU W 64 " pdb=" C GLU W 64 " pdb=" N LEU W 65 " ideal model delta sigma weight residual 122.09 125.57 -3.48 1.08e+00 8.57e-01 1.04e+01 angle pdb=" O GLU I 64 " pdb=" C GLU I 64 " pdb=" N LEU I 65 " ideal model delta sigma weight residual 122.09 125.57 -3.48 1.08e+00 8.57e-01 1.04e+01 ... (remaining 169801 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.37: 37781 17.37 - 34.74: 3303 34.74 - 52.11: 1675 52.11 - 69.48: 610 69.48 - 86.86: 101 Dihedral angle restraints: 43470 sinusoidal: 24346 harmonic: 19124 Sorted by residual: dihedral pdb=" CA MET Z 93 " pdb=" C MET Z 93 " pdb=" N PRO Z 94 " pdb=" CA PRO Z 94 " ideal model delta harmonic sigma weight residual -180.00 -155.90 -24.10 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA MET M 93 " pdb=" C MET M 93 " pdb=" N PRO M 94 " pdb=" CA PRO M 94 " ideal model delta harmonic sigma weight residual 180.00 -155.90 -24.10 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA MET b 93 " pdb=" C MET b 93 " pdb=" N PRO b 94 " pdb=" CA PRO b 94 " ideal model delta harmonic sigma weight residual -180.00 -155.90 -24.10 0 5.00e+00 4.00e-02 2.32e+01 ... (remaining 43467 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 4414 0.031 - 0.062: 1779 0.062 - 0.092: 563 0.092 - 0.123: 494 0.123 - 0.154: 114 Chirality restraints: 7364 Sorted by residual: chirality pdb=" CA LEU T 201 " pdb=" N LEU T 201 " pdb=" C LEU T 201 " pdb=" CB LEU T 201 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.91e-01 chirality pdb=" CA LEU O 201 " pdb=" N LEU O 201 " pdb=" C LEU O 201 " pdb=" CB LEU O 201 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.84e-01 chirality pdb=" CA LEU D 201 " pdb=" N LEU D 201 " pdb=" C LEU D 201 " pdb=" CB LEU D 201 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.81e-01 ... (remaining 7361 not shown) Planarity restraints: 13818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 57 " 0.304 9.50e-02 1.11e+02 3.68e-01 2.83e+03 pdb=" NE ARG A 57 " 0.388 2.00e-02 2.50e+03 pdb=" CZ ARG A 57 " 0.093 2.00e-02 2.50e+03 pdb=" NH1 ARG A 57 " -0.049 2.00e-02 2.50e+03 pdb=" NH2 ARG A 57 " -0.049 2.00e-02 2.50e+03 pdb="HH11 ARG A 57 " 0.494 2.00e-02 2.50e+03 pdb="HH12 ARG A 57 " -0.692 2.00e-02 2.50e+03 pdb="HH21 ARG A 57 " -0.430 2.00e-02 2.50e+03 pdb="HH22 ARG A 57 " 0.232 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG U 57 " -0.303 9.50e-02 1.11e+02 3.68e-01 2.83e+03 pdb=" NE ARG U 57 " -0.388 2.00e-02 2.50e+03 pdb=" CZ ARG U 57 " -0.093 2.00e-02 2.50e+03 pdb=" NH1 ARG U 57 " 0.049 2.00e-02 2.50e+03 pdb=" NH2 ARG U 57 " 0.050 2.00e-02 2.50e+03 pdb="HH11 ARG U 57 " -0.494 2.00e-02 2.50e+03 pdb="HH12 ARG U 57 " 0.692 2.00e-02 2.50e+03 pdb="HH21 ARG U 57 " 0.430 2.00e-02 2.50e+03 pdb="HH22 ARG U 57 " -0.232 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG P 57 " 0.303 9.50e-02 1.11e+02 3.68e-01 2.82e+03 pdb=" NE ARG P 57 " 0.388 2.00e-02 2.50e+03 pdb=" CZ ARG P 57 " 0.092 2.00e-02 2.50e+03 pdb=" NH1 ARG P 57 " -0.049 2.00e-02 2.50e+03 pdb=" NH2 ARG P 57 " -0.049 2.00e-02 2.50e+03 pdb="HH11 ARG P 57 " 0.494 2.00e-02 2.50e+03 pdb="HH12 ARG P 57 " -0.692 2.00e-02 2.50e+03 pdb="HH21 ARG P 57 " -0.430 2.00e-02 2.50e+03 pdb="HH22 ARG P 57 " 0.232 2.00e-02 2.50e+03 ... (remaining 13815 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 4756 2.16 - 2.77: 182324 2.77 - 3.38: 268408 3.38 - 3.99: 361777 3.99 - 4.60: 549347 Nonbonded interactions: 1366612 Sorted by model distance: nonbonded pdb="HE21 GLN J 141 " pdb="HE21 GLN a 141 " model vdw 1.547 2.100 nonbonded pdb=" O GLY P 128 " pdb=" H GLY O 127 " model vdw 1.584 1.850 nonbonded pdb="HE21 GLN K 141 " pdb="HE21 GLN Z 141 " model vdw 1.626 2.100 nonbonded pdb=" H GLY A 127 " pdb=" O GLY B 128 " model vdw 1.635 1.850 nonbonded pdb="HE21 GLN I 141 " pdb="HE21 GLN b 141 " model vdw 1.640 2.100 ... (remaining 1366607 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' } 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: 8.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 1.020 Extract box with map and model: 29.130 Check model and map are aligned: 1.040 Set scattering table: 0.640 Process input model: 224.900 Find NCS groups from input model: 3.640 Set up NCS constraints: 0.640 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: 0.020 Load rotamer database and sin/cos tables:11.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 281.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 46536 Z= 0.259 Angle : 0.693 6.393 62804 Z= 0.433 Chirality : 0.046 0.154 7364 Planarity : 0.006 0.111 8050 Dihedral : 17.551 86.856 17542 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.21 % Allowed : 17.41 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.11), residues: 5894 helix: 2.27 (0.11), residues: 2324 sheet: 0.48 (0.12), residues: 1428 loop : -0.62 (0.14), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS J 109 PHE 0.010 0.002 PHE T 149 TYR 0.016 0.002 TYR a 95 ARG 0.004 0.000 ARG b 71 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11788 Ramachandran restraints generated. 5894 Oldfield, 0 Emsley, 5894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11788 Ramachandran restraints generated. 