Starting phenix.real_space_refine on Mon Apr 15 07:14:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zyd_11557/04_2024/6zyd_11557_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zyd_11557/04_2024/6zyd_11557.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zyd_11557/04_2024/6zyd_11557.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zyd_11557/04_2024/6zyd_11557.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zyd_11557/04_2024/6zyd_11557_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zyd_11557/04_2024/6zyd_11557_trim_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 7 5.49 5 S 70 5.16 5 C 10927 2.51 5 N 2849 2.21 5 O 3080 1.98 5 H 14490 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E ARG 110": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 116": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 186": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 227": "OE1" <-> "OE2" Residue "E ARG 236": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 244": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 260": "OE1" <-> "OE2" Residue "C ARG 110": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 116": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 186": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 227": "OE1" <-> "OE2" Residue "C ARG 236": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 244": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 260": "OE1" <-> "OE2" Residue "A ARG 110": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 116": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 186": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 227": "OE1" <-> "OE2" Residue "A ARG 236": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 244": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 260": "OE1" <-> "OE2" Residue "B ARG 110": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 116": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 186": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 227": "OE1" <-> "OE2" Residue "B ARG 236": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 244": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 260": "OE1" <-> "OE2" Residue "D ARG 110": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 116": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 186": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 227": "OE1" <-> "OE2" Residue "D ARG 236": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 244": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 260": "OE1" <-> "OE2" Residue "F ARG 110": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 116": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 186": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 227": "OE1" <-> "OE2" Residue "F ARG 236": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 244": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 260": "OE1" <-> "OE2" Residue "G ARG 110": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 116": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 186": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 227": "OE1" <-> "OE2" Residue "G ARG 236": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 244": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 260": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 31423 Number of models: 1 Model: "" Number of chains: 14 Chain: "E" Number of atoms: 4438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 4438 Classifications: {'peptide': 323} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 7, 'TRANS': 315} Chain breaks: 1 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 67 Planarities with less than four sites: {'UNK:plan-1': 67} Unresolved non-hydrogen planarities: 67 Chain: "C" Number of atoms: 4438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 4438 Classifications: {'peptide': 323} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 7, 'TRANS': 315} Chain breaks: 1 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 67 Planarities with less than four sites: {'UNK:plan-1': 67} Unresolved non-hydrogen planarities: 67 Chain: "A" Number of atoms: 4438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 4438 Classifications: {'peptide': 323} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 7, 'TRANS': 315} Chain breaks: 1 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 67 Planarities with less than four sites: {'UNK:plan-1': 67} Unresolved non-hydrogen planarities: 67 Chain: "B" Number of atoms: 4438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 4438 Classifications: {'peptide': 323} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 7, 'TRANS': 315} Chain breaks: 1 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 67 Planarities with less than four sites: {'UNK:plan-1': 67} Unresolved non-hydrogen planarities: 67 Chain: "D" Number of atoms: 4438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 4438 Classifications: {'peptide': 323} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 7, 'TRANS': 315} Chain breaks: 1 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 67 Planarities with less than four sites: {'UNK:plan-1': 67} Unresolved non-hydrogen planarities: 67 Chain: "F" Number of atoms: 4438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 4438 Classifications: {'peptide': 323} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 7, 'TRANS': 315} Chain breaks: 1 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 67 Planarities with less than four sites: {'UNK:plan-1': 67} Unresolved non-hydrogen planarities: 67 Chain: "G" Number of atoms: 4438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 4438 Classifications: {'peptide': 323} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 7, 'TRANS': 315} Chain breaks: 1 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 67 Planarities with less than four sites: {'UNK:plan-1': 67} Unresolved non-hydrogen planarities: 67 Chain: "E" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Time building chain proxies: 14.29, per 1000 atoms: 0.45 Number of scatterers: 31423 At special positions: 0 Unit cell: (103.16, 104.223, 134.001, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 70 16.00 P 7 15.00 O 3080 8.00 N 2849 7.00 C 10927 6.00 H 14490 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: 24.77 Conformation dependent library (CDL) restraints added in 3.1 seconds 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4270 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 70 helices and 14 sheets defined 75.0% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.73 Creating SS restraints... Processing helix chain 'E' and resid -65 through -48 removed outlier: 3.679A pdb=" N UNK E -55 " --> pdb=" O UNK E -59 " (cutoff:3.500A) Processing helix chain 'E' and resid -38 through -34 Processing helix chain 'E' and resid -32 through -5 removed outlier: 3.726A pdb=" N UNK E -14 " --> pdb=" O UNK E -18 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N UNK E -13 " --> pdb=" O UNK E -17 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N UNK E -8 " --> pdb=" O UNK E -12 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N UNK E -5 " --> pdb=" O UNK E -9 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 109 removed outlier: 3.850A pdb=" N THR E 91 " --> pdb=" O ALA E 87 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS E 108 " --> pdb=" O GLN E 104 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N GLY E 109 " --> pdb=" O GLN E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 138 removed outlier: 3.638A pdb=" N VAL E 129 " --> pdb=" O THR E 125 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU E 130 " --> pdb=" O ILE E 126 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N GLU E 136 " --> pdb=" O LEU E 132 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N HIS E 137 " --> pdb=" O LEU E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 175 removed outlier: 5.322A pdb=" N ASP E 162 " --> pdb=" O MET E 158 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ILE E 163 " --> pdb=" O ALA E 159 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN E 166 " --> pdb=" O ASP E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 222 Processing helix chain 'E' and resid 229 through 231 No H-bonds generated for 'chain 'E' and resid 229 through 231' Processing helix chain 'E' and resid 245 through 264 removed outlier: 3.567A pdb=" N ALA E 248 " --> pdb=" O TYR E 245 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ALA E 249 " --> pdb=" O GLU E 246 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLY E 252 " --> pdb=" O ALA E 249 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL E 253 " --> pdb=" O LYS E 250 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS E 263 " --> pdb=" O GLU E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 320 Processing helix chain 'C' and resid -65 through -48 removed outlier: 3.680A pdb=" N UNK C -55 " --> pdb=" O UNK C -59 " (cutoff:3.500A) Processing helix chain 'C' and resid -38 through -34 Processing helix chain 'C' and resid -32 through -5 removed outlier: 3.725A pdb=" N UNK C -14 " --> pdb=" O UNK C -18 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N UNK C -13 " --> pdb=" O UNK C -17 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N UNK C -8 " --> pdb=" O UNK C -12 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N UNK C -5 " --> pdb=" O UNK C -9 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 109 removed outlier: 3.850A pdb=" N THR C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS C 108 " --> pdb=" O GLN C 104 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N GLY C 109 " --> pdb=" O GLN C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 138 removed outlier: 3.636A pdb=" N VAL C 129 " --> pdb=" O THR C 125 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU C 130 " --> pdb=" O ILE C 126 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N GLU C 136 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N HIS C 137 " --> pdb=" O LEU C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 175 removed outlier: 5.320A pdb=" N ASP C 162 " --> pdb=" O MET C 158 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ILE C 163 " --> pdb=" O ALA C 159 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASN C 166 " --> pdb=" O ASP