Starting phenix.real_space_refine on Wed Mar 20 17:26:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7svu_25453/03_2024/7svu_25453_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7svu_25453/03_2024/7svu_25453.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7svu_25453/03_2024/7svu_25453.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7svu_25453/03_2024/7svu_25453.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7svu_25453/03_2024/7svu_25453_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7svu_25453/03_2024/7svu_25453_updated.pdb" } resolution = 3.5 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= 0.176 sd= 0.689 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 89 5.49 5 Mg 11 5.21 5 S 116 5.16 5 C 17459 2.51 5 N 5051 2.21 5 O 5289 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 574": "OD1" <-> "OD2" Residue "I TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ASP 574": "OD1" <-> "OD2" Residue "K TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ASP 574": "OD1" <-> "OD2" Residue "X PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 28015 Number of models: 1 Model: "" Number of chains: 35 Chain: "1" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 560 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "2" Number of atoms: 588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 588 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain breaks: 1 Chain: "A" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "a" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "B" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "b" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "C" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "c" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "D" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "d" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "E" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "e" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "F" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "f" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "G" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "H" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "h" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "I" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "J" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "j" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "K" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "k" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "X" Number of atoms: 1314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1314 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 13, 'TRANS': 151} Chain: "Y" Number of atoms: 1314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1314 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 13, 'TRANS': 151} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 14.86, per 1000 atoms: 0.53 Number of scatterers: 28015 At special positions: 0 Unit cell: (136.99, 142.31, 168.91, 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 116 16.00 P 89 15.00 Mg 11 11.99 O 5289 8.00 N 5051 7.00 C 17459 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "ATOM 484 O5' DT 1 25 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.52 Conformation dependent library (CDL) restraints added in 4.3 seconds 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6156 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 171 helices and 11 sheets defined 52.4% alpha, 6.4% beta 22 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 10.66 Creating SS restraints... Processing helix chain 'A' and resid 20 through 28 Processing helix chain 'A' and resid 37 through 52 Processing helix chain 'A' and resid 66 through 76 removed outlier: 3.743A pdb=" N ARG A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 112 removed outlier: 3.874A pdb=" N PHE A 106 " --> pdb=" O PRO A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 133 Processing helix chain 'A' and resid 146 through 148 No H-bonds generated for 'chain 'A' and resid 146 through 148' Processing helix chain 'A' and resid 151 through 163 removed outlier: 3.760A pdb=" N PHE A 154 " --> pdb=" O PRO A 151 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG A 158 " --> pdb=" O ALA A 155 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP A 159 " --> pdb=" O ASP A 156 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE A 160 " --> pdb=" O VAL A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 182 removed outlier: 4.194A pdb=" N ARG A 182 " --> pdb=" O ALA A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 189 removed outlier: 3.954A pdb=" N ARG A 189 " --> pdb=" O GLN A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 214 Processing helix chain 'A' and resid 227 through 237 removed outlier: 4.355A pdb=" N ILE A 232 " --> pdb=" O GLU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 257 Processing helix chain 'A' and resid 265 through 274 removed outlier: 4.000A pdb=" N GLU A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) Processing helix chain 'a' and resid 575 through 580 removed outlier: 3.931A pdb=" N ARG a 579 " --> pdb=" O TYR a 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 28 Processing helix chain 'B' and resid 37 through 52 Processing helix chain 'B' and resid 66 through 76 removed outlier: 3.743A pdb=" N ARG B 76 " --> pdb=" O ALA B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 112 removed outlier: 3.874A pdb=" N PHE B 106 " --> pdb=" O PRO B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 133 Processing helix chain 'B' and resid 146 through 148 No H-bonds generated for 'chain 'B' and resid 146 through 148' Processing helix chain 'B' and resid 151 through 163 removed outlier: 3.760A pdb=" N PHE B 154 " --> pdb=" O PRO B 151 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG B 158 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP B 159 " --> pdb=" O ASP B 156 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE B 160 " --> pdb=" O VAL B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 182 removed outlier: 4.195A pdb=" N ARG B 182 " --> pdb=" O ALA B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 189 removed outlier: 3.955A pdb=" N ARG B 189 " --> pdb=" O GLN B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 214 Processing helix chain 'B' and resid 227 through 237 removed outlier: 4.356A pdb=" N ILE B 232 " --> pdb=" O GLU B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 257 Processing helix chain 'B' and resid 265 through 274 removed outlier: 4.000A pdb=" N GLU B 274 " --> pdb=" O GLU B 270 " (cutoff:3.500A) Processing helix chain 'b' and resid 575 through 580 removed outlier: 3.930A pdb=" N ARG b 579 " --> pdb=" O TYR b 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 28 Processing helix chain 'C' and resid 37 through 52 Processing helix chain 'C' and resid 66 through 76 removed outlier: 3.743A pdb=" N ARG C 76 " --> pdb=" O ALA C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 112 removed outlier: 3.874A pdb=" N PHE C 106 " --> pdb=" O PRO C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 133 Processing helix chain 'C' and resid 146 through 148 No H-bonds generated for 'chain 'C' and resid 146 through 148' Processing helix chain 'C' and resid 151 through 163 removed outlier: 3.760A pdb=" N PHE C 154 " --> pdb=" O PRO C 151 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG C 158 " --> pdb=" O ALA C 155 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP C 159 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE C 160 " --> pdb=" O VAL C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 182 removed outlier: 4.195A pdb=" N ARG C 182 " --> pdb=" O ALA C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 189 removed outlier: 3.954A pdb=" N ARG C 189 " --> pdb=" O GLN C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 214 Processing helix chain 'C' and resid 227 through 237 removed outlier: 4.355A pdb=" N ILE C 232 " --> pdb=" O GLU C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 257 Processing helix chain 'C' and resid 265 through 274 removed outlier: 4.002A pdb=" N GLU C 274 " --> pdb=" O GLU C 270 " (cutoff:3.500A) Processing helix chain 'c' and resid 575 through 580 removed outlier: 3.930A pdb=" N ARG c 579 " --> pdb=" O TYR c 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 28 Processing helix chain 'D' and resid 37 through 52 Processing helix chain 'D' and resid 66 through 76 removed outlier: 3.743A pdb=" N ARG D 76 " --> pdb=" O ALA D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 112 removed outlier: 3.874A pdb=" N PHE D 106 " --> pdb=" O PRO D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 133 Processing helix chain 'D' and resid 146 through 148 No H-bonds generated for 'chain 'D' and resid 146 through 148' Processing helix chain 'D' and resid 151 through 163 removed outlier: 3.759A pdb=" N PHE D 154 " --> pdb=" O PRO D 151 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG D 158 " --> pdb=" O ALA D 155 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP D 159 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE D 160 " --> pdb=" O VAL D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 182 removed outlier: 4.195A pdb=" N ARG D 182 " --> pdb=" O ALA D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 189 removed outlier: 3.955A pdb=" N ARG D 189 " --> pdb=" O GLN D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 214 Processing helix chain 'D' and resid 227 through 237 removed outlier: 4.356A pdb=" N ILE D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 257 Processing helix chain 'D' and resid 265 through 274 removed outlier: 4.001A pdb=" N GLU D 274 " --> pdb=" O GLU D 270 " (cutoff:3.500A) Processing helix chain 'd' and resid 575 through 580 removed outlier: 3.931A pdb=" N ARG d 579 " --> pdb=" O TYR d 575 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 28 Processing helix chain 'E' and resid 37 through 52 Processing helix chain 'E' and resid 66 through 76 removed outlier: 3.744A pdb=" N ARG E 76 " --> pdb=" O ALA E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 112 removed outlier: 3.873A pdb=" N PHE E 106 " --> pdb=" O PRO E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 133 Processing helix chain 'E' and resid 146 through 148 No H-bonds generated for 'chain 'E' and resid 146 through 148' Processing helix chain 'E' and resid 151 through 163 removed outlier: 3.760A pdb=" N PHE E 154 " --> pdb=" O PRO E 151 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG E 158 " --> pdb=" O ALA E 155 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP E 159 " --> pdb=" O ASP E 156 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE E 160 " --> pdb=" O VAL E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 182 removed outlier: 4.195A pdb=" N ARG E 182 " --> pdb=" O ALA E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 189 removed outlier: 3.954A pdb=" N ARG E 189 " --> pdb=" O GLN E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 214 Processing helix chain 'E' and resid 227 through 237 removed outlier: 4.355A pdb=" N ILE E 232 " --> pdb=" O GLU E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 241 through 257 Processing helix chain 'E' and resid 265 through 274 removed outlier: 4.002A pdb=" N GLU E 274 " --> pdb=" O GLU E 270 " (cutoff:3.500A) Processing helix chain 'e' and resid 575 through 580 removed outlier: 3.931A pdb=" N ARG e 579 " --> pdb=" O TYR e 575 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 28 Processing helix chain 'F' and resid 37 through 52 Processing helix chain 'F' and resid 66 through 76 removed outlier: 3.743A pdb=" N ARG F 76 " --> pdb=" O ALA F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 112 removed outlier: 3.874A pdb=" N PHE F 106 " --> pdb=" O PRO F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 124 No H-bonds generated for 'chain 'F' and resid 122 through 124' Processing helix chain 'F' and resid 127 through 133 Processing helix chain 'F' and resid 146 through 148 No H-bonds generated for 'chain 'F' and resid 146 through 148' Processing helix chain 'F' and resid 151 through 163 removed outlier: 3.759A pdb=" N PHE F 154 " --> pdb=" O PRO F 151 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG F 158 " --> pdb=" O ALA F 155 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP F 159 " --> pdb=" O ASP F 156 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE F 160 " --> pdb=" O VAL F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 182 removed outlier: 4.195A pdb=" N ARG F 182 " --> pdb=" O ALA F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 189 removed outlier: 3.954A pdb=" N ARG F 189 " --> pdb=" O GLN F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 214 Processing helix chain 'F' and resid 227 through 237 removed outlier: 4.356A pdb=" N ILE F 232 " --> pdb=" O GLU