5894 Oldfield, 0 Emsley, 5894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 964 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 805 time to evaluate : 6.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 TYR cc_start: 0.7751 (OUTLIER) cc_final: 0.5966 (t80) REVERT: F 221 TYR cc_start: 0.7937 (OUTLIER) cc_final: 0.5829 (t80) REVERT: O 221 TYR cc_start: 0.7692 (OUTLIER) cc_final: 0.5798 (t80) outliers start: 159 outliers final: 42 residues processed: 923 average time/residue: 3.8068 time to fit residues: 4169.1073 Evaluate side-chains 589 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 544 time to evaluate : 5.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain Y residue 3 THR Chi-restraints excluded: chain P residue 65 GLU Chi-restraints excluded: chain P residue 203 GLU Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 55 ARG Chi-restraints excluded: chain B residue 203 GLU Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 55 ARG Chi-restraints excluded: chain C residue 203 GLU Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 55 ARG Chi-restraints excluded: chain D residue 203 GLU Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 55 ARG Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 203 GLU Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 203 GLU Chi-restraints excluded: chain O residue 12 ILE Chi-restraints excluded: chain O residue 55 ARG Chi-restraints excluded: chain O residue 203 GLU Chi-restraints excluded: chain O residue 206 GLU Chi-restraints excluded: chain O residue 221 TYR Chi-restraints excluded: chain Q residue 12 ILE Chi-restraints excluded: chain Q residue 55 ARG Chi-restraints excluded: chain Q residue 203 GLU Chi-restraints excluded: chain R residue 12 ILE Chi-restraints excluded: chain R residue 55 ARG Chi-restraints excluded: chain R residue 203 GLU Chi-restraints excluded: chain R residue 206 GLU Chi-restraints excluded: chain S residue 12 ILE Chi-restraints excluded: chain S residue 203 GLU Chi-restraints excluded: chain T residue 12 ILE Chi-restraints excluded: chain T residue 203 GLU Chi-restraints excluded: chain U residue 12 ILE Chi-restraints excluded: chain U residue 55 ARG Chi-restraints excluded: chain U residue 203 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 496 optimal weight: 8.9990 chunk 445 optimal weight: 5.9990 chunk 247 optimal weight: 4.9990 chunk 152 optimal weight: 4.9990 chunk 300 optimal weight: 0.0980 chunk 238 optimal weight: 5.9990 chunk 460 optimal weight: 10.0000 chunk 178 optimal weight: 4.9990 chunk 280 optimal weight: 0.2980 chunk 343 optimal weight: 9.9990 chunk 533 optimal weight: 5.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN I 89 GLN K 89 GLN V 89 GLN W 89 GLN R 111 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 46536 Z= 0.263 Angle : 0.553 4.675 62804 Z= 0.306 Chirality : 0.045 0.141 7364 Planarity : 0.004 0.039 8050 Dihedral : 6.333 55.929 6634 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.14 % Allowed : 17.39 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.11), residues: 5894 helix: 2.50 (0.10), residues: 2380 sheet: 0.81 (0.13), residues: 1414 loop : -0.54 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS b 109 PHE 0.007 0.001 PHE Y 133 TYR 0.015 0.002 TYR Y 66 ARG 0.004 0.000 ARG E 57 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11788 Ramachandran restraints generated. 5894 Oldfield, 0 Emsley, 5894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11788 Ramachandran restraints generated. 5894 Oldfield, 0 Emsley, 5894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 555 time to evaluate : 5.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 TYR cc_start: 0.7896 (OUTLIER) cc_final: 0.6365 (t80) REVERT: K 141 GLN cc_start: 0.7518 (OUTLIER) cc_final: 0.7247 (mt0) REVERT: N 141 GLN cc_start: 0.7537 (OUTLIER) cc_final: 0.7176 (mt0) REVERT: F 221 TYR cc_start: 0.7969 (OUTLIER) cc_final: 0.6245 (t80) REVERT: O 221 TYR cc_start: 0.7869 (OUTLIER) cc_final: 0.6332 (t80) REVERT: T 221 TYR cc_start: 0.7869 (OUTLIER) cc_final: 0.6303 (t80) REVERT: U 221 TYR cc_start: 0.7949 (OUTLIER) cc_final: 0.6139 (t80) outliers start: 106 outliers final: 47 residues processed: 625 average time/residue: 3.2842 time to fit residues: 2505.2605 Evaluate side-chains 583 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 529 time to evaluate : 5.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 61 GLN Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain K residue 30 ASN Chi-restraints excluded: chain K residue 141 GLN Chi-restraints excluded: chain M residue 30 ASN Chi-restraints excluded: chain N residue 30 ASN Chi-restraints excluded: chain N residue 141 GLN Chi-restraints excluded: chain a residue 89 GLN Chi-restraints excluded: chain P residue 61 GLN Chi-restraints excluded: chain P residue 221 TYR Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 55 ARG Chi-restraints excluded: chain B residue 61 GLN Chi-restraints excluded: chain B residue 203 GLU Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 55 ARG Chi-restraints excluded: chain C residue 61 GLN Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain F residue 61 GLN Chi-restraints excluded: chain F residue 203 