C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 222 Processing helix chain 'C' and resid 229 through 231 No H-bonds generated for 'chain 'C' and resid 229 through 231' Processing helix chain 'C' and resid 245 through 264 removed outlier: 3.566A pdb=" N ALA C 248 " --> pdb=" O TYR C 245 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ALA C 249 " --> pdb=" O GLU C 246 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N GLY C 252 " --> pdb=" O ALA C 249 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL C 253 " --> pdb=" O LYS C 250 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS C 263 " --> pdb=" O GLU C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 320 Processing helix chain 'A' and resid -65 through -48 removed outlier: 3.680A pdb=" N UNK A -55 " --> pdb=" O UNK A -59 " (cutoff:3.500A) Processing helix chain 'A' and resid -38 through -34 Processing helix chain 'A' and resid -32 through -5 removed outlier: 3.724A pdb=" N UNK A -14 " --> pdb=" O UNK A -18 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N UNK A -13 " --> pdb=" O UNK A -17 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N UNK A -8 " --> pdb=" O UNK A -12 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N UNK A -5 " --> pdb=" O UNK A -9 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 109 removed outlier: 3.848A pdb=" N THR A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS A 108 " --> pdb=" O GLN A 104 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N GLY A 109 " --> pdb=" O GLN A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 138 removed outlier: 3.637A pdb=" N VAL A 129 " --> pdb=" O THR A 125 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU A 130 " --> pdb=" O ILE A 126 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N GLU A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N HIS A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 175 removed outlier: 5.321A pdb=" N ASP A 162 " --> pdb=" O MET A 158 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ILE A 163 " --> pdb=" O ALA A 159 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASN A 166 " --> pdb=" O ASP A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 222 Processing helix chain 'A' and resid 229 through 231 No H-bonds generated for 'chain 'A' and resid 229 through 231' Processing helix chain 'A' and resid 245 through 264 removed outlier: 3.567A pdb=" N ALA A 248 " --> pdb=" O TYR A 245 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ALA A 249 " --> pdb=" O GLU A 246 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N GLY A 252 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL A 253 " --> pdb=" O LYS A 250 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS A 263 " --> pdb=" O GLU A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 320 Processing helix chain 'B' and resid -65 through -48 removed outlier: 3.680A pdb=" N UNK B -55 " --> pdb=" O UNK B -59 " (cutoff:3.500A) Processing helix chain 'B' and resid -38 through -34 Processing helix chain 'B' and resid -32 through -5 removed outlier: 3.726A pdb=" N UNK B -14 " --> pdb=" O UNK B -18 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N UNK B -13 " --> pdb=" O UNK B -17 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N UNK B -8 " --> pdb=" O UNK B -12 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N UNK B -5 " --> pdb=" O UNK B -9 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 109 removed outlier: 3.850A pdb=" N THR B 91 " --> pdb=" O ALA B 87 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS B 108 " --> pdb=" O GLN B 104 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N GLY B 109 " --> pdb=" O GLN B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 138 removed outlier: 3.616A pdb=" N VAL B 129 " --> pdb=" O THR B 125 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU B 130 " --> pdb=" O ILE B 126 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N GLU B 136 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N HIS B 137 " --> pdb=" O LEU B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 175 removed outlier: 5.321A pdb=" N ASP B 162 " --> pdb=" O MET B 158 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ILE B 163 " --> pdb=" O ALA B 159 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASN B 166 " --> pdb=" O ASP B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 222 Processing helix chain 'B' and resid 229 through 231 No H-bonds generated for 'chain 'B' and resid 229 through 231' Processing helix chain 'B' and resid 245 through 264 removed outlier: 3.567A pdb=" N ALA B 248 " --> pdb=" O TYR B 245 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ALA B 249 " --> pdb=" O GLU B 246 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N GLY B 252 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL B 253 " --> pdb=" O LYS B 250 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS B 263 " --> pdb=" O GLU B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 320 Processing helix chain 'D' and resid -65 through -48 removed outlier: 3.679A pdb=" N UNK D -55 " --> pdb=" O UNK D -59 " (cutoff:3.500A) Processing helix chain 'D' and resid -38 through -34 Processing helix chain 'D' and resid -32 through -5 removed outlier: 3.724A pdb=" N UNK D -14 " --> pdb=" O UNK D -18 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N UNK D -13 " --> pdb=" O UNK D -17 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N UNK D -8 " --> pdb=" O UNK D -12 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N UNK D -5 " --> pdb=" O UNK D -9 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 109 removed outlier: 3.851A pdb=" N THR D 91 " --> pdb=" O ALA D 87 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS D 108 " --> pdb=" O GLN D 104 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N GLY D 109 " --> pdb=" O GLN D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 138 removed outlier: 3.636A pdb=" N VAL D 129 " --> pdb=" O THR D 125 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU D 130 " --> pdb=" O ILE D 126 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N GLU D 136 " --> pdb=" O LEU D 132 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N HIS D 137 " --> pdb=" O LEU D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 175 removed outlier: 5.323A pdb=" N ASP D 162 " --> pdb=" O MET D 158 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N ILE D 163 " --> pdb=" O ALA D 159 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASN D 166 " --> pdb=" O ASP D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 222 Processing helix chain 'D' and resid 229 through 231 No H-bonds generated for 'chain 'D' and resid 229 through 231' Processing helix chain 'D' and resid 245 through 264 removed outlier: 3.567A pdb=" N ALA D 248 " --> pdb=" O TYR D 245 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ALA D 249 " --> pdb=" O GLU D 246 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N GLY D 252 " --> pdb=" O ALA D 249 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL D 253 " --> pdb=" O LYS D 250 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS D 263 " --> pdb=" O GLU D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 320 Processing helix chain 'F' and resid -65 through -48 removed outlier: 3.680A pdb=" N UNK F -55 " --> pdb=" O UNK F -59 " (cutoff:3.500A) Processing helix chain 'F' and resid -38 through -34 Processing helix chain 'F' and resid -32 through -5 removed outlier: 3.725A pdb=" N UNK F -14 " --> pdb=" O UNK F -18 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N UNK F -13 " --> pdb=" O UNK F -17 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N UNK F -8 " --> pdb=" O UNK F -12 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N UNK F -5 " --> pdb=" O UNK F -9 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 109 removed outlier: 3.850A pdb=" N THR F 91 " --> pdb=" O ALA F 87 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS F 108 " --> pdb=" O GLN F 104 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N GLY F 109 " --> pdb=" O GLN F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 138 removed outlier: 3.636A pdb=" N VAL F 129 " --> pdb=" O THR F 125 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU F 130 " --> pdb=" O ILE F 126 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N GLU F 136 " --> pdb=" O LEU F 132 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N HIS F 137 " --> pdb=" O LEU F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 175 removed outlier: 5.322A pdb=" N ASP F 162 " --> pdb=" O MET F 158 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ILE F 163 " --> pdb=" O ALA F 159 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASN F 166 " --> pdb=" O ASP F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 218 through 222 Processing helix chain 'F' and resid 229 through 231 No H-bonds generated for 'chain 'F' and resid 229 through 231' Processing helix chain 'F' and resid 245 through 264 removed outlier: 3.567A pdb=" N ALA F 248 " --> pdb=" O TYR F 245 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ALA F 249 " --> pdb=" O GLU F 246 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLY F 252 " --> pdb=" O ALA F 249 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL F 253 " --> pdb=" O LYS F 250 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS F 263 " --> pdb=" O GLU F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 320 Processing helix chain 'G' and resid -65 through -48 removed outlier: 3.680A pdb=" N UNK G -55 " --> pdb=" O UNK G -59 " (cutoff:3.500A) Processing helix chain 'G' and resid -38 through -34 Processing helix chain 'G' and resid -32 through -5 removed outlier: 3.726A pdb=" N UNK G -14 " --> pdb=" O UNK G -18 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N UNK G -13 " --> pdb=" O UNK G -17 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N UNK G -8 " --> pdb=" O UNK G -12 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N UNK G -5 " --> pdb=" O UNK G -9 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 109 removed outlier: 3.850A pdb=" N THR G 91 " --> pdb=" O ALA G 87 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS G 108 " --> pdb=" O GLN G 104 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N GLY G 109 " --> pdb=" O GLN G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 138 