F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 241 through 257 Processing helix chain 'F' and resid 265 through 274 removed outlier: 4.000A pdb=" N GLU F 274 " --> pdb=" O GLU F 270 " (cutoff:3.500A) Processing helix chain 'f' and resid 575 through 580 removed outlier: 3.930A pdb=" N ARG f 579 " --> pdb=" O TYR f 575 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 28 Processing helix chain 'G' and resid 37 through 52 Processing helix chain 'G' and resid 66 through 76 removed outlier: 3.856A pdb=" N ARG G 76 " --> pdb=" O ALA G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 113 removed outlier: 4.070A pdb=" N PHE G 106 " --> pdb=" O PRO G 102 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU G 113 " --> pdb=" O ILE G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 133 Processing helix chain 'G' and resid 146 through 148 No H-bonds generated for 'chain 'G' and resid 146 through 148' Processing helix chain 'G' and resid 151 through 163 removed outlier: 3.778A pdb=" N PHE G 154 " --> pdb=" O PRO G 151 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG G 158 " --> pdb=" O ALA G 155 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP G 159 " --> pdb=" O ASP G 156 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE G 160 " --> pdb=" O VAL G 157 " (cutoff:3.500A) Processing helix chain 'G' and resid 174 through 182 removed outlier: 4.094A pdb=" N ARG G 182 " --> pdb=" O ALA G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 189 removed outlier: 3.555A pdb=" N GLU G 188 " --> pdb=" O GLU G 184 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARG G 189 " --> pdb=" O GLN G 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 184 through 189' Processing helix chain 'G' and resid 201 through 214 Processing helix chain 'G' and resid 227 through 237 removed outlier: 3.979A pdb=" N ILE G 232 " --> pdb=" O GLU G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 241 through 257 Processing helix chain 'G' and resid 265 through 274 removed outlier: 3.969A pdb=" N GLU G 274 " --> pdb=" O GLU G 270 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 28 Processing helix chain 'H' and resid 37 through 52 removed outlier: 3.725A pdb=" N THR H 41 " --> pdb=" O GLN H 37 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU H 42 " --> pdb=" O GLN H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 66 through 76 removed outlier: 3.585A pdb=" N ARG H 76 " --> pdb=" O ALA H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 112 removed outlier: 4.025A pdb=" N PHE H 106 " --> pdb=" O PRO H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 122 through 133 Processing helix chain 'H' and resid 146 through 148 No H-bonds generated for 'chain 'H' and resid 146 through 148' Processing helix chain 'H' and resid 151 through 163 removed outlier: 3.784A pdb=" N PHE H 154 " --> pdb=" O PRO H 151 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG H 158 " --> pdb=" O ALA H 155 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP H 159 " --> pdb=" O ASP H 156 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE H 160 " --> pdb=" O VAL H 157 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 182 removed outlier: 4.077A pdb=" N ARG H 182 " --> pdb=" O ALA H 178 " (cutoff:3.500A) Processing helix chain 'H' and resid 184 through 189 removed outlier: 3.572A pdb=" N GLU H 188 " --> pdb=" O GLU H 184 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ARG H 189 " --> pdb=" O GLN H 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 184 through 189' Processing helix chain 'H' and resid 201 through 214 Processing helix chain 'H' and resid 227 through 237 removed outlier: 4.260A pdb=" N ILE H 232 " --> pdb=" O GLU H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 241 through 257 Processing helix chain 'H' and resid 265 through 274 removed outlier: 4.068A pdb=" N GLU H 274 " --> pdb=" O GLU H 270 " (cutoff:3.500A) Processing helix chain 'h' and resid 577 through 580 No H-bonds generated for 'chain 'h' and resid 577 through 580' Processing helix chain 'I' and resid 20 through 28 Processing helix chain 'I' and resid 37 through 52 Processing helix chain 'I' and resid 66 through 76 removed outlier: 3.857A pdb=" N ARG I 76 " --> pdb=" O ALA I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 113 removed outlier: 4.069A pdb=" N PHE I 106 " --> pdb=" O PRO I 102 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU I 113 " --> pdb=" O ILE I 109 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 133 Processing helix chain 'I' and resid 146 through 148 No H-bonds generated for 'chain 'I' and resid 146 through 148' Processing helix chain 'I' and resid 151 through 163 removed outlier: 3.778A pdb=" N PHE I 154 " --> pdb=" O PRO I 151 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG I 158 " --> pdb=" O ALA I 155 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP I 159 " --> pdb=" O ASP I 156 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE I 160 " --> pdb=" O VAL I 157 " (cutoff:3.500A) Processing helix chain 'I' and resid 174 through 182 removed outlier: 4.093A pdb=" N ARG I 182 " --> pdb=" O ALA I 178 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 189 removed outlier: 3.554A pdb=" N GLU I 188 " --> pdb=" O GLU I 184 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ARG I 189 " --> pdb=" O GLN I 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 184 through 189' Processing helix chain 'I' and resid 201 through 214 Processing helix chain 'I' and resid 227 through 237 removed outlier: 3.980A pdb=" N ILE I 232 " --> pdb=" O GLU I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 241 through 257 Processing helix chain 'I' and resid 265 through 274 removed outlier: 3.969A pdb=" N GLU I 274 " --> pdb=" O GLU I 270 " (cutoff:3.500A) Processing helix chain 'J' and resid 20 through 28 Processing helix chain 'J' and resid 37 through 52 removed outlier: 3.726A pdb=" N THR J 41 " --> pdb=" O GLN J 37 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU J 42 " --> pdb=" O GLN J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 66 through 76 removed outlier: 3.585A pdb=" N ARG J 76 " --> pdb=" O ALA J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 102 through 112 removed outlier: 4.025A pdb=" N PHE J 106 " --> pdb=" O PRO J 102 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 133 Processing helix chain 'J' and resid 146 through 148 No H-bonds generated for 'chain 'J' and resid 146 through 148' Processing helix chain 'J' and resid 151 through 163 removed outlier: 3.783A pdb=" N PHE J 154 " --> pdb=" O PRO J 151 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG J 158 " --> pdb=" O ALA J 155 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP J 159 " --> pdb=" O ASP J 156 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE J 160 " --> pdb=" O VAL J 157 " (cutoff:3.500A) Processing helix chain 'J' and resid 174 through 182 removed outlier: 4.078A pdb=" N ARG J 182 " --> pdb=" O ALA J 178 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 189 removed outlier: 3.573A pdb=" N GLU J 188 " --> pdb=" O GLU J 184 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ARG J 189 " --> pdb=" O GLN J 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 184 through 189' Processing helix chain 'J' and resid 201 through 214 Processing helix chain 'J' and resid 227 through 237 removed outlier: 4.259A pdb=" N ILE J 232 " --> pdb=" O GLU J 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 241 through 257 Processing helix chain 'J' and resid 265 through 274 removed outlier: 4.068A pdb=" N GLU J 274 " --> pdb=" O GLU J 270 " (cutoff:3.500A) Processing helix chain 'j' and resid 577 through 580 No H-bonds generated for 'chain 'j' and resid 577 through 580' Processing helix chain 'K' and resid 20 through 28 Processing helix chain 'K' and resid 37 through 52 removed outlier: 3.726A pdb=" N THR K 41 " --> pdb=" O GLN K 37 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU K 42 " --> pdb=" O GLN K 38 " (cutoff:3.500A) Processing helix chain 'K' and resid 66 through 76 removed outlier: 3.585A pdb=" N ARG K 76 " --> pdb=" O ALA K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 102 through 112 removed outlier: 4.025A pdb=" N PHE K 106 " --> pdb=" O PRO K 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 122 through 133 Processing helix chain 'K' and resid 146 through 148 No H-bonds generated for 'chain 'K' and resid 146 through 148' Processing helix chain 'K' and resid 151 through 163 removed outlier: 3.784A pdb=" N PHE K 154 " --> pdb=" O PRO K 151 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG K 158 " --> pdb=" O ALA K 155 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP K 159 " --> pdb=" O ASP K 156 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE K 160 " --> pdb=" O VAL K 157 " (cutoff:3.500A) Processing helix chain 'K' and resid 174 through 182 removed outlier: 4.078A pdb=" N ARG K 182 " --> pdb=" O ALA K 178 " (cutoff:3.500A) Processing helix chain 'K' and resid 184 through 189 removed outlier: 3.573A pdb=" N GLU K 188 " --> pdb=" O GLU K 184 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ARG K 189 " --> pdb=" O GLN K 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 184 through 189' Processing helix chain 'K' and resid 201 through 214 Processing helix chain 'K' and resid 227 through 237 removed outlier: 4.259A pdb=" N ILE K 232 " --> pdb=" O GLU K 228 " (cutoff:3.500A) Processing helix chain 'K' and resid 241 through 257 Processing helix chain 'K' and resid 265 through 274 removed outlier: 4.068A pdb=" N GLU K 274 " --> pdb=" O GLU K 270 " (cutoff:3.500A) Processing helix chain 'k' and resid 577 through 580 No H-bonds generated for 'chain 'k' and resid 577 through 580' Processing helix chain 'X' and resid 22 through 32 Processing helix chain 'X' and resid 37 through 44 Processing helix chain 'X' and resid 48 through 52 Processing helix chain 'X' and resid 66 through 74 removed outlier: 3.983A pdb=" N ALA X 71 " --> pdb=" O LEU X 67 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N SER X 72 " --> pdb=" O GLU X 68 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N VAL X 73 " --> pdb=" O ALA X 69 " (cutoff:3.500A) Processing helix chain 'X' and resid 78 through 84 removed outlier: 3.798A pdb=" N MET X 84 " --> pdb=" O ARG X 80 " (cutoff:3.500A) Processing helix chain 'X' and resid 101 through 103 No H-bonds generated for 'chain 'X' and resid 101 through 103' Processing helix chain 'X' and resid 112 through 115 Processing helix chain 'X' and resid 143 through 145 No H-bonds generated for 'chain 'X' and resid 143 through 145' Processing helix chain 'X' and resid 159 through 163 removed outlier: 4.017A pdb=" N LYS X 163 " --> pdb=" O GLU X 160 " (cutoff:3.500A) Processing helix chain 'Y' and resid 22 through 32 Processing helix chain 'Y' and resid 37 through 44 Processing helix chain 'Y' and resid 48 through 52 Processing helix chain 'Y' and resid 66 through 74 removed outlier: 3.982A pdb=" N ALA Y 71 " --> pdb=" O LEU Y 67 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N SER Y 72 " --> pdb=" O GLU Y 68 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N VAL Y 73 " --> pdb=" O ALA Y 69 " (cutoff:3.500A) Processing helix chain 'Y' and resid 78 through 84 removed outlier: 3.798A pdb=" N MET Y 84 " --> pdb=" O ARG Y 80 " (cutoff:3.500A) Processing helix chain 'Y' and resid 101 through 103 No H-bonds generated for 'chain 'Y' and resid 101 through 103' Processing helix chain 'Y' and resid 112 through 115 Processing helix chain 'Y' and resid 143 through 145 No H-bonds generated for 'chain 'Y' and resid 143 through 145' Processing helix chain 'Y' and resid 159 through 163 removed outlier: 4.018A pdb=" N LYS Y 163 " --> pdb=" O GLU Y 160 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 193 through 196 removed outlier: 6.728A pdb=" N ARG A 57 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N PHE A 196 " --> pdb=" O ARG A 57 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL A 59 " --> pdb=" O PHE A 196 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 193 through 196 removed outlier: 6.729A pdb=" N ARG B 57 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N PHE B 196 " --> pdb=" O ARG B 57 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL B 59 " --> pdb=" O PHE B 196 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 193 through 196 removed outlier: 6.729A pdb=" N ARG C 57 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N PHE C 196 " --> pdb=" O ARG C 57 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL C 59 " --> pdb=" O PHE C 196 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 193 through 196 removed outlier: 6.729A pdb=" N ARG D 57 " --> pdb=" O LEU D 194 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N PHE D 196 " --> pdb=" O ARG D 57 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL D 59 " --> pdb=" O PHE D 196 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 193 through 196 removed outlier: 6.729A pdb=" N ARG E 57 " --> pdb=" O LEU E 194 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N PHE E 196 " --> pdb=" O ARG E 57 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL E 59 " --> pdb=" O PHE E 196 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 193 through 196 removed outlier: 6.729A pdb=" N ARG F 57 " --> pdb=" O LEU F 194 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N PHE F 196 " --> pdb=" O ARG F 57 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL F 59 " --> pdb=" O PHE F 196 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'G' and resid 193 through 195 removed outlier: 6.601A pdb=" N ARG G 57 " --> pdb=" O LEU G 194 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'H' and resid 193 through 195 removed outlier: 6.608A pdb=" N ARG H 57 " --> pdb=" O LEU H 194 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'I' and resid 193 through 195 removed outlier: 6.601A pdb=" N ARG I 57 " --> pdb=" O LEU I 194 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'J' and resid 193 through 195 removed outlier: 6.608A pdb=" N ARG J 57 " --> pdb=" O LEU J 194 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'K' and resid 193 through 195 removed outlier: 6.609A pdb=" N ARG K 57 " --> pdb=" O LEU K 194 " (cutoff:3.500A) 1068 hydrogen bonds defined for protein. 