GLU Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain G residue 61 GLN Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain O residue 12 ILE Chi-restraints excluded: chain O residue 55 ARG Chi-restraints excluded: chain O residue 61 GLN Chi-restraints excluded: chain O residue 203 GLU Chi-restraints excluded: chain O residue 221 TYR Chi-restraints excluded: chain Q residue 12 ILE Chi-restraints excluded: chain Q residue 61 GLN Chi-restraints excluded: chain Q residue 203 GLU Chi-restraints excluded: chain Q residue 221 TYR Chi-restraints excluded: chain R residue 12 ILE Chi-restraints excluded: chain R residue 61 GLN Chi-restraints excluded: chain R residue 203 GLU Chi-restraints excluded: chain R residue 221 TYR Chi-restraints excluded: chain S residue 61 GLN Chi-restraints excluded: chain S residue 203 GLU Chi-restraints excluded: chain S residue 221 TYR Chi-restraints excluded: chain T residue 12 ILE Chi-restraints excluded: chain T residue 203 GLU Chi-restraints excluded: chain T residue 221 TYR Chi-restraints excluded: chain U residue 12 ILE Chi-restraints excluded: chain U residue 55 ARG Chi-restraints excluded: chain U residue 61 GLN Chi-restraints excluded: chain U residue 203 GLU Chi-restraints excluded: chain U residue 221 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 296 optimal weight: 1.9990 chunk 165 optimal weight: 5.9990 chunk 444 optimal weight: 5.9990 chunk 363 optimal weight: 6.9990 chunk 147 optimal weight: 4.9990 chunk 534 optimal weight: 5.9990 chunk 577 optimal weight: 5.9990 chunk 476 optimal weight: 8.9990 chunk 530 optimal weight: 5.9990 chunk 182 optimal weight: 4.9990 chunk 429 optimal weight: 0.9980 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 89 GLN M 89 GLN N 89 GLN V 89 GLN W 89 GLN X 89 GLN b 89 GLN C 111 ASN G 98 GLN O 98 GLN R 111 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 46536 Z= 0.288 Angle : 0.523 4.754 62804 Z= 0.293 Chirality : 0.043 0.138 7364 Planarity : 0.004 0.043 8050 Dihedral : 5.583 56.273 6580 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.47 % Allowed : 16.65 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.11), residues: 5894 helix: 2.57 (0.10), residues: 2338 sheet: 0.84 (0.13), residues: 1414 loop : -0.61 (0.14), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS K 109 PHE 0.008 0.001 PHE O 149 TYR 0.013 0.001 TYR K 66 ARG 0.003 0.000 ARG R 55 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11788 Ramachandran restraints generated. 5894 Oldfield, 0 Emsley, 5894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11788 Ramachandran restraints generated. 5894 Oldfield, 0 Emsley, 5894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 542 time to evaluate : 5.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 141 GLN cc_start: 0.7572 (OUTLIER) cc_final: 0.7331 (mt0) REVERT: F 221 TYR cc_start: 0.7987 (OUTLIER) cc_final: 0.6181 (t80) REVERT: O 221 TYR cc_start: 0.7951 (OUTLIER) cc_final: 0.6192 (t80) outliers start: 73 outliers final: 42 residues processed: 585 average time/residue: 3.2972 time to fit residues: 2352.6252 Evaluate side-chains 571 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 526 time to evaluate : 5.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLN Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 89 GLN Chi-restraints excluded: chain K residue 30 ASN Chi-restraints excluded: chain K residue 141 GLN Chi-restraints excluded: chain W residue 30 ASN Chi-restraints excluded: chain Y residue 89 GLN Chi-restraints excluded: chain a residue 89 GLN Chi-restraints excluded: chain P residue 61 GLN Chi-restraints excluded: chain P residue 203 GLU Chi-restraints excluded: chain P residue 221 TYR Chi-restraints excluded: chain B residue 61 GLN Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 55 ARG Chi-restraints excluded: chain C residue 203 GLU Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain D residue 203 GLU Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 61 GLN Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 61 GLN Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain G residue 61 GLN Chi-restraints excluded: chain G residue 203 GLU Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain O residue 55 ARG Chi-restraints excluded: chain O residue 61 GLN Chi-restraints excluded: chain O residue 221 TYR Chi-restraints excluded: chain Q residue 61 GLN Chi-restraints excluded: chain Q residue 221 TYR Chi-restraints excluded: chain R residue 12 ILE Chi-restraints excluded: chain R residue 61 GLN Chi-restraints excluded: chain R residue 221 TYR Chi-restraints excluded: chain S residue 61 GLN Chi-restraints excluded: chain S residue 221 TYR Chi-restraints excluded: chain T residue 61 GLN Chi-restraints excluded: chain T residue 221 TYR Chi-restraints excluded: chain U residue 12 ILE Chi-restraints excluded: chain U residue 61 GLN Chi-restraints excluded: chain U residue 221 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 528 optimal weight: 0.3980 chunk 402 optimal weight: 5.9990 chunk 277 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 255 optimal weight: 0.9980 chunk 359 optimal weight: 7.9990 chunk 536 optimal weight: 4.9990 chunk 568 optimal