removed outlier: 3.637A pdb=" N VAL G 129 " --> pdb=" O THR G 125 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU G 130 " --> pdb=" O ILE G 126 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N GLU G 136 " --> pdb=" O LEU G 132 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N HIS G 137 " --> pdb=" O LEU G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 175 removed outlier: 5.323A pdb=" N ASP G 162 " --> pdb=" O MET G 158 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ILE G 163 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN G 166 " --> pdb=" O ASP G 162 " (cutoff:3.500A) Processing helix chain 'G' and resid 218 through 222 Processing helix chain 'G' and resid 229 through 231 No H-bonds generated for 'chain 'G' and resid 229 through 231' Processing helix chain 'G' and resid 245 through 264 removed outlier: 3.567A pdb=" N ALA G 248 " --> pdb=" O TYR G 245 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ALA G 249 " --> pdb=" O GLU G 246 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N GLY G 252 " --> pdb=" O ALA G 249 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL G 253 " --> pdb=" O LYS G 250 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS G 263 " --> pdb=" O GLU G 260 " (cutoff:3.500A) Processing helix chain 'G' and resid 299 through 320 Processing sheet with id= A, first strand: chain 'E' and resid 213 through 217 removed outlier: 5.579A pdb=" N THR E 207 " --> pdb=" O VAL E 196 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N VAL E 196 " --> pdb=" O THR E 207 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'E' and resid 235 through 243 removed outlier: 3.601A pdb=" N GLN E 280 " --> pdb=" O ASN E 287 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N MET E 289 " --> pdb=" O PHE E 278 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N PHE E 278 " --> pdb=" O MET E 289 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N TYR E 291 " --> pdb=" O VAL E 276 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N VAL E 276 " --> pdb=" O TYR E 291 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 213 through 217 removed outlier: 5.579A pdb=" N THR C 207 " --> pdb=" O VAL C 196 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N VAL C 196 " --> pdb=" O THR C 207 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 235 through 243 removed outlier: 3.601A pdb=" N GLN C 280 " --> pdb=" O ASN C 287 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N MET C 289 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N PHE C 278 " --> pdb=" O MET C 289 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N TYR C 291 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N VAL C 276 " --> pdb=" O TYR C 291 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 213 through 217 removed outlier: 5.580A pdb=" N THR A 207 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N VAL A 196 " --> pdb=" O THR A 207 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 235 through 243 removed outlier: 3.602A pdb=" N GLN A 280 " --> pdb=" O ASN A 287 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N MET A 289 " --> pdb=" O PHE A 278 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N PHE A 278 " --> pdb=" O MET A 289 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N TYR A 291 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N VAL A 276 " --> pdb=" O TYR A 291 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 213 through 217 removed outlier: 5.581A pdb=" N THR B 207 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N VAL B 196 " --> pdb=" O THR B 207 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 235 through 243 removed outlier: 3.601A pdb=" N GLN B 280 " --> pdb=" O ASN B 287 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N MET B 289 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N PHE B 278 " --> pdb=" O MET B 289 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N TYR B 291 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N VAL B 276 " --> pdb=" O TYR B 291 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 213 through 217 removed outlier: 5.581A pdb=" N THR D 207 " --> pdb=" O VAL D 196 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N VAL D 196 " --> pdb=" O THR D 207 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 235 through 243 removed outlier: 3.602A pdb=" N GLN D 280 " --> pdb=" O ASN D 287 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N MET D 289 " --> pdb=" O PHE D 278 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N PHE D 278 " --> pdb=" O MET D 289 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N TYR D 291 " --> pdb=" O VAL D 276 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N VAL D 276 " --> pdb=" O TYR D 291 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 213 through 217 removed outlier: 5.580A pdb=" N THR F 207 " --> pdb=" O VAL F 196 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N VAL F 196 " --> pdb=" O THR F 207 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 235 through 243 removed outlier: 3.602A pdb=" N GLN F 280 " --> pdb=" O ASN F 287 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N MET F 289 " --> pdb=" O PHE F 278 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N PHE F 278 " --> pdb=" O MET F 289 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N TYR F 291 " --> pdb=" O VAL F 276 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N VAL F 276 " --> pdb=" O TYR F 291 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 213 through 217 removed outlier: 5.581A pdb=" N THR G 207 " --> pdb=" O VAL G 196 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N VAL G 196 " --> pdb=" O THR G 207 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 235 through 243 removed outlier: 3.603A pdb=" N GLN G 280 " --> pdb=" O ASN G 287 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N MET G 289 " --> pdb=" O PHE G 278 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N PHE G 278 " --> pdb=" O MET G 289 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N TYR G 291 " --> pdb=" O VAL G 276 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N VAL G 276 " --> pdb=" O TYR G 291 " (cutoff:3.500A) 1078 hydrogen bonds defined for protein. 2898 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: 10.82 Time building geometry restraints manager: 25.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 14476 1.02 - 1.21: 21 1.21 - 1.41: 6972 1.41 - 1.61: 10087 1.61 - 1.81: 140 Bond restraints: 31696 Sorted by residual: bond pdb=" SG CYS C 292 " pdb=" HG CYS C 292 " ideal model delta sigma weight residual 1.200 1.340 -0.140 2.00e-02 2.50e+03 4.92e+01 bond pdb=" SG CYS A 292 " pdb=" HG CYS A 292 " ideal model delta sigma weight residual 1.200 1.340 -0.140 2.00e-02 2.50e+03 4.91e+01 bond pdb=" SG CYS E 292 " pdb=" HG CYS E 292 " ideal model delta sigma weight residual 1.200 1.340 -0.140 2.00e-02 2.50e+03 4.90e+01 bond pdb=" SG CYS G 292 " pdb=" HG CYS G 292 " ideal model delta sigma weight residual 1.200 1.340 -0.140 2.00e-02 2.50e+03 4.89e+01 bond pdb=" SG CYS B 292 " pdb=" HG CYS B 292 " ideal model delta sigma weight residual 1.200 1.339 -0.139 2.00e-02 2.50e+03 4.85e+01 ... (remaining 31691 not shown) Histogram of bond angle deviations from ideal: 78.71 - 89.75: 42 89.75 - 100.78: 56 100.78 - 111.81: 34124 111.81 - 122.84: 18478 122.84 - 133.87: 3356 Bond angle restraints: 56056 Sorted by residual: angle pdb=" CG2 THR A 113 " pdb=" CB THR A 113 " pdb=" HB THR A 113 " ideal model delta sigma weight residual 108.00 78.71 29.29 3.00e+00 1.11e-01 9.53e+01 angle pdb=" CG2 THR D 113 " pdb=" CB THR D 113 " pdb=" HB THR D 113 " ideal model delta sigma weight residual 108.00 78.72 29.28 3.00e+00 1.11e-01 9.53e+01 angle pdb=" CG2 THR E 113 " pdb=" CB THR E 113 " pdb=" HB THR E 113 " ideal model delta sigma weight residual 108.00 78.75 29.25 3.00e+00 1.11e-01 9.51e+01 angle pdb=" CG2 THR C 113 " pdb=" CB THR C 113 " pdb=" HB THR C 113 " ideal model delta sigma weight residual 108.00 78.76 29.24 3.00e+00 1.11e-01 9.50e+01 angle pdb=" CG2 THR B 113 " pdb=" CB THR B 113 " pdb=" HB THR B 113 " ideal model delta sigma weight residual 108.00 78.77 29.23 3.00e+00 1.11e-01 9.50e+01 ... (remaining 56051 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.28: 14735 35.28 - 70.56: 469 70.56 - 105.84: 28 105.84 - 141.12: 21 141.12 - 176.40: 21 Dihedral angle restraints: 15274 sinusoidal: 7686 harmonic: 7588 Sorted by residual: dihedral pdb=" CA ILE G 192 " pdb=" C ILE G 192 " pdb=" N GLU G 193 " pdb=" CA GLU G 193 " ideal model delta harmonic sigma weight residual 180.00 -154.09 -25.91 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA ILE C 192 " pdb=" C ILE C 192 " pdb=" N GLU C 193 " pdb=" CA GLU C 193 " ideal model delta harmonic sigma weight residual -180.00 -154.09 -25.91 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA ILE A 192 " pdb=" C ILE A 192 " pdb=" N GLU A 193 " pdb=" CA GLU A 193 " ideal model delta harmonic sigma weight residual -180.00 -154.11 -25.89 0 5.00e+00 4.00e-02 2.68e+01 ... (remaining 15271 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.293: 2758 0.293 - 0.585: 0 0.585 - 0.878: 0 0.878 - 1.170: 0 1.170 - 1.463: 14 Chirality restraints: 2772 Sorted by residual: chirality pdb=" CB THR G 113 " pdb=" CA THR G 113 " pdb=" OG1 THR G 113 " pdb=" CG2 THR G 113 " both_signs ideal model delta sigma weight residual False 2.55 1.09 1.46 2.00e-01 2.50e+01 5.35e+01 chirality pdb=" CB THR C 113 " pdb=" CA THR C 113 " pdb=" OG1 THR C 113 " pdb=" CG2 THR C 113 " both_signs ideal model delta sigma weight residual False 2.55 1.09 1.46 2.00e-01 2.50e+01 5.32e+01 chirality pdb=" CB THR F 113 " pdb=" CA THR F 113 " pdb=" OG1 THR F 113 " pdb=" CG2 THR F 113 " both_signs ideal model delta sigma weight residual False 2.55 1.09 1.46 2.00e-01 2.50e+01 5.31e+01 ... (remaining 2769 not shown) Planarity restraints: 4662 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 282 " -0.014 2.00e-02 2.50e+03 2.75e-02 7.58e+00 pdb=" N ASP B 283 " 0.047 2.00e-02 2.50e+03 pdb=" CA ASP B 283 " -0.012 2.00e-02 2.50e+03 pdb=" H ASP B 283 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA F 282 " 0.014 2.00e-02 2.50e+03 2.75e-02 7.56e+00 pdb=" N ASP F 283 " -0.047 2.00e-02 2.50e+03 pdb=" CA ASP F 283 " 0.012 2.00e-02 2.50e+03 pdb=" H ASP F 283 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU F 133 " 0.014 2.00e-02 2.50e+03 2.74e-02 7.49e+00 pdb=" N TYR F 134 " -0.047 2.00e-02 2.50e+03 pdb=" CA TYR F 134 " 0.012 2.00e-02 2.50e+03 pdb=" H TYR F 134 " 0.021 2.00e-02 2.50e+03 ... (remaining 4659 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.12: 892 2.12 - 2.74: 55381 2.74 - 3.36: 82956 3.36 - 3.98: 108543 3.98 - 4.60: 172377 Nonbonded interactions: 420149 Sorted by model distance: nonbonded pdb="HD12 ILE E 268 " pdb=" HG CYS E 292 " model vdw 1.506 2.440 nonbonded pdb="HD12 ILE F 268 " pdb=" HG CYS F 292 " model vdw 1.528 2.440 nonbonded pdb=" HA3 GLY E 144 " pdb="HD23 LEU F 133 " model vdw 1.672 2.440 nonbonded pdb="HD23 LEU C 133 " pdb=" HA3 GLY G 144 " model vdw 1.678 2.440 nonbonded pdb="HD23 LEU E 133 " pdb=" HA3 GLY D 144 " model vdw 1.692 2.440 ... (remaining 420144 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' } 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: 0.