2949 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 44 hydrogen bonds 88 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 8.57 Time building geometry restraints manager: 11.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 4484 1.29 - 1.42: 7161 1.42 - 1.55: 16626 1.55 - 1.69: 168 1.69 - 1.82: 170 Bond restraints: 28609 Sorted by residual: bond pdb=" C5 ATP J 302 " pdb=" N7 ATP J 302 " ideal model delta sigma weight residual 1.387 1.286 0.101 1.00e-02 1.00e+04 1.02e+02 bond pdb=" C4 ATP J 302 " pdb=" N9 ATP J 302 " ideal model delta sigma weight residual 1.374 1.278 0.096 1.00e-02 1.00e+04 9.19e+01 bond pdb=" C4 ATP A 302 " pdb=" C5 ATP A 302 " ideal model delta sigma weight residual 1.388 1.472 -0.084 1.00e-02 1.00e+04 7.04e+01 bond pdb=" C4 ATP D 302 " pdb=" C5 ATP D 302 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.95e+01 bond pdb=" C4 ATP G 302 " pdb=" C5 ATP G 302 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.93e+01 ... (remaining 28604 not shown) Histogram of bond angle deviations from ideal: 96.95 - 105.01: 953 105.01 - 113.08: 14932 113.08 - 121.14: 15839 121.14 - 129.21: 6832 129.21 - 137.27: 241 Bond angle restraints: 38797 Sorted by residual: angle pdb=" PA ATP J 302 " pdb=" O3A ATP J 302 " pdb=" PB ATP J 302 " ideal model delta sigma weight residual 136.83 109.85 26.98 1.00e+00 1.00e+00 7.28e+02 angle pdb=" PB ATP J 302 " pdb=" O3B ATP J 302 " pdb=" PG ATP J 302 " ideal model delta sigma weight residual 139.87 113.39 26.48 1.00e+00 1.00e+00 7.01e+02 angle pdb=" PB ATP B 302 " pdb=" O3B ATP B 302 " pdb=" PG ATP B 302 " ideal model delta sigma weight residual 139.87 120.44 19.43 1.00e+00 1.00e+00 3.78e+02 angle pdb=" PB ATP C 302 " pdb=" O3B ATP C 302 " pdb=" PG ATP C 302 " ideal model delta sigma weight residual 139.87 120.46 19.41 1.00e+00 1.00e+00 3.77e+02 angle pdb=" PB ATP A 302 " pdb=" O3B ATP A 302 " pdb=" PG ATP A 302 " ideal model delta sigma weight residual 139.87 120.47 19.40 1.00e+00 1.00e+00 3.76e+02 ... (remaining 38792 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.98: 16977 29.98 - 59.95: 665 59.95 - 89.93: 93 89.93 - 119.90: 1 119.90 - 149.88: 4 Dihedral angle restraints: 17740 sinusoidal: 8222 harmonic: 9518 Sorted by residual: dihedral pdb=" N ARG J 116 " pdb=" C ARG J 116 " pdb=" CA ARG J 116 " pdb=" CB ARG J 116 " ideal model delta harmonic sigma weight residual 122.80 138.90 -16.10 0 2.50e+00 1.60e-01 4.15e+01 dihedral pdb=" C TYR j 582 " pdb=" N TYR j 582 " pdb=" CA TYR j 582 " pdb=" CB TYR j 582 " ideal model delta harmonic sigma weight residual -122.60 -137.36 14.76 0 2.50e+00 1.60e-01 3.48e+01 dihedral pdb=" C TYR k 582 " pdb=" N TYR k 582 " pdb=" CA TYR k 582 " pdb=" CB TYR k 582 " ideal model delta harmonic sigma weight residual -122.60 -137.33 14.73 0 2.50e+00 1.60e-01 3.47e+01 ... (remaining 17737 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.134: 3637 0.134 - 0.267: 536 0.267 - 0.401: 83 0.401 - 0.534: 14 0.534 - 0.668: 12 Chirality restraints: 4282 Sorted by residual: chirality pdb=" CA TYR j 582 " pdb=" N TYR j 582 " pdb=" C TYR j 582 " pdb=" CB TYR j 582 " both_signs ideal model delta sigma weight residual False 2.51 1.84 0.67 2.00e-01 2.50e+01 1.11e+01 chirality pdb=" CA TYR k 582 " pdb=" N TYR k 582 " pdb=" C TYR k 582 " pdb=" CB TYR k 582 " both_signs ideal model delta sigma weight residual False 2.51 1.84 0.67 2.00e-01 2.50e+01 1.11e+01 chirality pdb=" CA TYR e 582 " pdb=" N TYR e 582 " pdb=" C TYR e 582 " pdb=" CB TYR e 582 " both_signs ideal model delta sigma weight residual False 2.51 1.84 0.67 2.00e-01 2.50e+01 1.11e+01 ... (remaining 4279 not shown) Planarity restraints: 4690 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 255 " -0.030 2.00e-02 2.50e+03 5.94e-02 3.52e+01 pdb=" C SER A 255 " 0.103 2.00e-02 2.50e+03 pdb=" O SER A 255 " -0.037 2.00e-02 2.50e+03 pdb=" N LEU A 256 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER F 255 " -0.030 2.00e-02 2.50e+03 5.93e-02 3.52e+01 pdb=" C SER F 255 " 0.103 2.00e-02 2.50e+03 pdb=" O SER F 255 " -0.037 2.00e-02 2.50e+03 pdb=" N LEU F 256 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER D 255 " 0.030 2.00e-02 2.50e+03 5.93e-02 3.52e+01 pdb=" C SER D 255 " -0.103 2.00e-02 2.50e+03 pdb=" O SER D 255 " 0.037 2.00e-02 2.50e+03 pdb=" N LEU D 256 " 0.036 2.00e-02 2.50e+03 ... (remaining 4687 not shown) Histogram of nonbonded interaction distances: 0.44 - 1.33: 16 1.33 - 2.22: 147 2.22 - 3.11: 23041 3.11 - 4.01: 69407 4.01 - 4.90: 124796 Warning: very small nonbonded interaction distances. Nonbonded interactions: 217407 Sorted by model distance: nonbonded pdb=" NH1 ARG A 85 " pdb=" CG LYS H 273 " model vdw 0.437 3.520 nonbonded pdb=" NH1 ARG B 85 " pdb=" CG LYS I 273 " model vdw 0.450 3.520 nonbonded pdb=" NH1 ARG D 85 " pdb=" CG LYS K 273 " model vdw 0.453 3.520 nonbonded pdb=" NH1 ARG C 85 " pdb=" CG LYS J 273 " model vdw 0.512 3.520 nonbonded pdb=" CZ ARG F 116 " pdb=" OE2 GLU K 184 " model vdw 0.871 3.270 ... (remaining 217402 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'X' selection = chain 'Y' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'h' selection = chain 'j' selection = chain 'k' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 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: 0.020 Extract box with map and model: 5.020 Check model and map are aligned: 0.430 Set scattering table: 0.270 Process input model: 76.640 Find NCS groups from input model: 1.910 Set up NCS constraints: 0.300 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 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 : 0.020 0.101 28609 Z= 1.289 Angle : 1.915 26.975 38797 Z= 1.453 Chirality : 0.108 0.668 4282 Planarity : 0.011 0.076 4690 Dihedral : 15.097 149.877 11584 Min Nonbonded Distance : 0.437 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.28 % Favored : 97.56 % Rotamer: Outliers : 0.42 % Allowed : 2.80 % Favored : 96.78 % Cbeta Deviations : 0.39 % 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: -0.41 (0.14), residues: 3239 helix: -0.71 (0.11), residues: 1810 sheet: 2.49 (0.30), residues: 253 loop : 0.13 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP Y 10 HIS 0.004 0.000 HIS Y 152 PHE 0.027 0.001 PHE F 125 TYR 0.026 0.002 TYR G 112 ARG 0.004 0.000 ARG Y 155 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1515 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 1503 time to evaluate : 3.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 LYS cc_start: 0.7247 (mttt) cc_final: 0.6639 (mtpp) REVERT: A 183 ASP cc_start: 0.7583 (t0) cc_final: 0.7348 (t70) REVERT: B 42 LEU cc_start: 0.8379 (tp) cc_final: 0.8071 (tt) REVERT: B 53 ARG cc_start: 0.8234 (mmt-90) cc_final: 0.6921 (mmt90) REVERT: B 104 ASP cc_start: 0.8384 (m-30) cc_final: 0.8058 (m-30) REVERT: B 132 VAL cc_start: 0.8763 (m) cc_final: 0.8378 (t) REVERT: C 36 LEU cc_start: 0.8563 (mt) cc_final: 0.8339 (mp) REVERT: C 78 LYS cc_start: 0.7228 (mttt) cc_final: 0.6364 (mtpp) REVERT: C 125 PHE cc_start: 0.8777 (m-10) cc_final: 0.8520 (m-80) REVERT: C 130 ILE cc_start: 0.9291 (mm) cc_final: 0.9071 (mt) REVERT: C 136 CYS cc_start: 0.6789 (t) cc_final: 0.6475 (t) REVERT: C 145 GLU cc_start: 0.7343 (mt-10) cc_final: 0.7118 (mt-10) REVERT: D 25 ILE cc_start: 0.6918 (mm) cc_final: 0.6690 (mm) REVERT: D 73 TYR cc_start: 0.8844 (t80) cc_final: 0.8555 (t80) REVERT: D 78 LYS cc_start: 0.8027 (mttt) cc_final: 0.7531 (mmmm) REVERT: D 132 VAL cc_start: 0.8744 (m) cc_final: 0.8376 (p) REVERT: E 33 ILE cc_start: 0.8898 (mt) cc_final: 0.8503 (mt) REVERT: E 47 ASP cc_start: 0.5398 (t70) cc_final: 0.5099 (t70) REVERT: E 53 ARG cc_start: 0.8154 (mmt-90) cc_final: 0.7895 (mpt180) REVERT: E 78 LYS cc_start: 0.7479 (mttt) cc_final: 0.6746 (mtpp) REVERT: E 89 VAL cc_start: 0.7578 (t) cc_final: 0.7289 (m) REVERT: E 93 TYR cc_start: 0.8633 (t80) cc_final: 0.8023 (t80) REVERT: E 144 ASP cc_start: 0.8459 (t0) cc_final: 0.8087 (t0) REVERT: E 159 ASP cc_start: 0.7352 (t70) cc_final: 0.6982 (t0) REVERT: E 163 ASP cc_start: 0.6178 (t70) cc_final: 0.5825 (t0) REVERT: F 34 VAL cc_start: 0.8419 (t) cc_final: 0.7988 (m) REVERT: F 41 THR cc_start: 0.8352 (m) cc_final: 0.8139 (m) REVERT: F 42 LEU cc_start: 0.8462 (tp) cc_final: 0.8215 (tt) REVERT: F 49 LYS cc_start: 0.8693 (mmtt) cc_final: 0.8442 (mmmm) REVERT: G 115 TYR cc_start: 0.7959 (t80) cc_final: 0.6409 (t80) REVERT: G 153 THR cc_start: 0.8722 (p) cc_final: 0.8503 (t) REVERT: G 180 ILE cc_start: 0.9060 (mt) cc_final: 0.8859 (mm) REVERT: G 268 LEU cc_start: 0.8967 (tp) cc_final: 0.8525 (tt) REVERT: G 269 GLN cc_start: 0.7805 (mt0) cc_final: 0.7566 (mt0) REVERT: G 275 TYR cc_start: 0.6406 (m-80) cc_final: 0.6003 (m-80) REVERT: H 64 THR cc_start: 0.8349 (p) cc_final: 0.8146 (p) REVERT: H 89 VAL cc_start: 0.8633 (t) cc_final: 0.8330 (m) REVERT: H 132 VAL cc_start: 0.8755 (m) cc_final: 0.8471 (t) REVERT: H 184 GLU cc_start: 0.6849 (mt-10) cc_final: 0.6374 (mt-10) REVERT: H 232 ILE cc_start: 0.8302 (mt) cc_final: 0.8091 (mt) REVERT: h 573 TRP cc_start: 0.7670 (m-90) cc_final: 0.7467 (m-90) REVERT: I 25 ILE cc_start: 0.7916 (mm) cc_final: 0.7688 (mm) REVERT: I 33 ILE cc_start: 0.8870 (mt) cc_final: 0.8649 (mm) REVERT: I 44 ASP cc_start: 0.7698 (m-30) cc_final: 0.7492 (m-30) REVERT: I 64 THR cc_start: 0.8336 (p) cc_final: 0.8135 (p) REVERT: I 240 TYR cc_start: 0.8569 (m-80) cc_final: 0.8331 (m-80) REVERT: I 268 LEU cc_start: 0.8837 (tp) cc_final: 0.8578 (tp) REVERT: I 269 GLN cc_start: 0.7871 (mt0) cc_final: 0.7670 (mt0) REVERT: J 29 LYS cc_start: 0.8469 (ttpt) cc_final: 0.8225 (ttpp) REVERT: J 47 ASP cc_start: 0.7743 (t70) cc_final: 0.7482 (t0) REVERT: J 91 VAL cc_start: 0.8841 (t) cc_final: 0.8631 (p) REVERT: J 104 ASP cc_start: 0.7781 (m-30) cc_final: 0.7559 (m-30) REVERT: J 124 ASP cc_start: 0.7962 (m-30) cc_final: 0.7404 (m-30) REVERT: J 129 THR cc_start: 0.8665 (m) cc_final: 0.8405 (t) REVERT: J 211 TRP cc_start: 0.8211 (t-100) cc_final: 0.7843 (t-100) REVERT: J 220 VAL cc_start: 0.8367 (OUTLIER) cc_final: 0.8042 (t) REVERT: J 235 SER cc_start: 0.8846 (t) cc_final: 0.8582 (p) REVERT: J 246 GLU cc_start: 0.6675 (tt0) cc_final: 0.6373 (tt0) REVERT: J 268 LEU cc_start: 0.8813 (tp) cc_final: 0.8550 (tt) REVERT: K 91 VAL cc_start: 0.8304 (t) cc_final: 0.7994 (m) REVERT: K 121 THR cc_start: 0.7298 (t) cc_final: 0.6825 (t) REVERT: K 145 GLU cc_start: 0.7354 (mt-10) cc_final: 0.7122 (mt-10) REVERT: K 164 LEU cc_start: 0.7717 (mt) cc_final: 0.7424 (mt) REVERT: K 220 VAL cc_start: 0.5870 (OUTLIER) cc_final: 0.5624 (t) REVERT: X 35 LEU cc_start: 0.8484 (pt) cc_final: 0.8070 (pp) REVERT: Y 13 LEU cc_start: 0.8212 (mm) cc_final: 0.7921 (mm) REVERT: Y 25 PHE cc_start: 0.7999 (t80) cc_final: 0.7507 (t80) outliers start: 12 outliers final: 7 residues processed: 1513 average time/residue: 0.4753 time to fit residues: 1060.9445 Evaluate side-chains 1135 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1126 time to evaluate : 3.