weight: 10.0000 chunk 280 optimal weight: 0.6980 chunk 508 optimal weight: 5.9990 chunk 153 optimal weight: 5.9990 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN K 89 GLN M 89 GLN N 89 GLN P 122 GLN C 111 ASN D 111 ASN F 122 GLN G 98 GLN G 122 GLN Q 122 GLN R 111 ASN R 122 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 46536 Z= 0.201 Angle : 0.488 4.848 62804 Z= 0.270 Chirality : 0.042 0.138 7364 Planarity : 0.004 0.046 8050 Dihedral : 4.814 56.067 6532 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.43 % Allowed : 16.26 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.11), residues: 5894 helix: 2.57 (0.10), residues: 2380 sheet: 0.91 (0.13), residues: 1414 loop : -0.54 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS W 109 PHE 0.006 0.001 PHE O 149 TYR 0.011 0.001 TYR L 66 ARG 0.005 0.000 ARG B 55 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11788 Ramachandran restraints generated. 5894 Oldfield, 0 Emsley, 5894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11788 Ramachandran restraints generated. 5894 Oldfield, 0 Emsley, 5894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 558 time to evaluate : 5.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 221 TYR cc_start: 0.7930 (OUTLIER) cc_final: 0.6192 (t80) outliers start: 71 outliers final: 43 residues processed: 597 average time/residue: 3.2618 time to fit residues: 2378.9227 Evaluate side-chains 578 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 534 time to evaluate : 5.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 89 GLN Chi-restraints excluded: chain A residue 61 GLN Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain V residue 17 GLU Chi-restraints excluded: chain V residue 89 GLN Chi-restraints excluded: chain W residue 17 GLU Chi-restraints excluded: chain Y residue 89 GLN Chi-restraints excluded: chain a residue 89 GLN Chi-restraints excluded: chain P residue 61 GLN Chi-restraints excluded: chain P residue 203 GLU Chi-restraints excluded: chain P residue 221 TYR Chi-restraints excluded: chain B residue 61 GLN Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 55 ARG Chi-restraints excluded: chain C residue 61 GLN Chi-restraints excluded: chain C residue 203 GLU Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain D residue 203 GLU Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 61 GLN Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain G residue 61 GLN Chi-restraints excluded: chain G residue 203 GLU Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain O residue 61 GLN Chi-restraints excluded: chain O residue 221 TYR Chi-restraints excluded: chain Q residue 61 GLN Chi-restraints excluded: chain Q residue 221 TYR Chi-restraints excluded: chain R residue 61 GLN Chi-restraints excluded: chain R residue 221 TYR Chi-restraints excluded: chain S residue 61 GLN Chi-restraints excluded: chain S residue 221 TYR Chi-restraints excluded: chain T residue 61 GLN Chi-restraints excluded: chain T residue 221 TYR Chi-restraints excluded: chain U residue 61 GLN Chi-restraints excluded: chain U residue 221 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 473 optimal weight: 10.0000 chunk 322 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 423 optimal weight: 5.9990 chunk 234 optimal weight: 6.9990 chunk 485 optimal weight: 4.9990 chunk 392 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 chunk 290 optimal weight: 4.9990 chunk 510 optimal weight: 4.9990 chunk 143 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN M 89 GLN N 89 GLN W 89 GLN Z 89 GLN C 111 ASN D 122 GLN O 98 GLN Q 98 GLN R 111 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 46536 Z= 0.397 Angle : 0.540 4.850 62804 Z= 0.303 Chirality : 0.044 0.134 7364 Planarity : 0.004 0.050 8050 Dihedral : 4.983 55.314 6522 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.41 % Allowed : 16.49 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.11), residues: 5894 helix: 2.48 (0.10), residues: 2338 sheet: 0.83 (0.13), residues: 1414 loop : -0.67 (0.14), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS Y 28 PHE 0.007 0.001 PHE P 149 TYR 0.014 0.001 TYR L 66 ARG 0.008 0.000 ARG L 71 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11788 Ramachandran restraints generated. 5894 Oldfield, 0 Emsley, 5894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11788 Ramachandran restraints generated. 5894 Oldfield, 0 Emsley, 5894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 529 time to evaluate : 5.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 70 outliers final: 46 residues processed: 562 average time/residue: 3.3394 time to fit residues: 2284.3457 Evaluate side-chains 559 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 513 time to evaluate : 5.