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.470 Extract box with map and model: 3.360 Check model and map are aligned: 0.470 Set scattering table: 0.250 Process input model: 94.910 Find NCS groups from input model: 1.520 Set up NCS constraints: 0.200 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: 0.000 Load rotamer database and sin/cos tables:13.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 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 : 0.017 0.107 17206 Z= 1.058 Angle : 1.196 16.094 23310 Z= 0.630 Chirality : 0.120 1.463 2772 Planarity : 0.007 0.067 2926 Dihedral : 19.712 176.400 6055 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % 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: -3.12 (0.17), residues: 1778 helix: -1.47 (0.13), residues: 938 sheet: -2.68 (0.28), residues: 259 loop : -2.47 (0.24), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP E 201 HIS 0.004 0.002 HIS B 265 PHE 0.013 0.002 PHE E 148 TYR 0.015 0.002 TYR D 291 ARG 0.013 0.001 ARG F 235 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Evaluate side-chains 214 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 2.499 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: E 130 LEU cc_start: 0.8585 (mt) cc_final: 0.8194 (pp) REVERT: E 256 GLU cc_start: 0.7625 (tt0) cc_final: 0.7385 (mt-10) REVERT: C 130 LEU cc_start: 0.8507 (mt) cc_final: 0.8084 (pp) REVERT: C 198 GLU cc_start: 0.8406 (tt0) cc_final: 0.8168 (tt0) REVERT: C 232 MET cc_start: 0.8051 (ptt) cc_final: 0.7837 (ptt) REVERT: A 130 LEU cc_start: 0.8544 (mt) cc_final: 0.8125 (pp) REVERT: B 130 LEU cc_start: 0.8504 (mt) cc_final: 0.8110 (pp) REVERT: B 227 GLU cc_start: 0.8173 (tt0) cc_final: 0.7917 (tt0) REVERT: D 130 LEU cc_start: 0.8501 (mt) cc_final: 0.8146 (pp) REVERT: D 227 GLU cc_start: 0.8138 (tt0) cc_final: 0.7925 (tt0) REVERT: D 256 GLU cc_start: 0.7716 (tt0) cc_final: 0.7435 (mt-10) REVERT: F 130 LEU cc_start: 0.8604 (mt) cc_final: 0.8163 (pp) REVERT: G 130 LEU cc_start: 0.8558 (mt) cc_final: 0.8094 (pp) REVERT: G 256 GLU cc_start: 0.7730 (tt0) cc_final: 0.7486 (mt-10) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 2.3134 time to fit residues: 560.0097 Evaluate side-chains 128 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 2.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 3.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 99 ASN E 272 GLN E 307 GLN E 329 GLN C 272 GLN C 307 GLN C 329 GLN A 272 GLN A 307 GLN A 329 GLN B 272 GLN B 307 GLN B 329 GLN D 272 GLN D 307 GLN D 329 GLN F 272 GLN F 307 GLN F 329 GLN G 99 ASN G 272 GLN G 307 GLN G 329 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.5165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.049 0.260 17206 Z= 3.163 Angle : 1.922 12.870 23310 Z= 1.069 Chirality : 0.167 1.463 2772 Planarity : 0.013 0.092 2926 Dihedral : 21.671 176.450 2723 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 40.55 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.45 % Favored : 90.38 % Rotamer: Outliers : 6.34 % Allowed : 17.36 % Favored : 76.30 % 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: -4.32 (0.15), residues: 1778 helix: -2.59 (0.13), residues: 938 sheet: -2.60 (0.28), residues: 259 loop : -3.07 (0.20), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.009 TRP A 302 HIS 0.007 0.002 HIS E 265 PHE 0.020 0.005 PHE C 138 TYR 0.036 0.006 TYR B 291 ARG 0.019 0.002 ARG C 235 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Evaluate side-chains 278 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 179 time to evaluate : 2.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 198 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.8106 (tt0) REVERT: C 118 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.8050 (tpp) REVERT: C 198 GLU cc_start: 0.8718 (tt0) cc_final: 0.8291 (tm-30) REVERT: C 232 MET cc_start: 0.9303 (ptt) cc_final: 0.9036 (ptm) REVERT: A 158 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.8128 (mtm) REVERT: B 198 GLU cc_start: 0.8435 (pt0) cc_final: 0.7928 (pp20) REVERT: B 227 GLU cc_start: 0.8718 (tt0) cc_final: 0.8404 (tt0) REVERT: B 232 MET cc_start: 0.9307 (ptt) cc_final: 0.9097 (ptt) REVERT: D 198 GLU cc_start: 0.8463 (pt0) cc_final: 0.7972 (pp20) REVERT: D 232 MET cc_start: 0.9242 (ptt) cc_final: 0.8850 (ptt) REVERT: F 118 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7935 (tpt) REVERT: G 246 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8152 (mp0) outliers start: 99 outliers final: 58 residues processed: 260 average time/residue: 1.8177 time to fit residues: 555.3035 Evaluate side-chains 232 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 169 time to evaluate : 2.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain E residue 198 GLU Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 223 SER Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain F residue 185 ILE Chi-restraints excluded: chain F residue 195 THR Chi-restraints excluded: chain F residue 198 GLU Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 210 ASP Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 246 GLU Chi-restraints excluded: chain G residue 198 GLU Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 210 ASP Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 233 THR Chi-restraints excluded: chain G residue 246 GLU Chi-restraints excluded: chain G residue 313 ILE Chi-restraints excluded: chain G residue 314 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 3.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.6375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.050 0.261 17206 Z= 3.188 Angle : 1.947 12.377 23310 Z= 1.080 Chirality : 0.169 1.509 2772 Planarity : 0.012 0.087 2926 Dihedral : 20.828 177.401 2723 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 46.71 Ramachandran Plot: Outliers : 0.11 % Allowed : 14.34 % Favored : 85.55 % Rotamer: Outliers : 14.80 % Allowed : 17.30 % Favored : 67.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -5.35 (0.14), residues: 1778 helix: -3.32 (0.12), residues: 966 sheet: -2.97 (0.27), residues: 259 loop : -3.77 (0.18), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.008 TRP F 302 HIS 0.009 0.003 HIS E 320 PHE 0.028 0.005 PHE B 221 TYR 0.033 0.006 TYR D 291 ARG 0.014 0.002 ARG B 231 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Evaluate side-chains 389 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 231 poor density : 158 time to evaluate : 2.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 111 ASP cc_start: 0.8768 (OUTLIER) cc_final: 0.8517 (t0) REVERT: E 136 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7407 (pm20) REVERT: E 198 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.8089 (tt0) REVERT: C 111 ASP cc_start: 0.8887 (OUTLIER) cc_final: 0.8543 (t70) REVERT: C 118 MET cc_start: 0.8248 (tpt) cc_final: 0.7941 (tpp) REVERT: C 136 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7334 (pm20) REVERT: C 198 GLU cc_start: 0.8627 (tt0) cc_final: 0.8227 (tm-30) REVERT: C 203 ILE cc_start: 0.9042 (OUTLIER) cc_final: 0.8822 (pp) REVERT: C 232 MET cc_start: 0.9330 (ptt) cc_final: 0.9104 (ptm) REVERT: A 158 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.8240 (mtm) REVERT: A 256 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8307 (mp0) REVERT: A 274 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8852 (tp) REVERT: B 158 MET cc_start: 0.8753 (OUTLIER) cc_final: 0.8290 (mtm) REVERT: B 198 GLU cc_start: 0.8499 (pt0) cc_final: 0.7976 (pp20) REVERT: B 199 ILE cc_start: 0.9583 (OUTLIER) cc_final: 0.9044 (mm) REVERT: B 203 ILE cc_start: 0.9118 (OUTLIER) cc_final: 0.8870 (pp) REVERT: B 227 GLU cc_start: 0.8612 (tt0) cc_final: 0.8296 (tt0) REVERT: B 232 MET cc_start: 0.9310 (ptt) cc_final: 0.9096 (ptt) REVERT: D 111 ASP cc_start: 0.8758 (OUTLIER) cc_final: 0.8519 (t70) REVERT: D 198 GLU cc_start: 0.8385 (pt0) cc_final: 0.7943 (pp20) REVERT: D 203 ILE cc_start: 0.9050 (OUTLIER) cc_final: 0.8802 (pp) REVERT: F 118 MET cc_start: 0.8255 (OUTLIER) cc_final: 0.7878 (tpt) REVERT: F 199 ILE cc_start: 0.9548 (OUTLIER) cc_final: 0.9265 (mm) REVERT: F 232 MET cc_start: 0.9178 (ptt) cc_final: 0.8961 (ptm) REVERT: F 274 LEU cc_start: 0.9297 (OUTLIER) cc_final: 0.8971 (tp) REVERT: G 111 ASP cc_start: 0.8774 (OUTLIER) cc_final: 0.8527 (t70) REVERT: G 246 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8178 (mp0) outliers start: 231 outliers final: 122 residues processed: 352 average time/residue: 1.3490 time to fit residues: 579.6025 Evaluate side-chains 292 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 151 time to evaluate : 2.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain E residue 198 GLU Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 223 SER Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 247 ASP Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 319 SER Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain F residue 81 ILE Chi-restraints excluded: chain F residue 111 ASP Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 185 ILE Chi-restraints excluded: chain F residue 195 THR Chi-restraints excluded: chain F residue 198 GLU Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 210 ASP Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 246 GLU Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 292 CYS Chi-restraints excluded: chain F residue 294 THR Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 165 SER Chi-restraints excluded: chain G residue 189 ASP Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 210 ASP Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 246 GLU Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain G residue 308 ASP Chi-restraints excluded: chain G residue 313 ILE Chi-restraints excluded: chain G residue 314 ILE Chi-restraints excluded: chain G residue 319 SER Chi-restraints excluded: chain G residue 330 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 3.