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 116 ARG Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 119 LYS Chi-restraints excluded: chain I residue 220 VAL Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 220 VAL Chi-restraints excluded: chain K residue 220 VAL Chi-restraints excluded: chain K residue 224 LEU Chi-restraints excluded: chain Y residue 158 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 270 optimal weight: 3.9990 chunk 242 optimal weight: 1.9990 chunk 134 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 163 optimal weight: 0.9990 chunk 129 optimal weight: 0.7980 chunk 250 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 152 optimal weight: 3.9990 chunk 186 optimal weight: 5.9990 chunk 290 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 GLN ** D 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 43 HIS f 577 GLN G 38 GLN G 98 GLN ** H 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 206 ASN J 38 GLN J 80 GLN K 38 GLN X 34 HIS X 57 HIS X 94 HIS Y 137 GLN Y 165 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 28609 Z= 0.240 Angle : 0.674 9.562 38797 Z= 0.366 Chirality : 0.044 0.233 4282 Planarity : 0.006 0.131 4690 Dihedral : 16.008 151.296 4713 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 4.17 % Allowed : 16.64 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.15), residues: 3239 helix: 0.78 (0.12), residues: 1832 sheet: 2.47 (0.31), residues: 253 loop : 0.00 (0.18), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP Y 114 HIS 0.010 0.001 HIS X 57 PHE 0.024 0.002 PHE X 158 TYR 0.015 0.001 TYR K 93 ARG 0.008 0.001 ARG C 85 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1294 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 1175 time to evaluate : 2.661 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: A 247 ILE cc_start: 0.7098 (mm) cc_final: 0.6508 (mm) REVERT: B 73 TYR cc_start: 0.8822 (t80) cc_final: 0.8519 (t80) REVERT: B 110 THR cc_start: 0.8570 (m) cc_final: 0.8365 (m) REVERT: B 275 TYR cc_start: 0.6702 (m-80) cc_final: 0.6227 (m-80) REVERT: C 112 TYR cc_start: 0.8971 (t80) cc_final: 0.8642 (t80) REVERT: C 125 PHE cc_start: 0.8820 (m-10) cc_final: 0.8406 (m-80) REVERT: C 129 THR cc_start: 0.8491 (OUTLIER) cc_final: 0.7976 (p) REVERT: C 136 CYS cc_start: 0.6795 (t) cc_final: 0.6424 (t) REVERT: C 144 ASP cc_start: 0.8216 (t0) cc_final: 0.7932 (m-30) REVERT: C 204 PHE cc_start: 0.6606 (t80) cc_final: 0.6247 (t80) REVERT: c 575 TYR cc_start: 0.8042 (t80) cc_final: 0.7632 (t80) REVERT: D 25 ILE cc_start: 0.7416 (mm) cc_final: 0.7044 (mm) REVERT: D 89 VAL cc_start: 0.8759 (t) cc_final: 0.8410 (m) REVERT: D 164 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8451 (mp) REVERT: D 177 ASP cc_start: 0.8003 (m-30) cc_final: 0.7724 (m-30) REVERT: D 186 VAL cc_start: 0.9355 (m) cc_final: 0.9048 (p) REVERT: D 213 GLN cc_start: 0.6606 (tm-30) cc_final: 0.6360 (tp40) REVERT: d 570 ILE cc_start: 0.7944 (mm) cc_final: 0.7660 (mm) REVERT: E 89 VAL cc_start: 0.7922 (t) cc_final: 0.7579 (m) REVERT: E 92 VAL cc_start: 0.9120 (m) cc_final: 0.8868 (p) REVERT: E 163 ASP cc_start: 0.6411 (t70) cc_final: 0.5999 (t0) REVERT: E 264 ASP cc_start: 0.5095 (p0) cc_final: 0.4659 (p0) REVERT: F 34 VAL cc_start: 0.8233 (t) cc_final: 0.8000 (m) REVERT: F 88 THR cc_start: 0.8030 (m) cc_final: 0.7564 (t) REVERT: F 140 MET cc_start: 0.6788 (OUTLIER) cc_final: 0.6485 (ttp) REVERT: F 144 ASP cc_start: 0.8217 (t70) cc_final: 0.7658 (t70) REVERT: F 145 GLU cc_start: 0.7154 (mt-10) cc_final: 0.6903 (mt-10) REVERT: F 234 THR cc_start: 0.8651 (m) cc_final: 0.8442 (m) REVERT: G 73 TYR cc_start: 0.8617 (t80) cc_final: 0.8293 (t80) REVERT: G 113 LEU cc_start: 0.8818 (mt) cc_final: 0.8609 (mp) REVERT: G 180 ILE cc_start: 0.8840 (mt) cc_final: 0.8636 (mm) REVERT: G 224 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8216 (mt) REVERT: G 268 LEU cc_start: 0.8934 (tp) cc_final: 0.8512 (tt) REVERT: H 62 SER cc_start: 0.7239 (p) cc_final: 0.6989 (p) REVERT: H 89 VAL cc_start: 0.8520 (t) cc_final: 0.8280 (m) REVERT: H 110 THR cc_start: 0.8799 (m) cc_final: 0.8512 (p) REVERT: H 163 ASP cc_start: 0.7194 (t70) cc_final: 0.6972 (t0) REVERT: H 208 VAL cc_start: 0.8122 (t) cc_final: 0.7779 (t) REVERT: H 247 ILE cc_start: 0.8610 (mm) cc_final: 0.8350 (mm) REVERT: I 64 THR cc_start: 0.8250 (p) cc_final: 0.8016 (p) REVERT: I 108 LYS cc_start: 0.8548 (mmmt) cc_final: 0.8289 (mmmm) REVERT: I 231 ARG cc_start: 0.7806 (ttm170) cc_final: 0.7592 (ttm-80) REVERT: I 245 ASP cc_start: 0.7893 (t70) cc_final: 0.7644 (t0) REVERT: J 28 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7870 (mm) REVERT: J 29 LYS cc_start: 0.8164 (ttpt) cc_final: 0.7883 (ttpp) REVERT: J 49 LYS cc_start: 0.8619 (mmmt) cc_final: 0.8410 (mmtm) REVERT: J 93 TYR cc_start: 0.8172 (t80) cc_final: 0.7794 (t80) REVERT: J 144 ASP cc_start: 0.7895 (t0) cc_final: 0.7248 (m-30) REVERT: J 209 GLU cc_start: 0.6779 (tt0) cc_final: 0.6551 (tt0) REVERT: J 234 THR cc_start: 0.8661 (t) cc_final: 0.8440 (m) REVERT: J 274 GLU cc_start: 0.6966 (mt-10) cc_final: 0.6658 (mt-10) REVERT: J 275 TYR cc_start: 0.7310 (m-80) cc_final: 0.7042 (m-80) REVERT: K 114 LYS cc_start: 0.8122 (mttm) cc_final: 0.7860 (tttm) REVERT: K 174 ASP cc_start: 0.7260 (m-30) cc_final: 0.6950 (m-30) REVERT: K 269 GLN cc_start: 0.8325 (tp40) cc_final: 0.7848 (tp40) REVERT: X 35 LEU cc_start: 0.8473 (pt) cc_final: 0.8113 (pp) REVERT: Y 22 LEU cc_start: 0.8182 (tt) cc_final: 0.7945 (tp) REVERT: Y 64 GLN cc_start: 0.7775 (mm-40) cc_final: 0.7327 (mm110) outliers start: 119 outliers final: 75 residues processed: 1211 average time/residue: 0.4052 time to fit residues: 747.1638 Evaluate side-chains 1154 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 1074 time to evaluate : 3.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 TRP Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 227 LYS Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain a residue 572 VAL Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain D residue 49 LYS Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 182 ARG Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain d residue 581 GLU Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 100 CYS Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 136 CYS Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 174 ASP Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain f residue 573 TRP Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain G residue 163 ASP Chi-restraints excluded: chain G residue 211 TRP Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 235 SER Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 263 ILE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 119 LYS Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 136 CYS Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain H residue 226 SER Chi-restraints excluded: chain H residue 255 SER Chi-restraints excluded: chain I residue 124 ASP Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 100 CYS Chi-restraints excluded: chain J residue 207 THR Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 255 SER Chi-restraints excluded: chain K residue 20 TRP Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 124 ASP Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain K residue 200 SER Chi-restraints excluded: chain K residue 213 GLN Chi-restraints excluded: chain X residue 36 SER Chi-restraints excluded: chain Y residue 36 SER Chi-restraints excluded: chain Y residue 154 CYS Chi-restraints excluded: chain Y residue 158 PHE Chi-restraints excluded: chain Y residue 161 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 161 optimal weight: 0.0870 chunk 90 optimal weight: 3.9990 chunk 241 optimal weight: 0.0570 chunk 197 optimal weight: 0.0270 chunk 80 optimal weight: 0.9990 chunk 291 optimal weight: 0.0870 chunk 314 optimal weight: 5.9990 chunk 259 optimal weight: 0.9990 chunk 288 optimal weight: 7.9990 chunk 99 optimal weight: 4.9990 chunk 233 optimal weight: 0.9980 overall best weight: 0.2512 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN ** E 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 43 HIS F 185 GLN f 577 GLN G 38 GLN ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 213 GLN J 38 GLN K 38 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.4520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 28609 Z= 0.162 Angle : 0.596 8.324 38797 Z= 0.315 Chirality : 0.042 0.381 4282 Planarity : 0.004 0.064 4690 Dihedral : 15.803 151.307 4703 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.36 % Allowed : 20.74 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.15), residues: 3239 helix: 1.18 (0.12), residues: 1788 sheet: 2.27 (0.30), residues: 253 loop : 0.00 (0.18), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP Y 114 HIS 0.005 0.001 HIS K 43 PHE 0.022 0.001 PHE X 158 TYR 0.017 0.001 TYR K 93 ARG 0.009 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1212 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 1116 time to evaluate : 3.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 ASP cc_start: 0.6753 (t0) cc_final: 0.6527 (t0) REVERT: A 189 ARG cc_start: 0.7410 (mpt180) cc_final: 0.7206 (mpt180) REVERT: A 246 GLU cc_start: 0.6004 (tp30) cc_final: 0.5744 (tm-30) REVERT: B 73 TYR cc_start: 0.8782 (t80) cc_final: 0.8523 (t80) REVERT: C 129 THR cc_start: 0.8390 (OUTLIER) cc_final: 0.8185 (m) REVERT: C 136 CYS cc_start: 0.6694 (t) cc_final: 0.6328 (t) REVERT: C 144 ASP cc_start: 0.8187 (t0) cc_final: 0.7890 (m-30) REVERT: C 173 THR cc_start: 0.8553 (OUTLIER) cc_final: 0.8337 (p) REVERT: c 575 TYR cc_start: 0.8033 (t80) cc_final: 0.7778 (t80) REVERT: D 25 ILE cc_start: 0.7316 (mm) cc_final: 0.6930 (mm) REVERT: D 89 VAL cc_start: 0.8743 (t) cc_final: 0.8448 (m) REVERT: D 164 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8440 (mp) REVERT: D 186 VAL cc_start: 0.9268 (m) cc_final: 0.8939 (p) REVERT: D 230 LEU cc_start: 0.8274 (tp) cc_final: 0.8020 (tp) REVERT: E 89 VAL cc_start: 0.7966 (t) cc_final: 0.7625 (m) REVERT: E 92 VAL cc_start: 0.9169 (m) cc_final: 0.8945 (p) REVERT: E 147 ASP cc_start: 0.8436 (p0) cc_final: 0.8213 (p0) REVERT: E 163 ASP cc_start: 0.6334 (t70) cc_final: 0.5921 (t0) REVERT: E 264 ASP cc_start: 0.5127 (p0) cc_final: 0.4703 (p0) REVERT: e 579 ARG cc_start: 0.8401 (ttm110) cc_final: 0.8152 (ttm110) REVERT: F 66 LYS cc_start: 0.8521 (mtmm) cc_final: 0.8115 (mtpp) REVERT: F 88 THR cc_start: 0.8034 (m) cc_final: 0.7545 (t) REVERT: F 111 GLU cc_start: 0.7214 (mt-10) cc_final: 0.6956 (mt-10) REVERT: F 144 ASP cc_start: 0.8248 (t70) cc_final: 0.7589 (t70) REVERT: F 180 ILE cc_start: 0.8409 (tp) cc_final: 0.8149 (tp) REVERT: F 240 TYR cc_start: 0.7531 (m-80) cc_final: 0.7234 (m-10) REVERT: G 73 TYR cc_start: 0.8549 (t80) cc_final: 0.8200 (t80) REVERT: G 92 VAL cc_start: 0.8624 (t) cc_final: 0.8281 (p) REVERT: G 113 LEU cc_start: 0.8774 (mt) cc_final: 0.8569 (mp) REVERT: H 41 THR cc_start: 0.8644 (m) cc_final: 0.8426 (t) REVERT: H 89 VAL cc_start: 0.8484 (t) cc_final: 0.8257 (m) REVERT: H 110 THR cc_start: 0.8589 (m) cc_final: 0.8364 (p) REVERT: H 188 GLU cc_start: 0.7930 (mp0) cc_final: 0.7595 (mp0) REVERT: H 247 ILE cc_start: 0.8686 (mm) cc_final: 0.8447 (mm) REVERT: I 42 LEU cc_start: 0.8861 (tp) cc_final: 0.8621 (tp) REVERT: I 46 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8464 (mp) REVERT: I 64 THR cc_start: 0.8144 (p) cc_final: 0.7898 (p) REVERT: I 128 ARG cc_start: 0.8232 (ttm170) cc_final: 0.7855 (mtp180) REVERT: I 214 MET cc_start: 0.7053 (mtp) cc_final: 0.6801 (mtp) REVERT: I 245 ASP cc_start: 0.7772 (t70) cc_final: 0.7467 (t0) REVERT: I 269 GLN cc_start: 0.7983 (mt0) cc_final: 0.7711 (mt0) REVERT: J 28 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7892 (mm) REVERT: J 49 LYS cc_start: 0.8578 (mmmt) cc_final: 0.8372 (mmtm) REVERT: J 91 VAL cc_start: 0.8695 (t) cc_final: 0.8390 (p) REVERT: J 111 GLU cc_start: 0.7271 (mt-10) cc_final: 0.6901 (mt-10) REVERT: J 234 THR cc_start: 0.8569 (t) cc_final: 0.8099 (p) REVERT: j 576 GLU cc_start: 0.6869 (mm-30) cc_final: 0.5853 (mm-30) REVERT: K 114 LYS cc_start: 0.8104 (mttm) cc_final: 0.7903 (tttm) REVERT: K 269 GLN cc_start: 0.8309 (tp40) cc_final: 0.7857 (tp-100) REVERT: Y 22 LEU cc_start: 0.8099 (tt) cc_final: 0.7718 (tp) REVERT: Y 25 PHE cc_start: 0.7646 (t80) cc_final: 0.7151 (t80) REVERT: Y 64 GLN cc_start: 0.7357 (mm-40) cc_final: 0.6999 (mm-40) REVERT: Y 80 ARG cc_start: 0.7359 (tpt170) cc_final: 0.7069 (tpt90) outliers start: 96 outliers final: 59 residues processed: 1147 average time/residue: 0.3987 time to fit residues: 703.0062 Evaluate side-chains 1129 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 1065 time to evaluate : 3.