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 89 GLN Chi-restraints excluded: chain A residue 61 GLN Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain J residue 89 GLN Chi-restraints excluded: chain K residue 30 ASN Chi-restraints excluded: chain Y residue 62 GLU Chi-restraints excluded: chain Y residue 89 GLN Chi-restraints excluded: chain Z residue 30 ASN Chi-restraints excluded: chain a residue 89 GLN Chi-restraints excluded: chain b residue 30 ASN Chi-restraints excluded: chain P residue 61 GLN Chi-restraints excluded: chain P residue 203 GLU Chi-restraints excluded: chain P residue 221 TYR Chi-restraints excluded: chain B residue 61 GLN Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 55 ARG Chi-restraints excluded: chain C residue 61 GLN Chi-restraints excluded: chain C residue 203 GLU Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain D residue 203 GLU Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 61 GLN Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain G residue 61 GLN Chi-restraints excluded: chain G residue 203 GLU Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain O residue 61 GLN Chi-restraints excluded: chain O residue 221 TYR Chi-restraints excluded: chain Q residue 59 ILE Chi-restraints excluded: chain Q residue 61 GLN Chi-restraints excluded: chain Q residue 221 TYR Chi-restraints excluded: chain R residue 61 GLN Chi-restraints excluded: chain R residue 221 TYR Chi-restraints excluded: chain S residue 61 GLN Chi-restraints excluded: chain S residue 63 SER Chi-restraints excluded: chain S residue 221 TYR Chi-restraints excluded: chain T residue 61 GLN Chi-restraints excluded: chain T residue 221 TYR Chi-restraints excluded: chain U residue 61 GLN Chi-restraints excluded: chain U residue 221 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 191 optimal weight: 3.9990 chunk 511 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 333 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 chunk 568 optimal weight: 8.9990 chunk 472 optimal weight: 8.9990 chunk 263 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 188 optimal weight: 4.9990 chunk 298 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN A 122 GLN M 89 GLN N 89 GLN W 89 GLN Y 191 GLN a 191 GLN C 111 ASN G 98 GLN G 111 ASN Q 98 GLN Q 111 ASN R 98 GLN R 111 ASN T 111 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 46536 Z= 0.301 Angle : 0.510 4.777 62804 Z= 0.285 Chirality : 0.043 0.140 7364 Planarity : 0.004 0.045 8050 Dihedral : 4.906 55.191 6522 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.23 % Allowed : 16.40 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.11), residues: 5894 helix: 2.52 (0.10), residues: 2338 sheet: 0.83 (0.13), residues: 1414 loop : -0.70 (0.14), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS W 109 PHE 0.007 0.001 PHE S 149 TYR 0.012 0.001 TYR L 66 ARG 0.005 0.000 ARG V 71 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11788 Ramachandran restraints generated. 5894 Oldfield, 0 Emsley, 5894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11788 Ramachandran restraints generated. 5894 Oldfield, 0 Emsley, 5894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 531 time to evaluate : 5.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 43 residues processed: 558 average time/residue: 3.3358 time to fit residues: 2263.5433 Evaluate side-chains 557 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 514 time to evaluate : 5.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 89 GLN Chi-restraints excluded: chain A residue 61 GLN Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain J residue 89 GLN Chi-restraints excluded: chain Y residue 62 GLU Chi-restraints excluded: chain Y residue 89 GLN Chi-restraints excluded: chain a residue 89 GLN Chi-restraints excluded: chain P residue 61 GLN Chi-restraints excluded: chain P residue 203 GLU Chi-restraints excluded: chain P residue 221 TYR Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 61 GLN Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain C residue 55 ARG Chi-restraints excluded: chain C residue 61 GLN Chi-restraints excluded: chain C residue 203 GLU Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain D residue 203 GLU Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 61 GLN Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 61 GLN Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain G residue 61 GLN Chi-restraints excluded: chain G residue 203 GLU Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain O residue 61 GLN Chi-restraints excluded: chain O residue 221 TYR Chi-restraints excluded: chain Q residue 61 GLN Chi-restraints excluded: chain Q residue 221 TYR Chi-restraints excluded: chain R residue 61 GLN Chi-restraints excluded: chain R residue 221 TYR Chi-restraints excluded: chain S residue 61 GLN Chi-restraints excluded: chain S residue 63 SER Chi-restraints excluded: chain S residue 221 TYR Chi-restraints excluded: chain T residue 61 GLN Chi-restraints excluded: chain T residue 221 TYR Chi-restraints excluded: chain U residue 61 GLN Chi-restraints excluded: chain U residue 221 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 548 optimal weight: 10.0000 chunk 64 optimal weight: 0.6980 chunk 324 optimal weight: 8.9990 chunk 415 optimal weight: 6.9990 chunk 321 optimal weight: 9.9990 chunk 478 optimal weight: 0.3980 chunk 317 optimal weight: 8.9990 chunk 566 optimal weight: 10.0000 chunk 354 optimal weight: 5.9990 chunk 345 optimal weight: 8.9990 chunk 261 optimal weight: 5.9990 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 191 