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.6743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.049 0.255 17206 Z= 3.172 Angle : 1.915 12.772 23310 Z= 1.065 Chirality : 0.166 1.491 2772 Planarity : 0.012 0.094 2926 Dihedral : 20.769 174.852 2723 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 51.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.15 % Favored : 82.85 % Rotamer: Outliers : 15.37 % Allowed : 18.90 % Favored : 65.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -5.78 (0.14), residues: 1778 helix: -3.63 (0.11), residues: 973 sheet: -3.10 (0.27), residues: 259 loop : -4.08 (0.18), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.008 TRP F 302 HIS 0.009 0.003 HIS E 320 PHE 0.051 0.005 PHE B 101 TYR 0.032 0.006 TYR D 291 ARG 0.013 0.002 ARG D 231 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Evaluate side-chains 385 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 145 time to evaluate : 2.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 111 ASP cc_start: 0.8815 (OUTLIER) cc_final: 0.8573 (t70) REVERT: E 136 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7393 (pm20) REVERT: E 148 PHE cc_start: 0.9153 (t80) cc_final: 0.8933 (t80) REVERT: E 198 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.8060 (tt0) REVERT: C 111 ASP cc_start: 0.8780 (OUTLIER) cc_final: 0.8513 (t70) REVERT: C 118 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.8043 (tpp) REVERT: C 136 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7498 (pm20) REVERT: C 198 GLU cc_start: 0.8626 (tt0) cc_final: 0.8190 (tm-30) REVERT: C 199 ILE cc_start: 0.9637 (OUTLIER) cc_final: 0.8908 (mm) REVERT: A 118 MET cc_start: 0.8219 (OUTLIER) cc_final: 0.7954 (tpp) REVERT: A 158 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.8196 (mtm) REVERT: B 117 ILE cc_start: 0.7149 (OUTLIER) cc_final: 0.6934 (mt) REVERT: B 158 MET cc_start: 0.8751 (OUTLIER) cc_final: 0.8303 (mtm) REVERT: B 198 GLU cc_start: 0.8430 (pt0) cc_final: 0.7959 (pp20) REVERT: B 199 ILE cc_start: 0.9580 (OUTLIER) cc_final: 0.9101 (mm) REVERT: B 227 GLU cc_start: 0.8599 (tt0) cc_final: 0.8310 (tt0) REVERT: B 232 MET cc_start: 0.9295 (ptt) cc_final: 0.9080 (ptt) REVERT: B 274 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8617 (tp) REVERT: D 198 GLU cc_start: 0.8418 (pt0) cc_final: 0.7995 (pp20) REVERT: D 203 ILE cc_start: 0.9020 (OUTLIER) cc_final: 0.8777 (pp) REVERT: F 118 MET cc_start: 0.8250 (OUTLIER) cc_final: 0.7852 (tpt) REVERT: F 199 ILE cc_start: 0.9535 (OUTLIER) cc_final: 0.9249 (mm) REVERT: F 274 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.8913 (tp) REVERT: G 111 ASP cc_start: 0.8809 (OUTLIER) cc_final: 0.8503 (t70) REVERT: G 246 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8138 (mp0) outliers start: 240 outliers final: 130 residues processed: 348 average time/residue: 1.2592 time to fit residues: 541.4316 Evaluate side-chains 285 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 136 time to evaluate : 2.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain E residue 198 GLU Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 211 ASN Chi-restraints excluded: chain E residue 223 SER Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 247 ASP Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 319 SER Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain A residue 138 PHE Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 138 PHE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 137 HIS Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 211 ASN Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain F residue 81 ILE Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 138 PHE Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain F residue 185 ILE Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 195 THR Chi-restraints excluded: chain F residue 198 GLU Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 210 ASP Chi-restraints excluded: chain F residue 211 ASN Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 246 GLU Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 292 CYS Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain G residue 92 ILE Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 137 HIS Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 165 SER Chi-restraints excluded: chain G residue 189 ASP Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 210 ASP Chi-restraints excluded: chain G residue 211 ASN Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 246 GLU Chi-restraints excluded: chain G residue 254 ILE Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain G residue 313 ILE Chi-restraints excluded: chain G residue 314 ILE Chi-restraints excluded: chain G residue 319 SER Chi-restraints excluded: chain G residue 330 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 3.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 99 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.6954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.049 0.254 17206 Z= 3.171 Angle : 1.910 13.018 23310 Z= 1.061 Chirality : 0.167 1.567 2772 Planarity : 0.013 0.097 2926 Dihedral : 20.868 176.902 2723 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 51.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.39 % Favored : 81.61 % Rotamer: Outliers : 16.40 % Allowed : 19.28 % Favored : 64.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -5.96 (0.13), residues: 1778 helix: -3.71 (0.11), residues: 973 sheet: -3.17 (0.26), residues: 259 loop : -4.33 (0.17), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.008 TRP F 302 HIS 0.010 0.003 HIS C 320 PHE 0.053 0.005 PHE E 101 TYR 0.032 0.006 TYR D 291 ARG 0.012 0.001 ARG D 231 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Evaluate side-chains 397 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 256 poor density : 141 time to evaluate : 2.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 111 ASP cc_start: 0.8878 (OUTLIER) cc_final: 0.8499 (t70) REVERT: E 136 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7337 (pm20) REVERT: E 148 PHE cc_start: 0.9145 (t80) cc_final: 0.8922 (t80) REVERT: E 198 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.8028 (tt0) REVERT: C 111 ASP cc_start: 0.8845 (OUTLIER) cc_final: 0.8529 (t70) REVERT: C 118 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.8046 (tpp) REVERT: C 136 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7445 (pm20) REVERT: C 198 GLU cc_start: 0.8637 (tt0) cc_final: 0.8016 (tm-30) REVERT: A 158 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.8282 (mtm) REVERT: A 214 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8140 (tp) REVERT: A 333 MET cc_start: 0.8601 (mmm) cc_final: 0.8398 (mmm) REVERT: B 117 ILE cc_start: 0.7129 (OUTLIER) cc_final: 0.6917 (mt) REVERT: B 158 MET cc_start: 0.8752 (OUTLIER) cc_final: 0.8388 (mtm) REVERT: B 198 GLU cc_start: 0.8409 (pt0) cc_final: 0.8078 (pp20) REVERT: B 199 ILE cc_start: 0.9594 (OUTLIER) cc_final: 0.9139 (mm) REVERT: B 227 GLU cc_start: 0.8613 (tt0) cc_final: 0.8364 (tt0) REVERT: B 232 MET cc_start: 0.9263 (ptt) cc_final: 0.9044 (ptt) REVERT: D 198 GLU cc_start: 0.8346 (pt0) cc_final: 0.8016 (pp20) REVERT: D 203 ILE cc_start: 0.9012 (OUTLIER) cc_final: 0.8766 (pp) REVERT: D 256 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7781 (tm-30) REVERT: F 118 MET cc_start: 0.8251 (OUTLIER) cc_final: 0.7873 (tpt) REVERT: F 199 ILE cc_start: 0.9531 (OUTLIER) cc_final: 0.9249 (mm) REVERT: F 274 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.8935 (tp) REVERT: G 111 ASP cc_start: 0.8856 (OUTLIER) cc_final: 0.8556 (t70) REVERT: G 198 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8012 (tm-30) REVERT: G 246 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8122 (mp0) REVERT: G 256 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7843 (tm-30) outliers start: 256 outliers final: 147 residues processed: 362 average time/residue: 1.3059 time to fit residues: 586.8494 Evaluate side-chains 299 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 134 time to evaluate : 2.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain E residue 198 GLU Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 211 ASN Chi-restraints excluded: chain E residue 223 SER Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 225 SER Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 247 ASP Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 319 SER Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 138 PHE Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 211 ASN Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain F residue 81 ILE Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 138 PHE Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain F residue 185 ILE Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 195 THR Chi-restraints excluded: chain F residue 198 GLU Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 210 ASP Chi-restraints excluded: chain F residue 211 ASN Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 225 SER Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 246 GLU Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 292 CYS Chi-restraints excluded: chain F residue 294 THR Chi-restraints excluded: chain F residue 316 ILE Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 165 SER Chi-restraints excluded: chain G residue 176 ASP Chi-restraints excluded: chain G residue 185 ILE Chi-restraints excluded: chain G residue 189 ASP Chi-restraints excluded: chain G residue 198 GLU Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 210 ASP Chi-restraints excluded: chain G residue 211 ASN Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 239 THR Chi-restraints excluded: chain G residue 246 GLU Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain G residue 313 ILE Chi-restraints excluded: chain G residue 314 ILE Chi-restraints excluded: chain G residue 319 SER Chi-restraints excluded: chain G residue 330 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 3.