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 TRP Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 227 LYS Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain a residue 572 VAL Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 262 LYS Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain D residue 49 LYS Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 182 ARG Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 174 ASP Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 174 ASP Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain G residue 199 LEU Chi-restraints excluded: chain G residue 211 TRP Chi-restraints excluded: chain G residue 223 ASN Chi-restraints excluded: chain G residue 235 SER Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain G residue 263 ILE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 119 LYS Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 136 CYS Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain H residue 255 SER Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 81 GLN Chi-restraints excluded: chain I residue 213 GLN Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain K residue 20 TRP Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 124 ASP Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain K residue 180 ILE Chi-restraints excluded: chain K residue 200 SER Chi-restraints excluded: chain K residue 213 GLN Chi-restraints excluded: chain X residue 7 VAL Chi-restraints excluded: chain X residue 36 SER Chi-restraints excluded: chain Y residue 36 SER Chi-restraints excluded: chain Y residue 154 CYS Chi-restraints excluded: chain Y residue 158 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 287 optimal weight: 5.9990 chunk 218 optimal weight: 0.5980 chunk 151 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 195 optimal weight: 2.9990 chunk 292 optimal weight: 10.0000 chunk 309 optimal weight: 3.9990 chunk 152 optimal weight: 0.5980 chunk 276 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 GLN D 81 GLN E 98 GLN E 213 GLN f 577 GLN ** G 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 223 ASN K 38 GLN X 126 GLN Y 83 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.5202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 28609 Z= 0.260 Angle : 0.622 9.634 38797 Z= 0.330 Chirality : 0.043 0.203 4282 Planarity : 0.004 0.042 4690 Dihedral : 15.740 151.122 4702 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 5.78 % Allowed : 21.02 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.15), residues: 3239 helix: 1.21 (0.13), residues: 1792 sheet: 2.16 (0.29), residues: 253 loop : -0.23 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP F 20 HIS 0.009 0.001 HIS Y 125 PHE 0.022 0.001 PHE X 158 TYR 0.018 0.002 TYR J 93 ARG 0.007 0.001 ARG H 191 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1298 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 1133 time to evaluate : 3.417 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: A 82 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7493 (mm-30) REVERT: A 159 ASP cc_start: 0.6810 (t0) cc_final: 0.6468 (t0) REVERT: A 163 ASP cc_start: 0.7394 (m-30) cc_final: 0.7027 (m-30) REVERT: A 180 ILE cc_start: 0.8512 (mm) cc_final: 0.8310 (mm) REVERT: A 246 GLU cc_start: 0.6118 (tp30) cc_final: 0.5911 (tm-30) REVERT: B 264 ASP cc_start: 0.6281 (OUTLIER) cc_final: 0.6006 (p0) REVERT: C 125 PHE cc_start: 0.8886 (m-80) cc_final: 0.8592 (m-80) REVERT: C 129 THR cc_start: 0.8584 (OUTLIER) cc_final: 0.8338 (m) REVERT: C 136 CYS cc_start: 0.6927 (t) cc_final: 0.6425 (t) REVERT: C 144 ASP cc_start: 0.8300 (t0) cc_final: 0.7961 (m-30) REVERT: c 575 TYR cc_start: 0.8111 (t80) cc_final: 0.7864 (t80) REVERT: D 25 ILE cc_start: 0.7477 (mm) cc_final: 0.7105 (mm) REVERT: D 89 VAL cc_start: 0.8884 (t) cc_final: 0.8553 (m) REVERT: D 164 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8604 (mp) REVERT: D 186 VAL cc_start: 0.9327 (m) cc_final: 0.8975 (p) REVERT: D 235 SER cc_start: 0.8862 (t) cc_final: 0.8386 (p) REVERT: E 46 LEU cc_start: 0.8668 (mt) cc_final: 0.8157 (mp) REVERT: E 89 VAL cc_start: 0.8540 (t) cc_final: 0.8190 (m) REVERT: E 163 ASP cc_start: 0.7023 (t70) cc_final: 0.6605 (t0) REVERT: E 177 ASP cc_start: 0.7549 (m-30) cc_final: 0.7093 (m-30) REVERT: E 264 ASP cc_start: 0.5796 (p0) cc_final: 0.5285 (p0) REVERT: F 66 LYS cc_start: 0.8694 (mtmm) cc_final: 0.7917 (mtmm) REVERT: F 88 THR cc_start: 0.8189 (m) cc_final: 0.7828 (t) REVERT: F 92 VAL cc_start: 0.7947 (t) cc_final: 0.7176 (m) REVERT: F 140 MET cc_start: 0.7270 (OUTLIER) cc_final: 0.7016 (ttp) REVERT: F 144 ASP cc_start: 0.8307 (t70) cc_final: 0.8092 (t0) REVERT: F 180 ILE cc_start: 0.8547 (tp) cc_final: 0.8205 (tp) REVERT: F 220 VAL cc_start: 0.6575 (p) cc_final: 0.5273 (t) REVERT: G 38 GLN cc_start: 0.7952 (mm-40) cc_final: 0.7686 (mt0) REVERT: G 73 TYR cc_start: 0.8755 (t80) cc_final: 0.8432 (t80) REVERT: G 92 VAL cc_start: 0.8809 (t) cc_final: 0.8571 (p) REVERT: G 129 THR cc_start: 0.8544 (m) cc_final: 0.8298 (p) REVERT: G 205 LYS cc_start: 0.8077 (tttt) cc_final: 0.7814 (ttpt) REVERT: G 247 ILE cc_start: 0.9030 (mm) cc_final: 0.8825 (mm) REVERT: H 41 THR cc_start: 0.8711 (m) cc_final: 0.8472 (t) REVERT: H 89 VAL cc_start: 0.8578 (t) cc_final: 0.8370 (m) REVERT: H 110 THR cc_start: 0.8709 (m) cc_final: 0.8501 (p) REVERT: H 188 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7482 (mp0) REVERT: I 42 LEU cc_start: 0.8926 (tp) cc_final: 0.8702 (tp) REVERT: I 46 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8528 (mp) REVERT: I 53 ARG cc_start: 0.7708 (mmt-90) cc_final: 0.7490 (mmt180) REVERT: I 64 THR cc_start: 0.8242 (p) cc_final: 0.7997 (p) REVERT: I 108 LYS cc_start: 0.8704 (mmmt) cc_final: 0.8417 (mmmm) REVERT: I 128 ARG cc_start: 0.8283 (ttm170) cc_final: 0.7950 (mtm180) REVERT: I 213 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7575 (mt0) REVERT: I 245 ASP cc_start: 0.7864 (t70) cc_final: 0.7527 (t0) REVERT: I 269 GLN cc_start: 0.8172 (mt0) cc_final: 0.7827 (mt0) REVERT: J 28 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8002 (mm) REVERT: J 29 LYS cc_start: 0.7860 (ttmm) cc_final: 0.7641 (ttmm) REVERT: J 40 LYS cc_start: 0.8390 (ttmm) cc_final: 0.8093 (mttp) REVERT: J 91 VAL cc_start: 0.8765 (t) cc_final: 0.8521 (p) REVERT: J 111 GLU cc_start: 0.7266 (mt-10) cc_final: 0.6994 (mt-10) REVERT: J 144 ASP cc_start: 0.7917 (t0) cc_final: 0.7469 (m-30) REVERT: K 123 SER cc_start: 0.7022 (p) cc_final: 0.6740 (t) REVERT: K 269 GLN cc_start: 0.8510 (tp40) cc_final: 0.7940 (tp-100) REVERT: X 35 LEU cc_start: 0.8621 (pt) cc_final: 0.8228 (pp) REVERT: Y 11 LEU cc_start: 0.8681 (mp) cc_final: 0.8321 (mt) REVERT: Y 25 PHE cc_start: 0.7686 (t80) cc_final: 0.7191 (t80) REVERT: Y 64 GLN cc_start: 0.7926 (mm-40) cc_final: 0.7409 (mm110) outliers start: 165 outliers final: 104 residues processed: 1190 average time/residue: 0.4219 time to fit residues: 784.4720 Evaluate side-chains 1189 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 1077 time to evaluate : 3.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 TRP Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 227 LYS Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain a residue 572 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 262 LYS Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain b residue 572 VAL Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 182 ARG Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain d residue 574 ASP Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 174 ASP Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain E residue 255 SER Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 71 ASP Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 174 ASP Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain G residue 166 ILE Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 223 ASN Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 136 CYS Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain H residue 223 ASN Chi-restraints excluded: chain H residue 255 SER Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 104 ASP Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain I residue 213 GLN Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 100 CYS Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain J residue 174 ASP Chi-restraints excluded: chain J residue 207 THR Chi-restraints excluded: chain J residue 225 LYS Chi-restraints excluded: chain J residue 235 SER Chi-restraints excluded: chain j residue 578 LEU Chi-restraints excluded: chain K residue 38 GLN Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 166 ILE Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain K residue 180 ILE Chi-restraints excluded: chain K residue 200 SER Chi-restraints excluded: chain K residue 213 GLN Chi-restraints excluded: chain K residue 226 SER Chi-restraints excluded: chain K residue 246 GLU Chi-restraints excluded: chain X residue 7 VAL Chi-restraints excluded: chain X residue 36 SER Chi-restraints excluded: chain Y residue 14 ILE Chi-restraints excluded: chain Y residue 36 SER Chi-restraints excluded: chain Y residue 154 CYS Chi-restraints excluded: chain Y residue 158 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 257 optimal weight: 5.9990 chunk 175 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 230 optimal weight: 3.9990 chunk 127 optimal weight: 0.7980 chunk 263 optimal weight: 4.9990 chunk 213 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 157 optimal weight: 3.9990 chunk 277 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 ASN C 38 GLN C 98 GLN D 81 GLN D 213 GLN F 185 GLN ** H 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 213 GLN I 223 ASN J 38 GLN K 38 GLN X 125 HIS Y 83 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.5978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 28609 Z= 0.377 Angle : 0.690 9.870 38797 Z= 0.371 Chirality : 0.045 0.174 4282 Planarity : 0.005 0.054 4690 Dihedral : 15.761 149.690 4698 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 6.65 % Allowed : 22.77 % Favored : 70.58 % 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: 0.52 (0.15), residues: 3239 helix: 0.76 (0.12), residues: 1820 sheet: 2.03 (0.28), residues: 253 loop : -0.59 (0.18), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP Y 120 HIS 0.014 0.002 HIS Y 125 PHE 0.022 0.002 PHE X 158 TYR 0.018 0.002 TYR A 73 ARG 0.011 0.001 ARG C 85 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1322 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 1132 time to evaluate : 3.325 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: A 254 ARG cc_start: 0.6199 (mmm-85) cc_final: 0.5818 (mmm-85) REVERT: C 129 THR cc_start: 0.8698 (OUTLIER) cc_final: 0.8464 (m) REVERT: C 136 CYS cc_start: 0.6985 (t) cc_final: 0.6660 (t) REVERT: C 144 ASP cc_start: 0.8490 (t0) cc_final: 0.8049 (m-30) REVERT: C 275 TYR cc_start: 0.8489 (m-80) cc_final: 0.8156 (m-80) REVERT: D 25 ILE cc_start: 0.7813 (mm) cc_final: 0.7449 (mm) REVERT: D 61 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7522 (mt-10) REVERT: D 89 VAL cc_start: 0.8863 (t) cc_final: 0.8512 (m) REVERT: D 186 VAL cc_start: 0.9362 (m) cc_final: 0.9128 (p) REVERT: D 214 MET cc_start: 0.6453 (mmm) cc_final: 0.6250 (mmm) REVERT: D 230 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8200 (tp) REVERT: E 46 LEU cc_start: 0.8731 (mt) cc_final: 0.8301 (mp) REVERT: E 89 VAL cc_start: 0.8662 (t) cc_final: 0.8367 (m) REVERT: E 117 VAL cc_start: 0.7621 (t) cc_final: 0.7266 (m) REVERT: E 163 ASP cc_start: 0.7385 (t70) cc_final: 0.7106 (t70) REVERT: E 177 ASP cc_start: 0.7803 (m-30) cc_final: 0.7310 (m-30) REVERT: E 183 ASP cc_start: 0.7394 (t0) cc_final: 0.7130 (t0) REVERT: E 186 VAL cc_start: 0.9215 (m) cc_final: 0.8896 (p) REVERT: E 234 THR cc_start: 0.8371 (m) cc_final: 0.8164 (t) REVERT: F 66 LYS cc_start: 0.8587 (mtmm) cc_final: 0.7989 (mtmm) REVERT: F 88 THR cc_start: 0.8140 (m) cc_final: 0.7865 (t) REVERT: F 140 MET cc_start: 0.7614 (OUTLIER) cc_final: 0.7314 (ttp) REVERT: F 144 ASP cc_start: 0.8147 (t70) cc_final: 0.7924 (t70) REVERT: F 180 ILE cc_start: 0.8911 (tp) cc_final: 0.8681 (tp) REVERT: F 215 VAL cc_start: 0.5935 (t) cc_final: 0.5637 (p) REVERT: f 579 ARG cc_start: 0.5915 (ttm170) cc_final: 0.5703 (ttm-80) REVERT: G 54 LYS cc_start: 0.8522 (mtmt) cc_final: 0.8280 (mttt) REVERT: G 92 VAL cc_start: 0.8919 (t) cc_final: 0.8701 (p) REVERT: G 108 LYS cc_start: 0.8570 (ttmm) cc_final: 0.8322 (tttm) REVERT: G 224 LEU cc_start: 0.8931 (mp) cc_final: 0.8688 (mt) REVERT: H 89 VAL cc_start: 0.8753 (t) cc_final: 0.8515 (m) REVERT: H 110 THR cc_start: 0.8760 (m) cc_final: 0.8533 (p) REVERT: H 144 ASP cc_start: 0.8376 (OUTLIER) cc_final: 0.8129 (t70) REVERT: H 184 GLU cc_start: 0.7418 (mp0) cc_final: 0.6819 (mp0) REVERT: H 188 GLU cc_start: 0.8185 (mp0) cc_final: 0.7495 (mp0) REVERT: I 42 LEU cc_start: 0.9009 (tp) cc_final: 0.8773 (tp) REVERT: I 46 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8661 (mp) REVERT: I 64 THR cc_start: 0.8370 (p) cc_final: 0.8168 (p) REVERT: I 93 TYR cc_start: 0.8852 (t80) cc_final: 0.8497 (t80) REVERT: I 128 ARG cc_start: 0.8307 (ttm170) cc_final: 0.7993 (mtm180) REVERT: I 268 LEU cc_start: 0.9109 (tp) cc_final: 0.8822 (tp) REVERT: J 28 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8186 (mm) REVERT: J 91 VAL cc_start: 0.8974 (t) cc_final: 0.8699 (p) REVERT: J 94 ILE cc_start: 0.8780 (mm) cc_final: 0.8563 (mm) REVERT: K 273 LYS cc_start: 0.8264 (ttpt) cc_final: 0.8061 (ttpt) REVERT: X 156 MET cc_start: 0.5069 (mtm) cc_final: 0.4852 (mtm) REVERT: Y 64 GLN cc_start: 0.7806 (mm-40) cc_final: 0.7388 (mm110) REVERT: Y 83 GLN cc_start: 0.7357 (OUTLIER) cc_final: 0.7155 (pt0) outliers start: 190 outliers final: 134 residues processed: 1201 average time/residue: 0.4046 time to fit residues: 748.2972 Evaluate side-chains 1226 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 1085 time to evaluate : 3.