GLN A 98 GLN A 111 ASN M 89 GLN N 89 GLN X 89 GLN Y 191 GLN Z 89 GLN C 111 ASN D 111 ASN G 98 GLN G 111 ASN Q 98 GLN Q 111 ASN R 98 GLN R 111 ASN T 111 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 46536 Z= 0.308 Angle : 0.508 4.785 62804 Z= 0.284 Chirality : 0.043 0.135 7364 Planarity : 0.004 0.044 8050 Dihedral : 4.881 54.993 6520 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.17 % Allowed : 16.04 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.11), residues: 5894 helix: 2.53 (0.10), residues: 2338 sheet: 0.81 (0.13), residues: 1414 loop : -0.68 (0.14), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS W 28 PHE 0.007 0.001 PHE B 149 TYR 0.012 0.001 TYR X 66 ARG 0.005 0.000 ARG H 71 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11788 Ramachandran restraints generated. 5894 Oldfield, 0 Emsley, 5894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11788 Ramachandran restraints generated. 5894 Oldfield, 0 Emsley, 5894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 521 time to evaluate : 5.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 17 GLU cc_start: 0.6771 (OUTLIER) cc_final: 0.6212 (pp20) REVERT: b 17 GLU cc_start: 0.6780 (OUTLIER) cc_final: 0.6210 (pp20) outliers start: 58 outliers final: 42 residues processed: 548 average time/residue: 3.3528 time to fit residues: 2237.0317 Evaluate side-chains 558 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 514 time to evaluate : 5.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 89 GLN Chi-restraints excluded: chain A residue 61 GLN Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain J residue 89 GLN Chi-restraints excluded: chain K residue 17 GLU Chi-restraints excluded: chain Y residue 62 GLU Chi-restraints excluded: chain Y residue 89 GLN Chi-restraints excluded: chain a residue 89 GLN Chi-restraints excluded: chain b residue 17 GLU Chi-restraints excluded: chain P residue 12 ILE Chi-restraints excluded: chain P residue 61 GLN Chi-restraints excluded: chain P residue 203 GLU Chi-restraints excluded: chain P residue 221 TYR Chi-restraints excluded: chain B residue 61 GLN Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain C residue 55 ARG Chi-restraints excluded: chain C residue 61 GLN Chi-restraints excluded: chain C residue 203 GLU Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain D residue 203 GLU Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 61 GLN Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 61 GLN Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain G residue 61 GLN Chi-restraints excluded: chain G residue 203 GLU Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain O residue 61 GLN Chi-restraints excluded: chain O residue 221 TYR Chi-restraints excluded: chain Q residue 61 GLN Chi-restraints excluded: chain Q residue 221 TYR Chi-restraints excluded: chain R residue 61 GLN Chi-restraints excluded: chain R residue 221 TYR Chi-restraints excluded: chain S residue 61 GLN Chi-restraints excluded: chain S residue 221 TYR Chi-restraints excluded: chain T residue 61 GLN Chi-restraints excluded: chain T residue 221 TYR Chi-restraints excluded: chain U residue 61 GLN Chi-restraints excluded: chain U residue 221 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 350 optimal weight: 9.9990 chunk 226 optimal weight: 5.9990 chunk 338 optimal weight: 0.4980 chunk 170 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 360 optimal weight: 3.9990 chunk 386 optimal weight: 2.9990 chunk 280 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 445 optimal weight: 3.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN M 89 GLN N 89 GLN X 89 GLN Z 89 GLN C 111 ASN D 111 ASN G 111 ASN Q 111 ASN R 98 GLN R 111 ASN T 111 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 46536 Z= 0.213 Angle : 0.481 4.702 62804 Z= 0.267 Chirality : 0.042 0.139 7364 Planarity : 0.004 0.041 8050 Dihedral : 4.737 55.141 6520 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.19 % Allowed : 16.10 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.11), residues: 5894 helix: 2.53 (0.10), residues: 2380 sheet: 0.83 (0.13), residues: 1414 loop : -0.57 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS N 28 PHE 0.007 0.001 PHE E 149 TYR 0.010 0.001 TYR L 66 ARG 0.005 0.000 ARG Y 71 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11788 Ramachandran restraints generated. 5894 Oldfield, 0 Emsley, 5894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11788 Ramachandran restraints generated. 5894 Oldfield, 0 Emsley, 5894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 533 time to evaluate : 5.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 17 GLU cc_start: 0.6733 (OUTLIER) cc_final: 0.6167 (pp20) outliers start: 59 outliers final: 44 residues processed: 561 average time/residue: 3.3321 time to fit residues: 2271.4422 Evaluate side-chains 564 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 519 time to evaluate : 5.