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.7094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.049 0.252 17206 Z= 3.170 Angle : 1.910 12.817 23310 Z= 1.061 Chirality : 0.166 1.505 2772 Planarity : 0.013 0.100 2926 Dihedral : 20.785 177.187 2723 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 53.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 19.97 % Favored : 79.98 % Rotamer: Outliers : 15.95 % Allowed : 20.76 % Favored : 63.29 % 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: -6.08 (0.13), residues: 1778 helix: -3.74 (0.10), residues: 973 sheet: -3.21 (0.26), residues: 259 loop : -4.52 (0.16), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.008 TRP F 302 HIS 0.010 0.004 HIS C 320 PHE 0.038 0.005 PHE A 101 TYR 0.033 0.006 TYR C 134 ARG 0.011 0.001 ARG C 231 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Evaluate side-chains 387 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 249 poor density : 138 time to evaluate : 2.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 136 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7301 (pm20) REVERT: E 140 MET cc_start: 0.7566 (OUTLIER) cc_final: 0.7316 (mpt) REVERT: E 148 PHE cc_start: 0.9170 (t80) cc_final: 0.8939 (t80) REVERT: E 198 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.8057 (tt0) REVERT: E 256 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7914 (tm-30) REVERT: C 111 ASP cc_start: 0.8759 (OUTLIER) cc_final: 0.8459 (t70) REVERT: C 118 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.8137 (tpp) REVERT: C 136 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7432 (pm20) REVERT: C 198 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.7989 (tm-30) REVERT: C 203 ILE cc_start: 0.9038 (OUTLIER) cc_final: 0.8800 (pp) REVERT: A 118 MET cc_start: 0.8181 (OUTLIER) cc_final: 0.7955 (tpp) REVERT: A 140 MET cc_start: 0.7322 (OUTLIER) cc_final: 0.6988 (mpt) REVERT: A 158 MET cc_start: 0.8648 (OUTLIER) cc_final: 0.8245 (mtm) REVERT: A 214 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8146 (tp) REVERT: B 117 ILE cc_start: 0.7144 (OUTLIER) cc_final: 0.6940 (mt) REVERT: B 158 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.8394 (mtm) REVERT: B 198 GLU cc_start: 0.8394 (pt0) cc_final: 0.8094 (pp20) REVERT: B 199 ILE cc_start: 0.9585 (OUTLIER) cc_final: 0.9118 (mm) REVERT: B 203 ILE cc_start: 0.9104 (OUTLIER) cc_final: 0.8838 (pp) REVERT: B 214 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.7859 (tp) REVERT: B 227 GLU cc_start: 0.8634 (tt0) cc_final: 0.8377 (tt0) REVERT: B 232 MET cc_start: 0.9221 (ptt) cc_final: 0.9000 (ptt) REVERT: D 140 MET cc_start: 0.7661 (OUTLIER) cc_final: 0.7382 (mpt) REVERT: D 198 GLU cc_start: 0.8337 (pt0) cc_final: 0.8015 (pp20) REVERT: D 203 ILE cc_start: 0.9006 (OUTLIER) cc_final: 0.8756 (pp) REVERT: D 256 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7870 (tm-30) REVERT: F 93 LYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7762 (mmpt) REVERT: F 118 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.7885 (tpt) REVERT: F 199 ILE cc_start: 0.9551 (OUTLIER) cc_final: 0.9259 (mm) REVERT: F 274 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.8934 (tp) REVERT: G 111 ASP cc_start: 0.8844 (OUTLIER) cc_final: 0.8519 (t70) REVERT: G 140 MET cc_start: 0.7026 (OUTLIER) cc_final: 0.6779 (mpt) REVERT: G 246 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8120 (mp0) REVERT: G 316 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8571 (mt) outliers start: 249 outliers final: 165 residues processed: 357 average time/residue: 1.2951 time to fit residues: 568.8968 Evaluate side-chains 329 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 136 time to evaluate : 2.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain E residue 198 GLU Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 211 ASN Chi-restraints excluded: chain E residue 223 SER Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 247 ASP Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 319 SER Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 140 MET Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 138 PHE Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 112 ILE Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 140 MET Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 211 ASN Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 225 SER Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain F residue 81 ILE Chi-restraints excluded: chain F residue 93 LYS Chi-restraints excluded: chain F residue 112 ILE Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 138 PHE Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain F residue 185 ILE Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 195 THR Chi-restraints excluded: chain F residue 198 GLU Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 210 ASP Chi-restraints excluded: chain F residue 211 ASN Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 225 SER Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 246 GLU Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 292 CYS Chi-restraints excluded: chain F residue 294 THR Chi-restraints excluded: chain F residue 316 ILE Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain G residue 107 LYS Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 140 MET Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 165 SER Chi-restraints excluded: chain G residue 171 ILE Chi-restraints excluded: chain G residue 176 ASP Chi-restraints excluded: chain G residue 185 ILE Chi-restraints excluded: chain G residue 189 ASP Chi-restraints excluded: chain G residue 198 GLU Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 210 ASP Chi-restraints excluded: chain G residue 211 ASN Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 239 THR Chi-restraints excluded: chain G residue 246 GLU Chi-restraints excluded: chain G residue 254 ILE Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 268 ILE Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain G residue 313 ILE Chi-restraints excluded: chain G residue 314 ILE Chi-restraints excluded: chain G residue 316 ILE Chi-restraints excluded: chain G residue 319 SER Chi-restraints excluded: chain G residue 330 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 3.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.7181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.049 0.251 17206 Z= 3.171 Angle : 1.913 12.901 23310 Z= 1.062 Chirality : 0.167 1.517 2772 Planarity : 0.013 0.101 2926 Dihedral : 20.716 178.084 2723 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 53.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.92 % Favored : 79.08 % Rotamer: Outliers : 15.12 % Allowed : 22.55 % Favored : 62.33 % 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: -6.10 (0.13), residues: 1778 helix: -3.71 (0.11), residues: 966 sheet: -3.24 (0.26), residues: 259 loop : -4.62 (0.16), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.008 TRP F 302 HIS 0.013 0.004 HIS F 137 PHE 0.040 0.005 PHE E 101 TYR 0.031 0.006 TYR D 291 ARG 0.011 0.001 ARG D 231 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Evaluate side-chains 372 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 136 time to evaluate : 2.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 136 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7315 (pm20) REVERT: E 140 MET cc_start: 0.7592 (OUTLIER) cc_final: 0.7298 (mpt) REVERT: E 148 PHE cc_start: 0.9162 (t80) cc_final: 0.8936 (t80) REVERT: E 198 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.8048 (tt0) REVERT: C 118 MET cc_start: 0.8399 (OUTLIER) cc_final: 0.8072 (tpp) REVERT: C 136 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7427 (pm20) REVERT: C 198 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8044 (tm-30) REVERT: C 203 ILE cc_start: 0.9031 (OUTLIER) cc_final: 0.8790 (pp) REVERT: A 140 MET cc_start: 0.7290 (OUTLIER) cc_final: 0.6919 (mpt) REVERT: A 158 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.8292 (mtm) REVERT: A 214 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8143 (tp) REVERT: B 158 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.8368 (mtm) REVERT: B 198 GLU cc_start: 0.8393 (pt0) cc_final: 0.8098 (pp20) REVERT: B 199 ILE cc_start: 0.9599 (OUTLIER) cc_final: 0.9139 (mm) REVERT: B 214 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.7860 (tp) REVERT: B 227 GLU cc_start: 0.8620 (tt0) cc_final: 0.8364 (tt0) REVERT: B 232 MET cc_start: 0.9190 (ptt) cc_final: 0.8973 (ptt) REVERT: D 140 MET cc_start: 0.7611 (mpt) cc_final: 0.7379 (mpt) REVERT: D 198 GLU cc_start: 0.8335 (pt0) cc_final: 0.7995 (pp20) REVERT: D 203 ILE cc_start: 0.9004 (OUTLIER) cc_final: 0.8748 (pp) REVERT: D 256 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7934 (tm-30) REVERT: F 93 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7686 (mmpt) REVERT: F 118 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.7897 (tpt) REVERT: F 199 ILE cc_start: 0.9565 (OUTLIER) cc_final: 0.9254 (mm) REVERT: F 274 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.8943 (tp) REVERT: G 111 ASP cc_start: 0.8849 (OUTLIER) cc_final: 0.8545 (t70) REVERT: G 246 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.8118 (mp0) outliers start: 236 outliers final: 175 residues processed: 349 average time/residue: 1.3255 time to fit residues: 566.4853 Evaluate side-chains 332 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 136 time to evaluate : 2.