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 TRP Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain a residue 572 VAL Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain b residue 572 VAL Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 182 ARG Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain d residue 574 ASP Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 174 ASP Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 174 ASP Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 100 CYS Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 166 ILE Chi-restraints excluded: chain G residue 202 GLU Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 221 SER Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 223 ASN Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 136 CYS Chi-restraints excluded: chain H residue 144 ASP Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain H residue 223 ASN Chi-restraints excluded: chain H residue 226 SER Chi-restraints excluded: chain H residue 255 SER Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 54 LYS Chi-restraints excluded: chain I residue 56 CYS Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 104 ASP Chi-restraints excluded: chain I residue 124 ASP Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain I residue 136 CYS Chi-restraints excluded: chain I residue 184 GLU Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 31 LYS Chi-restraints excluded: chain J residue 38 GLN Chi-restraints excluded: chain J residue 100 CYS Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain J residue 207 THR Chi-restraints excluded: chain J residue 220 VAL Chi-restraints excluded: chain J residue 225 LYS Chi-restraints excluded: chain J residue 246 GLU Chi-restraints excluded: chain J residue 247 ILE Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain j residue 578 LEU Chi-restraints excluded: chain K residue 56 CYS Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 94 ILE Chi-restraints excluded: chain K residue 117 VAL Chi-restraints excluded: chain K residue 140 MET Chi-restraints excluded: chain K residue 163 ASP Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain K residue 180 ILE Chi-restraints excluded: chain K residue 203 ASP Chi-restraints excluded: chain K residue 213 GLN Chi-restraints excluded: chain K residue 226 SER Chi-restraints excluded: chain K residue 233 LEU Chi-restraints excluded: chain K residue 246 GLU Chi-restraints excluded: chain X residue 7 VAL Chi-restraints excluded: chain Y residue 74 VAL Chi-restraints excluded: chain Y residue 83 GLN Chi-restraints excluded: chain Y residue 154 CYS Chi-restraints excluded: chain Y residue 158 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 104 optimal weight: 0.9980 chunk 278 optimal weight: 0.2980 chunk 61 optimal weight: 2.9990 chunk 181 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 309 optimal weight: 4.9990 chunk 257 optimal weight: 0.4980 chunk 143 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 102 optimal weight: 0.5980 chunk 162 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 269 GLN C 38 GLN C 98 GLN D 81 GLN ** H 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 213 GLN I 269 GLN Y 64 GLN Y 83 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.6182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28609 Z= 0.181 Angle : 0.600 9.790 38797 Z= 0.315 Chirality : 0.042 0.182 4282 Planarity : 0.004 0.066 4690 Dihedral : 15.470 148.975 4698 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.27 % Allowed : 26.80 % Favored : 68.93 % 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: 0.79 (0.15), residues: 3239 helix: 0.98 (0.12), residues: 1820 sheet: 2.14 (0.28), residues: 253 loop : -0.49 (0.19), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP Y 120 HIS 0.005 0.001 HIS Y 125 PHE 0.026 0.001 PHE X 158 TYR 0.021 0.001 TYR G 115 ARG 0.012 0.000 ARG C 85 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1234 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 1112 time to evaluate : 3.315 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: A 247 ILE cc_start: 0.6994 (mm) cc_final: 0.6616 (mm) REVERT: B 42 LEU cc_start: 0.8203 (tp) cc_final: 0.7882 (tt) REVERT: B 110 THR cc_start: 0.8622 (m) cc_final: 0.8421 (m) REVERT: C 129 THR cc_start: 0.8538 (OUTLIER) cc_final: 0.8291 (m) REVERT: C 136 CYS cc_start: 0.6849 (t) cc_final: 0.6598 (t) REVERT: C 144 ASP cc_start: 0.8352 (t0) cc_final: 0.8019 (m-30) REVERT: C 275 TYR cc_start: 0.8389 (m-80) cc_final: 0.7975 (m-80) REVERT: D 25 ILE cc_start: 0.7607 (mm) cc_final: 0.7218 (mm) REVERT: D 89 VAL cc_start: 0.8750 (t) cc_final: 0.8453 (m) REVERT: D 111 GLU cc_start: 0.7483 (mt-10) cc_final: 0.7194 (mt-10) REVERT: D 144 ASP cc_start: 0.8181 (t0) cc_final: 0.7959 (m-30) REVERT: D 186 VAL cc_start: 0.9326 (m) cc_final: 0.9073 (p) REVERT: d 582 TYR cc_start: 0.7168 (t80) cc_final: 0.6724 (t80) REVERT: E 46 LEU cc_start: 0.8705 (mt) cc_final: 0.8282 (mp) REVERT: E 87 PRO cc_start: 0.8666 (Cg_exo) cc_final: 0.8455 (Cg_endo) REVERT: E 89 VAL cc_start: 0.8701 (t) cc_final: 0.8398 (m) REVERT: E 132 VAL cc_start: 0.8873 (m) cc_final: 0.8667 (p) REVERT: E 164 LEU cc_start: 0.8408 (mt) cc_final: 0.8139 (mm) REVERT: E 177 ASP cc_start: 0.7775 (m-30) cc_final: 0.7291 (m-30) REVERT: E 183 ASP cc_start: 0.7287 (t0) cc_final: 0.6987 (t0) REVERT: E 186 VAL cc_start: 0.9158 (m) cc_final: 0.8874 (p) REVERT: E 188 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7618 (mm-30) REVERT: E 234 THR cc_start: 0.8310 (m) cc_final: 0.7954 (t) REVERT: F 88 THR cc_start: 0.8104 (m) cc_final: 0.7861 (t) REVERT: F 94 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.8315 (mt) REVERT: F 144 ASP cc_start: 0.8070 (t70) cc_final: 0.7818 (t70) REVERT: F 180 ILE cc_start: 0.8796 (tp) cc_final: 0.8573 (tp) REVERT: F 275 TYR cc_start: 0.5655 (m-80) cc_final: 0.5313 (m-80) REVERT: f 579 ARG cc_start: 0.5921 (ttm170) cc_final: 0.5684 (ttm-80) REVERT: G 73 TYR cc_start: 0.8705 (t80) cc_final: 0.8404 (t80) REVERT: G 92 VAL cc_start: 0.8889 (t) cc_final: 0.8659 (p) REVERT: G 108 LYS cc_start: 0.8592 (ttmm) cc_final: 0.8312 (tttm) REVERT: G 224 LEU cc_start: 0.8835 (mp) cc_final: 0.8635 (mt) REVERT: H 110 THR cc_start: 0.8688 (m) cc_final: 0.8454 (p) REVERT: H 188 GLU cc_start: 0.8074 (mp0) cc_final: 0.7269 (mp0) REVERT: H 191 ARG cc_start: 0.8149 (tpp80) cc_final: 0.7634 (tpp80) REVERT: I 42 LEU cc_start: 0.8972 (tp) cc_final: 0.8711 (tp) REVERT: I 46 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8511 (mp) REVERT: I 128 ARG cc_start: 0.8231 (ttm170) cc_final: 0.7924 (mtm180) REVERT: I 268 LEU cc_start: 0.9051 (tp) cc_final: 0.8765 (tp) REVERT: J 28 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.7960 (mm) REVERT: J 40 LYS cc_start: 0.8235 (ttmm) cc_final: 0.7891 (mttp) REVERT: J 91 VAL cc_start: 0.8904 (t) cc_final: 0.8672 (p) REVERT: J 94 ILE cc_start: 0.8603 (mm) cc_final: 0.8369 (mm) REVERT: J 205 LYS cc_start: 0.8405 (tptp) cc_final: 0.8166 (tptp) REVERT: J 234 THR cc_start: 0.8573 (t) cc_final: 0.8136 (p) REVERT: K 124 ASP cc_start: 0.6042 (OUTLIER) cc_final: 0.5831 (m-30) REVERT: K 202 GLU cc_start: 0.7826 (pm20) cc_final: 0.7382 (pm20) REVERT: K 269 GLN cc_start: 0.8485 (tp40) cc_final: 0.8034 (tp-100) REVERT: X 35 LEU cc_start: 0.8593 (pt) cc_final: 0.8134 (pp) REVERT: Y 55 ARG cc_start: 0.6308 (mtm110) cc_final: 0.5960 (mtm110) REVERT: Y 83 GLN cc_start: 0.7150 (OUTLIER) cc_final: 0.6734 (pt0) outliers start: 122 outliers final: 83 residues processed: 1157 average time/residue: 0.4379 time to fit residues: 790.4499 Evaluate side-chains 1183 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 1094 time to evaluate : 3.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 TRP Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain a residue 572 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 182 ARG Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 100 CYS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 124 ASP Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 174 ASP Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 174 ASP Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain f residue 578 LEU Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 221 SER Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 223 ASN Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 223 ASN Chi-restraints excluded: chain H residue 255 SER Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 184 GLU Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 31 LYS Chi-restraints excluded: chain J residue 100 CYS Chi-restraints excluded: chain J residue 173 THR Chi-restraints excluded: chain J residue 174 ASP Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 247 ILE Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain j residue 578 LEU Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 117 VAL Chi-restraints excluded: chain K residue 124 ASP Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain K residue 177 ASP Chi-restraints excluded: chain K residue 180 ILE Chi-restraints excluded: chain K residue 226 SER Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 246 GLU Chi-restraints excluded: chain X residue 14 ILE Chi-restraints excluded: chain X residue 36 SER Chi-restraints excluded: chain Y residue 14 ILE Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Y residue 83 GLN Chi-restraints excluded: chain Y residue 154 CYS Chi-restraints excluded: chain Y residue 158 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 298 optimal weight: 0.1980 chunk 34 optimal weight: 0.6980 chunk 176 optimal weight: 0.9980 chunk 226 optimal weight: 3.9990 chunk 175 optimal weight: 0.6980 chunk 260 optimal weight: 5.9990 chunk 172 optimal weight: 0.8980 chunk 308 optimal weight: 0.5980 chunk 193 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 chunk 142 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN B 38 GLN B 185 GLN B 206 ASN C 38 GLN f 577 GLN ** H 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 213 GLN I 269 GLN J 38 GLN Y 83 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.6322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 28609 Z= 0.179 Angle : 0.594 10.988 38797 Z= 0.311 Chirality : 0.041 0.172 4282 Planarity : 0.004 0.054 4690 Dihedral : 15.372 149.797 4698 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.89 % Allowed : 27.36 % Favored : 68.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.15), residues: 3239 helix: 1.04 (0.12), residues: 1842 sheet: 2.13 (0.27), residues: 253 loop : -0.41 (0.19), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP X 10 HIS 0.004 0.001 HIS Y 125 PHE 0.028 0.001 PHE X 158 TYR 0.019 0.001 TYR G 93 ARG 0.010 0.000 ARG C 85 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1229 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 1118 time to evaluate : 3.238 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: A 246 GLU cc_start: 0.4748 (tm-30) cc_final: 0.3446 (tm-30) REVERT: B 245 ASP cc_start: 0.7638 (t70) cc_final: 0.7318 (t0) REVERT: C 129 THR cc_start: 0.8549 (OUTLIER) cc_final: 0.8304 (m) REVERT: C 136 CYS cc_start: 0.6849 (t) cc_final: 0.6605 (t) REVERT: C 144 ASP cc_start: 0.8339 (t0) cc_final: 0.7986 (m-30) REVERT: C 275 TYR cc_start: 0.8349 (m-80) cc_final: 0.7905 (m-80) REVERT: D 25 ILE cc_start: 0.7520 (mm) cc_final: 0.7147 (mm) REVERT: D 53 ARG cc_start: 0.7802 (mmt-90) cc_final: 0.7488 (mmt-90) REVERT: D 89 VAL cc_start: 0.8754 (t) cc_final: 0.8442 (m) REVERT: D 93 TYR cc_start: 0.8218 (t80) cc_final: 0.7990 (t80) REVERT: D 139 GLU cc_start: 0.7304 (mm-30) cc_final: 0.6733 (mm-30) REVERT: D 144 ASP cc_start: 0.8139 (t0) cc_final: 0.7887 (m-30) REVERT: D 153 THR cc_start: 0.9054 (t) cc_final: 0.8809 (p) REVERT: D 186 VAL cc_start: 0.9323 (m) cc_final: 0.9058 (p) REVERT: D 214 MET cc_start: 0.6534 (mmm) cc_final: 0.6325 (mmm) REVERT: D 229 MET cc_start: 0.6727 (mmm) cc_final: 0.6234 (mmm) REVERT: E 89 VAL cc_start: 0.8717 (t) cc_final: 0.8425 (m) REVERT: E 177 ASP cc_start: 0.7770 (m-30) cc_final: 0.7260 (m-30) REVERT: E 186 VAL cc_start: 0.9149 (m) cc_final: 0.8863 (t) REVERT: E 188 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7622 (mm-30) REVERT: E 234 THR cc_start: 0.8208 (m) cc_final: 0.8007 (t) REVERT: F 88 THR cc_start: 0.8138 (m) cc_final: 0.7920 (t) REVERT: F 94 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8317 (mt) REVERT: F 144 ASP cc_start: 0.8067 (t70) cc_final: 0.7796 (t70) REVERT: F 148 ARG cc_start: 0.8474 (mtt180) cc_final: 0.8247 (mtp180) REVERT: F 180 ILE cc_start: 0.8832 (tp) cc_final: 0.8513 (tp) REVERT: G 73 TYR cc_start: 0.8724 (t80) cc_final: 0.8398 (t80) REVERT: G 92 VAL cc_start: 0.8854 (t) cc_final: 0.8626 (p) REVERT: G 108 LYS cc_start: 0.8576 (ttmm) cc_final: 0.8294 (tttm) REVERT: G 224 LEU cc_start: 0.8876 (mp) cc_final: 0.8612 (mt) REVERT: H 110 THR cc_start: 0.8698 (m) cc_final: 0.8465 (p) REVERT: H 188 GLU cc_start: 0.8052 (mp0) cc_final: 0.7314 (mp0) REVERT: H 191 ARG cc_start: 0.8057 (tpp80) cc_final: 0.7631 (tpp80) REVERT: I 42 LEU cc_start: 0.8972 (tp) cc_final: 0.8681 (tp) REVERT: I 46 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8520 (mp) REVERT: I 114 LYS cc_start: 0.8641 (mtpp) cc_final: 0.8440 (mtmt) REVERT: I 128 ARG cc_start: 0.8222 (ttm170) cc_final: 0.7909 (mtm180) REVERT: I 162 GLU cc_start: 0.6403 (mp0) cc_final: 0.6121 (mp0) REVERT: I 268 LEU cc_start: 0.9073 (tp) cc_final: 0.8872 (tp) REVERT: J 40 LYS cc_start: 0.8221 (ttmm) cc_final: 0.7934 (mttp) REVERT: J 91 VAL cc_start: 0.8888 (t) cc_final: 0.8651 (p) REVERT: J 234 THR cc_start: 0.8570 (t) cc_final: 0.8206 (p) REVERT: K 38 GLN cc_start: 0.6632 (tp40) cc_final: 0.6423 (tp40) REVERT: K 202 GLU cc_start: 0.7768 (pm20) cc_final: 0.7429 (pm20) REVERT: K 269 GLN cc_start: 0.8466 (tp40) cc_final: 0.7898 (tp-100) REVERT: X 35 LEU cc_start: 0.8574 (pt) cc_final: 0.8149 (pp) REVERT: Y 83 GLN cc_start: 0.7259 (OUTLIER) cc_final: 0.6847 (pt0) outliers start: 111 outliers final: 82 residues processed: 1151 average time/residue: 0.4020 time to fit residues: 710.3566 Evaluate side-chains 1170 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 1084 time to evaluate : 2.