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 89 GLN Chi-restraints excluded: chain A residue 61 GLN Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 89 GLN Chi-restraints excluded: chain K residue 17 GLU Chi-restraints excluded: chain V residue 89 GLN Chi-restraints excluded: chain Y residue 62 GLU Chi-restraints excluded: chain Y residue 89 GLN Chi-restraints excluded: chain a residue 89 GLN Chi-restraints excluded: chain b residue 17 GLU Chi-restraints excluded: chain P residue 61 GLN Chi-restraints excluded: chain P residue 203 GLU Chi-restraints excluded: chain P residue 221 TYR Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 61 GLN Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain C residue 55 ARG Chi-restraints excluded: chain C residue 61 GLN Chi-restraints excluded: chain C residue 203 GLU Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain D residue 203 GLU Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 61 GLN Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 61 GLN Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain G residue 61 GLN Chi-restraints excluded: chain G residue 203 GLU Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain O residue 61 GLN Chi-restraints excluded: chain O residue 221 TYR Chi-restraints excluded: chain Q residue 61 GLN Chi-restraints excluded: chain Q residue 221 TYR Chi-restraints excluded: chain R residue 61 GLN Chi-restraints excluded: chain R residue 221 TYR Chi-restraints excluded: chain S residue 61 GLN Chi-restraints excluded: chain S residue 221 TYR Chi-restraints excluded: chain T residue 221 TYR Chi-restraints excluded: chain U residue 61 GLN Chi-restraints excluded: chain U residue 221 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 515 optimal weight: 10.0000 chunk 542 optimal weight: 7.9990 chunk 495 optimal weight: 7.9990 chunk 528 optimal weight: 5.9990 chunk 317 optimal weight: 10.0000 chunk 230 optimal weight: 3.9990 chunk 414 optimal weight: 10.0000 chunk 162 optimal weight: 5.9990 chunk 477 optimal weight: 8.9990 chunk 499 optimal weight: 7.9990 chunk 526 optimal weight: 0.9980 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 111 ASN N 89 GLN X 89 GLN C 111 ASN D 111 ASN G 98 GLN G 111 ASN Q 98 GLN Q 111 ASN R 111 ASN T 111 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 46536 Z= 0.374 Angle : 0.523 4.837 62804 Z= 0.294 Chirality : 0.044 0.133 7364 Planarity : 0.004 0.042 8050 Dihedral : 4.913 54.793 6520 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.07 % Allowed : 16.26 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.11), residues: 5894 helix: 2.51 (0.10), residues: 2338 sheet: 0.80 (0.13), residues: 1414 loop : -0.68 (0.14), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 28 PHE 0.007 0.001 PHE C 149 TYR 0.013 0.001 TYR L 66 ARG 0.005 0.000 ARG L 71 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11788 Ramachandran restraints generated. 5894 Oldfield, 0 Emsley, 5894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11788 Ramachandran restraints generated. 5894 Oldfield, 0 Emsley, 5894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 510 time to evaluate : 5.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 17 GLU cc_start: 0.6805 (OUTLIER) cc_final: 0.6234 (pp20) REVERT: b 17 GLU cc_start: 0.6803 (OUTLIER) cc_final: 0.6232 (pp20) outliers start: 53 outliers final: 40 residues processed: 534 average time/residue: 3.3899 time to fit residues: 2198.9981 Evaluate side-chains 543 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 501 time to evaluate : 5.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 89 GLN Chi-restraints excluded: chain A residue 61 GLN Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain J residue 89 GLN Chi-restraints excluded: chain K residue 17 GLU Chi-restraints excluded: chain L residue 24 ASN Chi-restraints excluded: chain Y residue 62 GLU Chi-restraints excluded: chain Y residue 89 GLN Chi-restraints excluded: chain a residue 89 GLN Chi-restraints excluded: chain b residue 17 GLU Chi-restraints excluded: chain P residue 61 GLN Chi-restraints excluded: chain P residue 203 GLU Chi-restraints excluded: chain P residue 221 TYR Chi-restraints excluded: chain B residue 61 GLN Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain C residue 55 ARG Chi-restraints excluded: chain C residue 61 GLN Chi-restraints excluded: chain C residue 203 GLU Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain D residue 203 GLU Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 61 GLN Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 61 GLN Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain G residue 61 GLN Chi-restraints excluded: chain G residue 203 GLU Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain O residue 61 GLN Chi-restraints excluded: chain O residue 221 TYR Chi-restraints excluded: chain Q residue 61 GLN Chi-restraints excluded: chain Q residue 221 TYR Chi-restraints excluded: chain R residue 61 GLN Chi-restraints excluded: chain R residue 221 TYR Chi-restraints excluded: chain S residue 61 GLN Chi-restraints excluded: chain S residue 221 TYR Chi-restraints excluded: chain T residue 221 TYR Chi-restraints excluded: chain U residue 61 GLN Chi-restraints excluded: chain U residue 221 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 346 optimal weight: 6.9990 chunk 558 optimal weight: 2.9990 chunk 340 optimal weight: 5.9990 chunk 264 optimal weight: 1.9990 chunk 388 optimal weight: 0.9980 chunk 585 optimal weight: 0.9990 chunk 539 optimal weight: 1.9990 chunk 466 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 360 optimal weight: 0.9980 chunk 286 optimal weight: 5.