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain E residue 198 GLU Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 211 ASN Chi-restraints excluded: chain E residue 223 SER Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 225 SER Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 247 ASP Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 319 SER Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 140 MET Chi-restraints excluded: chain A residue 148 PHE Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 138 PHE Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 112 ILE Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 211 ASN Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 225 SER Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain F residue 81 ILE Chi-restraints excluded: chain F residue 93 LYS Chi-restraints excluded: chain F residue 112 ILE Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 138 PHE Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain F residue 185 ILE Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 195 THR Chi-restraints excluded: chain F residue 198 GLU Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 210 ASP Chi-restraints excluded: chain F residue 211 ASN Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 225 SER Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 246 GLU Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 292 CYS Chi-restraints excluded: chain F residue 294 THR Chi-restraints excluded: chain F residue 316 ILE Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain G residue 92 ILE Chi-restraints excluded: chain G residue 107 LYS Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 158 MET Chi-restraints excluded: chain G residue 165 SER Chi-restraints excluded: chain G residue 176 ASP Chi-restraints excluded: chain G residue 185 ILE Chi-restraints excluded: chain G residue 189 ASP Chi-restraints excluded: chain G residue 198 GLU Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 210 ASP Chi-restraints excluded: chain G residue 211 ASN Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 239 THR Chi-restraints excluded: chain G residue 246 GLU Chi-restraints excluded: chain G residue 254 ILE Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain G residue 313 ILE Chi-restraints excluded: chain G residue 314 ILE Chi-restraints excluded: chain G residue 319 SER Chi-restraints excluded: chain G residue 330 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 3.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.7234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.049 0.250 17206 Z= 3.171 Angle : 1.919 12.780 23310 Z= 1.063 Chirality : 0.166 1.515 2772 Planarity : 0.013 0.103 2926 Dihedral : 20.628 177.863 2723 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 54.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.26 % Favored : 78.74 % Rotamer: Outliers : 15.31 % Allowed : 23.06 % Favored : 61.63 % 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: -6.13 (0.13), residues: 1778 helix: -3.72 (0.11), residues: 973 sheet: -3.29 (0.26), residues: 259 loop : -4.63 (0.16), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.008 TRP F 302 HIS 0.012 0.004 HIS F 137 PHE 0.038 0.005 PHE A 101 TYR 0.034 0.006 TYR C 134 ARG 0.011 0.001 ARG D 231 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Evaluate side-chains 376 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 239 poor density : 137 time to evaluate : 2.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 148 PHE cc_start: 0.9181 (t80) cc_final: 0.8953 (t80) REVERT: E 198 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.8050 (tt0) REVERT: E 256 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8099 (tm-30) REVERT: C 118 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.8062 (tpp) REVERT: C 136 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7493 (pm20) REVERT: C 198 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8049 (tm-30) REVERT: C 203 ILE cc_start: 0.9029 (OUTLIER) cc_final: 0.8786 (pp) REVERT: A 158 MET cc_start: 0.8680 (OUTLIER) cc_final: 0.8294 (mtm) REVERT: A 198 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7839 (tt0) REVERT: A 214 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8145 (tp) REVERT: B 158 MET cc_start: 0.8800 (mmm) cc_final: 0.8365 (mtm) REVERT: B 198 GLU cc_start: 0.8383 (pt0) cc_final: 0.8091 (pp20) REVERT: B 199 ILE cc_start: 0.9594 (OUTLIER) cc_final: 0.9145 (mm) REVERT: B 203 ILE cc_start: 0.9108 (OUTLIER) cc_final: 0.8847 (pp) REVERT: B 214 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.7859 (tp) REVERT: B 227 GLU cc_start: 0.8629 (tt0) cc_final: 0.8370 (tt0) REVERT: B 232 MET cc_start: 0.9171 (ptt) cc_final: 0.8953 (ptt) REVERT: D 140 MET cc_start: 0.7738 (mpt) cc_final: 0.7501 (mpt) REVERT: D 198 GLU cc_start: 0.8322 (pt0) cc_final: 0.8002 (pp20) REVERT: D 203 ILE cc_start: 0.9002 (OUTLIER) cc_final: 0.8754 (pp) REVERT: D 256 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7941 (tm-30) REVERT: F 118 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.7902 (tpt) REVERT: F 199 ILE cc_start: 0.9551 (OUTLIER) cc_final: 0.9238 (mm) REVERT: F 274 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.8938 (tp) REVERT: G 111 ASP cc_start: 0.8833 (OUTLIER) cc_final: 0.8514 (t70) REVERT: G 246 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.8119 (mp0) REVERT: G 256 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7998 (tm-30) REVERT: G 316 ILE cc_start: 0.8773 (OUTLIER) cc_final: 0.8573 (mt) outliers start: 239 outliers final: 182 residues processed: 350 average time/residue: 1.3403 time to fit residues: 582.2428 Evaluate side-chains 337 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 134 time to evaluate : 2.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 138 PHE Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain E residue 198 GLU Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 211 ASN Chi-restraints excluded: chain E residue 223 SER Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 225 SER Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 247 ASP Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain E residue 285 SER Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 319 SER Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 148 PHE Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 138 PHE Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 112 ILE Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 211 ASN Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 225 SER Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain F residue 81 ILE Chi-restraints excluded: chain F residue 112 ILE Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 138 PHE Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 148 PHE Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain F residue 185 ILE Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 195 THR Chi-restraints excluded: chain F residue 198 GLU Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 210 ASP Chi-restraints excluded: chain F residue 211 ASN Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 225 SER Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 246 GLU Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 292 CYS Chi-restraints excluded: chain F residue 294 THR Chi-restraints excluded: chain F residue 316 ILE Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 107 LYS Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 158 MET Chi-restraints excluded: chain G residue 165 SER Chi-restraints excluded: chain G residue 171 ILE Chi-restraints excluded: chain G residue 176 ASP Chi-restraints excluded: chain G residue 185 ILE Chi-restraints excluded: chain G residue 189 ASP Chi-restraints excluded: chain G residue 198 GLU Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 210 ASP Chi-restraints excluded: chain G residue 211 ASN Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 239 THR Chi-restraints excluded: chain G residue 246 GLU Chi-restraints excluded: chain G residue 254 ILE Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 256 GLU Chi-restraints excluded: chain G residue 268 ILE Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain G residue 313 ILE Chi-restraints excluded: chain G residue 314 ILE Chi-restraints excluded: chain G residue 316 ILE Chi-restraints excluded: chain G residue 319 SER Chi-restraints excluded: chain G residue 330 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 3.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.7315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.049 0.250 17206 Z= 3.172 Angle : 1.920 12.720 23310 Z= 1.065 Chirality : 0.167 1.518 2772 Planarity : 0.013 0.103 2926 Dihedral : 20.582 179.027 2723 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 55.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 21.37 % Favored : 78.57 % Rotamer: Outliers : 14.54 % Allowed : 24.34 % Favored : 61.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -6.14 (0.13), residues: 1778 helix: -3.72 (0.11), residues: 973 sheet: -3.30 (0.26), residues: 259 loop : -4.67 (0.16), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.008 TRP F 302 HIS 0.017 0.005 HIS D 137 PHE 0.039 0.005 PHE A 101 TYR 0.033 0.006 TYR E 134 ARG 0.011 0.001 ARG D 231 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Evaluate side-chains 359 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 132 time to evaluate : 2.626 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: E 140 MET cc_start: 0.7652 (OUTLIER) cc_final: 0.7390 (mpt) REVERT: E 148 PHE cc_start: 0.9150 (t80) cc_final: 0.8911 (t80) REVERT: E 198 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.8055 (tt0) REVERT: E 256 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8104 (tm-30) REVERT: C 118 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.8064 (tpp) REVERT: C 136 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7541 (pm20) REVERT: C 198 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8054 (tm-30) REVERT: C 203 ILE cc_start: 0.9032 (OUTLIER) cc_final: 0.8790 (pp) REVERT: A 158 MET cc_start: 0.8714 (OUTLIER) cc_final: 0.8314 (mtm) REVERT: A 198 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7830 (tt0) REVERT: A 214 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8148 (tp) REVERT: B 158 MET cc_start: 0.8796 (mmm) cc_final: 0.8409 (mtm) REVERT: B 198 GLU cc_start: 0.8380 (pt0) cc_final: 0.8086 (pp20) REVERT: B 199 ILE cc_start: 0.9586 (OUTLIER) cc_final: 0.9130 (mm) REVERT: B 214 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.7857 (tp) REVERT: B 227 GLU cc_start: 0.8613 (tt0) cc_final: 0.8357 (tt0) REVERT: B 232 MET cc_start: 0.9145 (ptt) cc_final: 0.8933 (ptt) REVERT: D 140 MET cc_start: 0.7799 (mpt) cc_final: 0.7532 (mpt) REVERT: D 198 GLU cc_start: 0.8374 (pt0) cc_final: 0.8035 (pp20) REVERT: D 203 ILE cc_start: 0.9000 (OUTLIER) cc_final: 0.8757 (pp) REVERT: D 256 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7932 (tm-30) REVERT: F 118 MET cc_start: 0.8278 (OUTLIER) cc_final: 0.7905 (tpt) REVERT: F 199 ILE cc_start: 0.9552 (OUTLIER) cc_final: 0.9242 (mm) REVERT: F 274 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.8941 (tp) REVERT: G 111 ASP cc_start: 0.8855 (OUTLIER) cc_final: 0.8555 (t70) REVERT: G 246 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8116 (mp0) REVERT: G 256 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.8002 (tm-30) REVERT: G 316 ILE cc_start: 0.8791 (OUTLIER) cc_final: 0.8590 (mt) outliers start: 227 outliers final: 183 residues processed: 337 average time/residue: 1.2756 time to fit residues: 529.7656 Evaluate side-chains 333 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 129 time to evaluate : 2.