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 TRP Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain a residue 572 VAL Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain D residue 49 LYS Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 182 ARG Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 100 CYS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 124 ASP Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 174 ASP Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 174 ASP Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 221 SER Chi-restraints excluded: chain G residue 223 ASN Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 136 CYS Chi-restraints excluded: chain H residue 223 ASN Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 56 CYS Chi-restraints excluded: chain I residue 104 ASP Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain J residue 100 CYS Chi-restraints excluded: chain J residue 220 VAL Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain J residue 247 ILE Chi-restraints excluded: chain J residue 255 SER Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain j residue 578 LEU Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 117 VAL Chi-restraints excluded: chain K residue 127 ASP Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain K residue 177 ASP Chi-restraints excluded: chain K residue 180 ILE Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 246 GLU Chi-restraints excluded: chain X residue 7 VAL Chi-restraints excluded: chain X residue 14 ILE Chi-restraints excluded: chain Y residue 3 GLU Chi-restraints excluded: chain Y residue 35 LEU Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Y residue 83 GLN Chi-restraints excluded: chain Y residue 154 CYS Chi-restraints excluded: chain Y residue 158 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 190 optimal weight: 5.9990 chunk 123 optimal weight: 5.9990 chunk 184 optimal weight: 0.0670 chunk 92 optimal weight: 0.9980 chunk 60 optimal weight: 6.9990 chunk 59 optimal weight: 0.7980 chunk 196 optimal weight: 0.4980 chunk 210 optimal weight: 0.4980 chunk 152 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 chunk 242 optimal weight: 4.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 GLN B 185 GLN C 38 GLN F 43 HIS ** f 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 38 GLN X 126 GLN Y 83 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.6434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 28609 Z= 0.181 Angle : 0.607 11.935 38797 Z= 0.315 Chirality : 0.041 0.174 4282 Planarity : 0.004 0.048 4690 Dihedral : 15.305 150.076 4698 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 4.03 % Allowed : 27.46 % Favored : 68.51 % 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: 0.96 (0.15), residues: 3239 helix: 1.12 (0.13), residues: 1812 sheet: 2.13 (0.27), residues: 253 loop : -0.37 (0.19), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP Y 120 HIS 0.004 0.000 HIS Y 125 PHE 0.028 0.001 PHE X 158 TYR 0.023 0.001 TYR K 75 ARG 0.010 0.000 ARG Y 124 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1216 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 1101 time to evaluate : 3.202 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: A 111 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7170 (tm-30) REVERT: a 570 ILE cc_start: 0.7447 (mm) cc_final: 0.7164 (mm) REVERT: B 42 LEU cc_start: 0.8165 (tp) cc_final: 0.7914 (tt) REVERT: B 61 GLU cc_start: 0.7067 (OUTLIER) cc_final: 0.6582 (mp0) REVERT: B 245 ASP cc_start: 0.7612 (t70) cc_final: 0.7337 (t0) REVERT: B 250 GLU cc_start: 0.7530 (tp30) cc_final: 0.7290 (tp30) REVERT: C 129 THR cc_start: 0.8556 (OUTLIER) cc_final: 0.8294 (m) REVERT: C 136 CYS cc_start: 0.6811 (t) cc_final: 0.6570 (t) REVERT: C 144 ASP cc_start: 0.8307 (t0) cc_final: 0.7948 (m-30) REVERT: C 176 LEU cc_start: 0.8924 (tp) cc_final: 0.8724 (tt) REVERT: C 275 TYR cc_start: 0.8340 (m-80) cc_final: 0.7893 (m-80) REVERT: D 25 ILE cc_start: 0.7482 (mm) cc_final: 0.7094 (mm) REVERT: D 53 ARG cc_start: 0.7786 (mmt-90) cc_final: 0.7476 (mmt-90) REVERT: D 89 VAL cc_start: 0.8765 (t) cc_final: 0.8494 (m) REVERT: D 93 TYR cc_start: 0.8140 (t80) cc_final: 0.7891 (t80) REVERT: D 139 GLU cc_start: 0.7217 (mm-30) cc_final: 0.6750 (mm-30) REVERT: D 144 ASP cc_start: 0.8094 (t0) cc_final: 0.7860 (m-30) REVERT: D 186 VAL cc_start: 0.9314 (m) cc_final: 0.9052 (p) REVERT: D 229 MET cc_start: 0.6441 (mmm) cc_final: 0.6023 (mmm) REVERT: d 582 TYR cc_start: 0.6963 (t80) cc_final: 0.6723 (t80) REVERT: E 53 ARG cc_start: 0.8700 (mmt-90) cc_final: 0.6989 (mmt-90) REVERT: E 89 VAL cc_start: 0.8710 (t) cc_final: 0.8435 (m) REVERT: E 177 ASP cc_start: 0.7755 (m-30) cc_final: 0.7266 (m-30) REVERT: E 186 VAL cc_start: 0.9151 (m) cc_final: 0.8862 (t) REVERT: E 188 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7713 (mm-30) REVERT: E 189 ARG cc_start: 0.7132 (mpt-90) cc_final: 0.6911 (mpt-90) REVERT: E 234 THR cc_start: 0.8279 (m) cc_final: 0.7971 (t) REVERT: F 66 LYS cc_start: 0.8429 (mtmm) cc_final: 0.8160 (mtmm) REVERT: F 88 THR cc_start: 0.8165 (m) cc_final: 0.7949 (t) REVERT: F 94 ILE cc_start: 0.8527 (OUTLIER) cc_final: 0.8312 (mt) REVERT: F 144 ASP cc_start: 0.8047 (t70) cc_final: 0.7761 (t70) REVERT: F 148 ARG cc_start: 0.8469 (mtt180) cc_final: 0.8234 (mtt180) REVERT: F 180 ILE cc_start: 0.8838 (tp) cc_final: 0.8528 (tp) REVERT: G 73 TYR cc_start: 0.8735 (t80) cc_final: 0.8429 (t80) REVERT: G 92 VAL cc_start: 0.8871 (t) cc_final: 0.8635 (p) REVERT: G 108 LYS cc_start: 0.8576 (ttmm) cc_final: 0.8320 (tttm) REVERT: G 224 LEU cc_start: 0.8852 (mp) cc_final: 0.8599 (mt) REVERT: H 110 THR cc_start: 0.8683 (m) cc_final: 0.8472 (p) REVERT: H 184 GLU cc_start: 0.7289 (mp0) cc_final: 0.6558 (mp0) REVERT: H 188 GLU cc_start: 0.8032 (mp0) cc_final: 0.7364 (mp0) REVERT: I 42 LEU cc_start: 0.8951 (tp) cc_final: 0.8740 (tp) REVERT: I 46 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8560 (mp) REVERT: I 76 ARG cc_start: 0.8321 (tpp80) cc_final: 0.7840 (ttt90) REVERT: I 128 ARG cc_start: 0.8208 (ttm170) cc_final: 0.7888 (mtm180) REVERT: I 162 GLU cc_start: 0.6355 (mp0) cc_final: 0.6141 (mp0) REVERT: I 269 GLN cc_start: 0.8339 (mt0) cc_final: 0.8120 (mt0) REVERT: J 28 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.8006 (mm) REVERT: J 40 LYS cc_start: 0.8211 (ttmm) cc_final: 0.7957 (mttp) REVERT: J 91 VAL cc_start: 0.8745 (t) cc_final: 0.8495 (p) REVERT: J 234 THR cc_start: 0.8622 (t) cc_final: 0.8218 (p) REVERT: K 74 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.7576 (ptt-90) REVERT: K 269 GLN cc_start: 0.8447 (tp40) cc_final: 0.7886 (tp-100) REVERT: X 35 LEU cc_start: 0.8574 (pt) cc_final: 0.8128 (pp) REVERT: Y 11 LEU cc_start: 0.8638 (mp) cc_final: 0.8335 (mt) REVERT: Y 83 GLN cc_start: 0.7245 (OUTLIER) cc_final: 0.6925 (pt0) REVERT: Y 142 MET cc_start: 0.5323 (tpp) cc_final: 0.4664 (ttt) outliers start: 115 outliers final: 93 residues processed: 1141 average time/residue: 0.3935 time to fit residues: 694.5546 Evaluate side-chains 1182 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 1081 time to evaluate : 3.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 TRP Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain a residue 572 VAL Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain D residue 49 LYS Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 182 ARG Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 100 CYS Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 174 ASP Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 174 ASP Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain f residue 578 LEU Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 221 SER Chi-restraints excluded: chain G residue 223 ASN Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 218 LEU Chi-restraints excluded: chain H residue 223 ASN Chi-restraints excluded: chain H residue 226 SER Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 56 CYS Chi-restraints excluded: chain I residue 184 GLU Chi-restraints excluded: chain I residue 213 GLN Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 31 LYS Chi-restraints excluded: chain J residue 173 THR Chi-restraints excluded: chain J residue 220 VAL Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 247 ILE Chi-restraints excluded: chain J residue 255 SER Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 74 ARG Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 117 VAL Chi-restraints excluded: chain K residue 127 ASP Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain K residue 177 ASP Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 246 GLU Chi-restraints excluded: chain X residue 7 VAL Chi-restraints excluded: chain X residue 14 ILE Chi-restraints excluded: chain Y residue 3 GLU Chi-restraints excluded: chain Y residue 35 LEU Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Y residue 83 GLN Chi-restraints excluded: chain Y residue 154 CYS Chi-restraints excluded: chain Y residue 158 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 280 optimal weight: 0.4980 chunk 295 optimal weight: 0.2980 chunk 269 optimal weight: 0.1980 chunk 287 optimal weight: 7.9990 chunk 172 optimal weight: 0.5980 chunk 125 optimal weight: 0.6980 chunk 225 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 259 optimal weight: 0.9980 chunk 271 optimal weight: 0.6980 chunk 286 optimal weight: 7.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 GLN C 38 GLN F 43 HIS ** f 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 269 GLN K 38 GLN Y 83 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.6558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 28609 Z= 0.185 Angle : 0.629 13.024 38797 Z= 0.324 Chirality : 0.041 0.195 4282 Planarity : 0.004 0.047 4690 Dihedral : 15.223 150.360 4698 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.82 % Allowed : 28.86 % Favored : 67.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.15), residues: 3239 helix: 1.12 (0.13), residues: 1812 sheet: 2.13 (0.27), residues: 253 loop : -0.37 (0.19), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP X 10 HIS 0.003 0.000 HIS Y 125 PHE 0.029 0.001 PHE X 158 TYR 0.020 0.001 TYR G 115 ARG 0.007 0.000 ARG X 80 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1209 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 1100 time to evaluate : 3.