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN K 89 GLN L 24 ASN N 89 GLN V 89 GLN X 89 GLN Z 89 GLN b 89 GLN C 111 ASN D 111 ASN G 111 ASN O 98 GLN Q 111 ASN R 98 GLN R 111 ASN T 111 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.154 46536 Z= 0.290 Angle : 0.597 59.195 62804 Z= 0.347 Chirality : 0.043 0.137 7364 Planarity : 0.004 0.042 8050 Dihedral : 4.918 54.727 6520 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.99 % Allowed : 16.36 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.11), residues: 5894 helix: 2.51 (0.10), residues: 2338 sheet: 0.78 (0.13), residues: 1414 loop : -0.68 (0.14), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 28 PHE 0.007 0.001 PHE L 25 TYR 0.012 0.001 TYR M 66 ARG 0.004 0.000 ARG V 71 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11788 Ramachandran restraints generated. 5894 Oldfield, 0 Emsley, 5894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11788 Ramachandran restraints generated. 5894 Oldfield, 0 Emsley, 5894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 505 time to evaluate : 5.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 17 GLU cc_start: 0.6790 (OUTLIER) cc_final: 0.6234 (pp20) REVERT: b 17 GLU cc_start: 0.6793 (OUTLIER) cc_final: 0.6228 (pp20) outliers start: 49 outliers final: 40 residues processed: 528 average time/residue: 3.2663 time to fit residues: 2108.2996 Evaluate side-chains 543 residues out of total 4956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 501 time to evaluate : 5.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 89 GLN Chi-restraints excluded: chain A residue 61 GLN Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain J residue 89 GLN Chi-restraints excluded: chain K residue 17 GLU Chi-restraints excluded: chain Y residue 62 GLU Chi-restraints excluded: chain Y residue 89 GLN Chi-restraints excluded: chain a residue 89 GLN Chi-restraints excluded: chain b residue 17 GLU Chi-restraints excluded: chain P residue 12 ILE Chi-restraints excluded: chain P residue 61 GLN Chi-restraints excluded: chain P residue 203 GLU Chi-restraints excluded: chain P residue 221 TYR Chi-restraints excluded: chain B residue 61 GLN Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain C residue 55 ARG Chi-restraints excluded: chain C residue 61 GLN Chi-restraints excluded: chain C residue 203 GLU Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain D residue 203 GLU Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 61 GLN Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 61 GLN Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain G residue 61 GLN Chi-restraints excluded: chain G residue 203 GLU Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain O residue 61 GLN Chi-restraints excluded: chain O residue 221 TYR Chi-restraints excluded: chain Q residue 61 GLN Chi-restraints excluded: chain Q residue 221 TYR Chi-restraints excluded: chain R residue 61 GLN Chi-restraints excluded: chain R residue 221 TYR Chi-restraints excluded: chain S residue 61 GLN Chi-restraints excluded: chain S residue 221 TYR Chi-restraints excluded: chain T residue 221 TYR Chi-restraints excluded: chain U residue 61 GLN Chi-restraints excluded: chain U residue 221 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 370 optimal weight: 8.9990 chunk 496 optimal weight: 8.9990 chunk 142 optimal weight: 4.9990 chunk 430 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 467 optimal weight: 4.9990 chunk 195 optimal weight: 3.9990 chunk 479 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN K 89 GLN ** L 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 89 GLN V 89 GLN X 89 GLN Z 89 GLN b 89 GLN C 111 ASN D 111 ASN E 62 ASN G 98 GLN G 111 ASN O 98 GLN Q 98 GLN Q 111 ASN R 98 GLN R 111 ASN T 111 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.075110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2495 r_free = 0.2495 target = 0.050419 restraints weight = 216691.295| |-----------------------------------------------------------------------------| r_work (start): 0.2505 rms_B_bonded: 2.29 r_work: 0.2375 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2261 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9069 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.154 46536 Z= 0.290 Angle : 0.597 59.195 62804 Z= 0.347 Chirality : 0.043 0.137 7364 Planarity : 0.004 0.042 8050 Dihedral : 4.918 54.727 6520 Min Nonbonded Distance : 1.429 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.99 % Allowed : 16.32 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.11), residues: 5894 helix: 2.51 (0.10), residues: 2338 sheet: 0.78 (0.13), residues: 1414 loop : -0.68 (0.14), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 28 PHE 0.007 0.001 PHE L 25 TYR 0.012 0.001 TYR M 66 ARG 0.004 0.000 ARG V 71 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 34775.14 seconds wall clock time: 598 minutes 11.56 seconds (35891.56 seconds total)