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 138 PHE Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain E residue 198 GLU Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 211 ASN Chi-restraints excluded: chain E residue 223 SER Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 225 SER Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 247 ASP Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 319 SER Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 148 PHE Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 138 PHE Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 112 ILE Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 211 ASN Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 225 SER Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain F residue 81 ILE Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 112 ILE Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 138 PHE Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 148 PHE Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain F residue 185 ILE Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 195 THR Chi-restraints excluded: chain F residue 198 GLU Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 210 ASP Chi-restraints excluded: chain F residue 211 ASN Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 225 SER Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 246 GLU Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 292 CYS Chi-restraints excluded: chain F residue 294 THR Chi-restraints excluded: chain F residue 316 ILE Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 107 LYS Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 158 MET Chi-restraints excluded: chain G residue 165 SER Chi-restraints excluded: chain G residue 171 ILE Chi-restraints excluded: chain G residue 176 ASP Chi-restraints excluded: chain G residue 185 ILE Chi-restraints excluded: chain G residue 189 ASP Chi-restraints excluded: chain G residue 198 GLU Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 210 ASP Chi-restraints excluded: chain G residue 211 ASN Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 239 THR Chi-restraints excluded: chain G residue 246 GLU Chi-restraints excluded: chain G residue 254 ILE Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 256 GLU Chi-restraints excluded: chain G residue 268 ILE Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain G residue 313 ILE Chi-restraints excluded: chain G residue 314 ILE Chi-restraints excluded: chain G residue 316 ILE Chi-restraints excluded: chain G residue 319 SER Chi-restraints excluded: chain G residue 330 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 3.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.7343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.049 0.249 17206 Z= 3.172 Angle : 1.925 12.937 23310 Z= 1.066 Chirality : 0.167 1.518 2772 Planarity : 0.013 0.104 2926 Dihedral : 20.564 178.948 2723 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 56.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.65 % Favored : 78.35 % Rotamer: Outliers : 14.09 % Allowed : 24.92 % Favored : 60.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -6.18 (0.13), residues: 1778 helix: -3.74 (0.11), residues: 973 sheet: -3.33 (0.26), residues: 259 loop : -4.69 (0.16), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.008 TRP F 302 HIS 0.020 0.005 HIS G 137 PHE 0.039 0.005 PHE C 101 TYR 0.038 0.006 TYR B 134 ARG 0.010 0.001 ARG D 231 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Evaluate side-chains 349 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 129 time to evaluate : 2.620 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: E 140 MET cc_start: 0.7708 (OUTLIER) cc_final: 0.7465 (mpt) REVERT: E 148 PHE cc_start: 0.9164 (t80) cc_final: 0.8930 (t80) REVERT: E 198 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.8042 (tt0) REVERT: E 256 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.8099 (tm-30) REVERT: C 118 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.8065 (tpp) REVERT: C 136 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.7520 (pm20) REVERT: C 198 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8049 (tm-30) REVERT: C 203 ILE cc_start: 0.9029 (OUTLIER) cc_final: 0.8786 (pp) REVERT: A 158 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.8318 (mtm) REVERT: A 198 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7809 (tt0) REVERT: A 214 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8147 (tp) REVERT: B 158 MET cc_start: 0.8763 (mmm) cc_final: 0.8248 (mtm) REVERT: B 198 GLU cc_start: 0.8376 (pt0) cc_final: 0.8082 (pp20) REVERT: B 199 ILE cc_start: 0.9574 (OUTLIER) cc_final: 0.9121 (mm) REVERT: B 203 ILE cc_start: 0.9102 (OUTLIER) cc_final: 0.8828 (pp) REVERT: B 214 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.7858 (tp) REVERT: B 227 GLU cc_start: 0.8621 (tt0) cc_final: 0.8383 (tt0) REVERT: B 232 MET cc_start: 0.9114 (ptt) cc_final: 0.8906 (ptt) REVERT: D 140 MET cc_start: 0.7819 (mpt) cc_final: 0.7577 (mpt) REVERT: D 198 GLU cc_start: 0.8372 (pt0) cc_final: 0.8033 (pp20) REVERT: D 203 ILE cc_start: 0.8999 (OUTLIER) cc_final: 0.8755 (pp) REVERT: D 256 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7941 (tm-30) REVERT: F 118 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.7908 (tpt) REVERT: F 199 ILE cc_start: 0.9552 (OUTLIER) cc_final: 0.9241 (mm) REVERT: F 274 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.8939 (tp) REVERT: G 111 ASP cc_start: 0.8806 (OUTLIER) cc_final: 0.8508 (t70) REVERT: G 246 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8117 (mp0) REVERT: G 256 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.8000 (tm-30) outliers start: 220 outliers final: 183 residues processed: 329 average time/residue: 1.3760 time to fit residues: 563.6959 Evaluate side-chains 333 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 129 time to evaluate : 2.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 138 PHE Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain E residue 198 GLU Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 211 ASN Chi-restraints excluded: chain E residue 223 SER Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 225 SER Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 247 ASP Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain E residue 285 SER Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 319 SER Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 148 PHE Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 138 PHE Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 112 ILE Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 211 ASN Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 225 SER Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain F residue 81 ILE Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 112 ILE Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 138 PHE Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 148 PHE Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain F residue 185 ILE Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 195 THR Chi-restraints excluded: chain F residue 198 GLU Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 210 ASP Chi-restraints excluded: chain F residue 211 ASN Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 225 SER Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 246 GLU Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 292 CYS Chi-restraints excluded: chain F residue 294 THR Chi-restraints excluded: chain F residue 316 ILE Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 107 LYS Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 158 MET Chi-restraints excluded: chain G residue 165 SER Chi-restraints excluded: chain G residue 176 ASP Chi-restraints excluded: chain G residue 185 ILE Chi-restraints excluded: chain G residue 189 ASP Chi-restraints excluded: chain G residue 198 GLU Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 210 ASP Chi-restraints excluded: chain G residue 211 ASN Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 239 THR Chi-restraints excluded: chain G residue 246 GLU Chi-restraints excluded: chain G residue 254 ILE Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 256 GLU Chi-restraints excluded: chain G residue 268 ILE Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain G residue 313 ILE Chi-restraints excluded: chain G residue 314 ILE Chi-restraints excluded: chain G residue 319 SER Chi-restraints excluded: chain G residue 330 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 3.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.097113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.060364 restraints weight = 113286.029| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 2.53 r_work: 0.2674 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2573 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.7364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.049 0.250 17206 Z= 3.174 Angle : 1.924 12.720 23310 Z= 1.065 Chirality : 0.167 1.516 2772 Planarity : 0.013 0.104 2926 Dihedral : 20.471 179.575 2723 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 56.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.71 % Favored : 78.29 % Rotamer: Outliers : 14.41 % Allowed : 24.66 % Favored : 60.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -6.19 (0.13), residues: 1778 helix: -3.75 (0.11), residues: 973 sheet: -3.32 (0.26), residues: 259 loop : -4.71 (0.16), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.008 TRP F 302 HIS 0.017 0.005 HIS G 137 PHE 0.038 0.005 PHE A 101 TYR 0.035 0.006 TYR C 134 ARG 0.010 0.001 ARG D 231 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14669.65 seconds wall clock time: 259 minutes 25.21 seconds (15565.21 seconds total)