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LEU cc_start: 0.8553 (tp) cc_final: 0.8302 (tp) REVERT: A 246 GLU cc_start: 0.5129 (tm-30) cc_final: 0.4891 (tm-30) REVERT: a 570 ILE cc_start: 0.7370 (mm) cc_final: 0.7104 (mm) REVERT: B 42 LEU cc_start: 0.8154 (tp) cc_final: 0.7862 (tt) REVERT: B 245 ASP cc_start: 0.7613 (t70) cc_final: 0.7336 (t0) REVERT: B 250 GLU cc_start: 0.7527 (tp30) cc_final: 0.7290 (tp30) REVERT: C 129 THR cc_start: 0.8547 (t) cc_final: 0.8277 (m) REVERT: C 136 CYS cc_start: 0.6743 (t) cc_final: 0.6542 (t) REVERT: C 144 ASP cc_start: 0.8274 (t0) cc_final: 0.7912 (m-30) REVERT: C 275 TYR cc_start: 0.8310 (m-80) cc_final: 0.7870 (m-80) REVERT: D 25 ILE cc_start: 0.7548 (mm) cc_final: 0.7210 (mm) REVERT: D 53 ARG cc_start: 0.7779 (mmt-90) cc_final: 0.7491 (mmt-90) REVERT: D 89 VAL cc_start: 0.8741 (t) cc_final: 0.8464 (m) REVERT: D 93 TYR cc_start: 0.8152 (t80) cc_final: 0.7920 (t80) REVERT: D 139 GLU cc_start: 0.7193 (mm-30) cc_final: 0.6733 (mm-30) REVERT: D 144 ASP cc_start: 0.8065 (t0) cc_final: 0.7832 (m-30) REVERT: D 186 VAL cc_start: 0.9314 (m) cc_final: 0.9053 (p) REVERT: D 229 MET cc_start: 0.6583 (mmm) cc_final: 0.6135 (mmm) REVERT: E 53 ARG cc_start: 0.8114 (mmt-90) cc_final: 0.7768 (mmt-90) REVERT: E 89 VAL cc_start: 0.8737 (t) cc_final: 0.8460 (m) REVERT: E 177 ASP cc_start: 0.7723 (m-30) cc_final: 0.7243 (m-30) REVERT: E 186 VAL cc_start: 0.9139 (m) cc_final: 0.8836 (t) REVERT: E 188 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7724 (mm-30) REVERT: F 66 LYS cc_start: 0.8430 (mtmm) cc_final: 0.8171 (mtmm) REVERT: F 94 ILE cc_start: 0.8521 (OUTLIER) cc_final: 0.8319 (mt) REVERT: F 148 ARG cc_start: 0.8487 (mtt180) cc_final: 0.8149 (mtt180) REVERT: F 180 ILE cc_start: 0.8857 (tp) cc_final: 0.8541 (tp) REVERT: G 73 TYR cc_start: 0.8722 (t80) cc_final: 0.8429 (t80) REVERT: G 92 VAL cc_start: 0.8861 (t) cc_final: 0.8618 (p) REVERT: G 108 LYS cc_start: 0.8567 (ttmm) cc_final: 0.8314 (tttm) REVERT: G 224 LEU cc_start: 0.8846 (mp) cc_final: 0.8598 (mt) REVERT: H 110 THR cc_start: 0.8684 (m) cc_final: 0.8469 (p) REVERT: H 184 GLU cc_start: 0.7275 (mp0) cc_final: 0.6620 (mp0) REVERT: H 188 GLU cc_start: 0.7987 (mp0) cc_final: 0.7367 (mp0) REVERT: I 42 LEU cc_start: 0.8953 (tp) cc_final: 0.8728 (tp) REVERT: I 46 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8552 (mp) REVERT: I 76 ARG cc_start: 0.8392 (tpp80) cc_final: 0.7915 (ttt90) REVERT: I 128 ARG cc_start: 0.8200 (ttm170) cc_final: 0.7897 (mtm180) REVERT: I 269 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.8171 (mt0) REVERT: J 40 LYS cc_start: 0.8216 (ttmm) cc_final: 0.7958 (mttp) REVERT: J 91 VAL cc_start: 0.8749 (t) cc_final: 0.8482 (p) REVERT: J 111 GLU cc_start: 0.7119 (mt-10) cc_final: 0.6723 (mp0) REVERT: J 156 ASP cc_start: 0.7551 (m-30) cc_final: 0.7327 (m-30) REVERT: J 205 LYS cc_start: 0.8442 (tptp) cc_final: 0.8081 (tptt) REVERT: J 234 THR cc_start: 0.8588 (t) cc_final: 0.8229 (p) REVERT: K 269 GLN cc_start: 0.8432 (tp40) cc_final: 0.7868 (tp-100) REVERT: X 35 LEU cc_start: 0.8546 (pt) cc_final: 0.8126 (pp) REVERT: Y 11 LEU cc_start: 0.8611 (mp) cc_final: 0.8353 (mt) REVERT: Y 25 PHE cc_start: 0.7604 (t80) cc_final: 0.7198 (t80) REVERT: Y 83 GLN cc_start: 0.7252 (OUTLIER) cc_final: 0.6917 (pt0) REVERT: Y 142 MET cc_start: 0.5255 (tpp) cc_final: 0.4616 (ttt) outliers start: 109 outliers final: 83 residues processed: 1135 average time/residue: 0.3981 time to fit residues: 699.2983 Evaluate side-chains 1163 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 1076 time to evaluate : 3.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain a residue 572 VAL Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain D residue 49 LYS Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain E residue 100 CYS Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 174 ASP Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 174 ASP Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain f residue 578 LEU Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 221 SER Chi-restraints excluded: chain G residue 223 ASN Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 218 LEU Chi-restraints excluded: chain H residue 223 ASN Chi-restraints excluded: chain H residue 226 SER Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 56 CYS Chi-restraints excluded: chain I residue 85 ARG Chi-restraints excluded: chain I residue 104 ASP Chi-restraints excluded: chain I residue 184 GLU Chi-restraints excluded: chain I residue 213 GLN Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain I residue 269 GLN Chi-restraints excluded: chain J residue 31 LYS Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain J residue 173 THR Chi-restraints excluded: chain J residue 220 VAL Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 232 ILE Chi-restraints excluded: chain J residue 247 ILE Chi-restraints excluded: chain J residue 255 SER Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain K residue 38 GLN Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 117 VAL Chi-restraints excluded: chain K residue 127 ASP Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain K residue 177 ASP Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 246 GLU Chi-restraints excluded: chain X residue 7 VAL Chi-restraints excluded: chain X residue 14 ILE Chi-restraints excluded: chain Y residue 3 GLU Chi-restraints excluded: chain Y residue 35 LEU Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Y residue 83 GLN Chi-restraints excluded: chain Y residue 154 CYS Chi-restraints excluded: chain Y residue 158 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 188 optimal weight: 0.7980 chunk 303 optimal weight: 0.0870 chunk 185 optimal weight: 0.7980 chunk 144 optimal weight: 2.9990 chunk 211 optimal weight: 1.9990 chunk 318 optimal weight: 1.9990 chunk 293 optimal weight: 0.9980 chunk 253 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 196 optimal weight: 4.9990 chunk 155 optimal weight: 0.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 GLN B 185 GLN C 38 GLN ** f 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 269 GLN K 38 GLN Y 83 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.6640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 28609 Z= 0.196 Angle : 0.651 15.040 38797 Z= 0.334 Chirality : 0.042 0.204 4282 Planarity : 0.004 0.069 4690 Dihedral : 15.200 150.499 4698 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.43 % Allowed : 29.60 % Favored : 66.97 % 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: 0.94 (0.15), residues: 3239 helix: 1.13 (0.13), residues: 1812 sheet: 2.14 (0.27), residues: 253 loop : -0.43 (0.19), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP Y 120 HIS 0.004 0.001 HIS Y 125 PHE 0.030 0.001 PHE X 158 TYR 0.022 0.001 TYR A 73 ARG 0.016 0.000 ARG Y 124 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1189 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 1091 time to evaluate : 2.954 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: A 42 LEU cc_start: 0.8572 (tp) cc_final: 0.8330 (tp) REVERT: a 570 ILE cc_start: 0.7379 (mm) cc_final: 0.7131 (mm) REVERT: B 42 LEU cc_start: 0.8159 (tp) cc_final: 0.7899 (tt) REVERT: B 245 ASP cc_start: 0.7624 (t70) cc_final: 0.7338 (t0) REVERT: B 250 GLU cc_start: 0.7530 (tp30) cc_final: 0.7298 (tp30) REVERT: C 129 THR cc_start: 0.8535 (OUTLIER) cc_final: 0.8280 (m) REVERT: C 136 CYS cc_start: 0.6873 (t) cc_final: 0.6671 (t) REVERT: C 144 ASP cc_start: 0.8317 (t0) cc_final: 0.7988 (m-30) REVERT: C 275 TYR cc_start: 0.8190 (m-80) cc_final: 0.7767 (m-80) REVERT: D 25 ILE cc_start: 0.7564 (mm) cc_final: 0.7217 (mm) REVERT: D 53 ARG cc_start: 0.7810 (mmt-90) cc_final: 0.7497 (mmt-90) REVERT: D 89 VAL cc_start: 0.8742 (t) cc_final: 0.8475 (m) REVERT: D 93 TYR cc_start: 0.8164 (t80) cc_final: 0.7937 (t80) REVERT: D 139 GLU cc_start: 0.7189 (mm-30) cc_final: 0.6696 (mm-30) REVERT: D 144 ASP cc_start: 0.8049 (t0) cc_final: 0.7839 (m-30) REVERT: D 186 VAL cc_start: 0.9317 (m) cc_final: 0.9042 (p) REVERT: D 229 MET cc_start: 0.6553 (mmm) cc_final: 0.6067 (mmm) REVERT: D 238 GLU cc_start: 0.7562 (mp0) cc_final: 0.7338 (mp0) REVERT: E 89 VAL cc_start: 0.8730 (t) cc_final: 0.8465 (m) REVERT: E 107 LYS cc_start: 0.8869 (tttt) cc_final: 0.8554 (tttm) REVERT: E 139 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7520 (mm-30) REVERT: E 177 ASP cc_start: 0.7747 (m-30) cc_final: 0.7258 (m-30) REVERT: E 186 VAL cc_start: 0.9140 (m) cc_final: 0.8868 (t) REVERT: E 188 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7722 (mm-30) REVERT: F 66 LYS cc_start: 0.8409 (mtmm) cc_final: 0.8176 (mtmm) REVERT: F 94 ILE cc_start: 0.8509 (OUTLIER) cc_final: 0.8303 (mt) REVERT: F 144 ASP cc_start: 0.8161 (t70) cc_final: 0.7847 (t0) REVERT: F 153 THR cc_start: 0.8884 (p) cc_final: 0.8633 (t) REVERT: F 180 ILE cc_start: 0.8888 (tp) cc_final: 0.8541 (tp) REVERT: G 73 TYR cc_start: 0.8750 (t80) cc_final: 0.8439 (t80) REVERT: G 92 VAL cc_start: 0.8893 (t) cc_final: 0.8651 (p) REVERT: G 108 LYS cc_start: 0.8570 (ttmm) cc_final: 0.8317 (tttm) REVERT: G 224 LEU cc_start: 0.8843 (mp) cc_final: 0.8605 (mt) REVERT: H 110 THR cc_start: 0.8687 (m) cc_final: 0.8476 (p) REVERT: H 122 VAL cc_start: 0.9039 (OUTLIER) cc_final: 0.8795 (t) REVERT: H 159 ASP cc_start: 0.7388 (m-30) cc_final: 0.7157 (m-30) REVERT: I 42 LEU cc_start: 0.8944 (tp) cc_final: 0.8741 (tp) REVERT: I 46 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8551 (mp) REVERT: I 76 ARG cc_start: 0.8437 (tpp80) cc_final: 0.7970 (ttt90) REVERT: I 89 VAL cc_start: 0.8624 (t) cc_final: 0.8226 (m) REVERT: I 128 ARG cc_start: 0.8197 (ttm170) cc_final: 0.7899 (mtm180) REVERT: I 269 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.8112 (mt0) REVERT: J 28 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.8005 (mm) REVERT: J 40 LYS cc_start: 0.8223 (ttmm) cc_final: 0.7962 (mttp) REVERT: J 91 VAL cc_start: 0.8720 (t) cc_final: 0.8457 (p) REVERT: J 156 ASP cc_start: 0.7523 (m-30) cc_final: 0.7302 (m-30) REVERT: J 234 THR cc_start: 0.8589 (t) cc_final: 0.8250 (p) REVERT: K 269 GLN cc_start: 0.8437 (tp40) cc_final: 0.7845 (tp-100) REVERT: X 35 LEU cc_start: 0.8557 (pt) cc_final: 0.8123 (pp) REVERT: Y 11 LEU cc_start: 0.8610 (mp) cc_final: 0.8324 (mt) REVERT: Y 25 PHE cc_start: 0.7609 (t80) cc_final: 0.7207 (t80) REVERT: Y 83 GLN cc_start: 0.7106 (OUTLIER) cc_final: 0.6820 (pt0) REVERT: Y 124 ARG cc_start: 0.6539 (tpt90) cc_final: 0.6303 (tpt90) REVERT: Y 142 MET cc_start: 0.5290 (tpp) cc_final: 0.4633 (ttt) outliers start: 98 outliers final: 81 residues processed: 1126 average time/residue: 0.4179 time to fit residues: 738.1665 Evaluate side-chains 1158 residues out of total 2855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 1070 time to evaluate : 3.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain a residue 572 VAL Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain D residue 49 LYS Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 174 ASP Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 174 ASP Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain f residue 578 LEU Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 221 SER Chi-restraints excluded: chain G residue 223 ASN Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 218 LEU Chi-restraints excluded: chain H residue 223 ASN Chi-restraints excluded: chain H residue 226 SER Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 56 CYS Chi-restraints excluded: chain I residue 85 ARG Chi-restraints excluded: chain I residue 104 ASP Chi-restraints excluded: chain I residue 213 GLN Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain I residue 269 GLN Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain J residue 173 THR Chi-restraints excluded: chain J residue 220 VAL Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 247 ILE Chi-restraints excluded: chain J residue 255 SER Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain K residue 38 GLN Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 117 VAL Chi-restraints excluded: chain K residue 127 ASP Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain K residue 177 ASP Chi-restraints excluded: chain K residue 226 SER Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 246 GLU Chi-restraints excluded: chain X residue 7 VAL Chi-restraints excluded: chain X residue 14 ILE Chi-restraints excluded: chain Y residue 3 GLU Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Y residue 83 GLN Chi-restraints excluded: chain Y residue 154 CYS Chi-restraints excluded: chain Y residue 158 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 201 optimal weight: 5.9990 chunk 270 optimal weight: 0.3980 chunk 77 optimal weight: 0.6980 chunk 234 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 254 optimal weight: 0.8980 chunk 106 optimal weight: 7.9990 chunk 261 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 GLN F 43 HIS ** f 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 80 GLN ** H 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 GLN K 185 GLN Y 83 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.114332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.096186 restraints weight = 55809.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.099155 restraints weight = 24062.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.100987 restraints weight = 13023.280| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.6717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 28609 Z= 0.200 Angle : 0.652 15.195 38797 Z= 0.335 Chirality : 0.042 0.200 4282 Planarity : 0.004 0.065 4690 Dihedral : 15.187 150.470 4698 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.43 % Allowed : 30.12 % Favored : 66.44 % 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: 0.86 (0.15), residues: 3239 helix: 1.10 (0.12), residues: 1830 sheet: 1.78 (0.31), residues: 165 loop : -0.28 (0.18), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP Y 120 HIS 0.005 0.001 HIS Y 125 PHE 0.029 0.001 PHE X 158 TYR 0.022 0.001 TYR A 73 ARG 0.015 0.000 ARG C 85 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10436.85 seconds wall clock time: 186 minutes 34.90 seconds (11194.90 seconds total)