Starting phenix.real_space_refine on Thu Feb 15 00:44:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpa_0742/02_2024/6kpa_0742_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpa_0742/02_2024/6kpa_0742.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpa_0742/02_2024/6kpa_0742.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpa_0742/02_2024/6kpa_0742.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpa_0742/02_2024/6kpa_0742_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpa_0742/02_2024/6kpa_0742_trim_updated.pdb" } resolution = 2.75 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= 0.004 sd= 0.338 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: 7 Type Number sf(0) Gaussians P 24 5.49 5 Mg 24 5.21 5 S 120 5.16 5 C 20316 2.51 5 N 5160 2.21 5 O 5976 1.98 5 H 31225 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 62845 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "B" Number of atoms: 5185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5185 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "C" Number of atoms: 5180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5180 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "D" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "E" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "F" Number of atoms: 5185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5185 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "G" Number of atoms: 5185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5185 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "H" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "I" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "J" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "K" Number of atoms: 5184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5184 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "L" Number of atoms: 5180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5180 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "A" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "H" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "I" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "J" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "K" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "L" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 19.91, per 1000 atoms: 0.32 Number of scatterers: 62845 At special positions: 0 Unit cell: (145.32, 145.32, 145.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 120 16.00 P 24 15.00 Mg 24 11.99 O 5976 8.00 N 5160 7.00 C 20316 6.00 H 31225 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 41.15 Conformation dependent library (CDL) restraints added in 4.8 seconds 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7176 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 216 helices and 12 sheets defined 54.3% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.62 Creating SS restraints... Processing helix chain 'A' and resid 25 through 36 removed outlier: 3.984A pdb=" N VAL A 29 " --> pdb=" O ASN A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 56 removed outlier: 3.637A pdb=" N LEU A 53 " --> pdb=" O LYS A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 68 Processing helix chain 'A' and resid 83 through 89 Processing helix chain 'A' and resid 91 through 97 removed outlier: 3.762A pdb=" N GLY A 97 " --> pdb=" O PRO A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 112 No H-bonds generated for 'chain 'A' and resid 109 through 112' Processing helix chain 'A' and resid 136 through 141 Processing helix chain 'A' and resid 160 through 170 Processing helix chain 'A' and resid 185 through 196 removed outlier: 4.278A pdb=" N LEU A 190 " --> pdb=" O GLU A 186 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLU A 195 " --> pdb=" O ASP A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 217 Processing helix chain 'A' and resid 221 through 228 removed outlier: 3.631A pdb=" N LEU A 225 " --> pdb=" O PRO A 221 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU A 226 " --> pdb=" O GLU A 222 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU A 227 " --> pdb=" O ALA A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 244 Processing helix chain 'A' and resid 248 through 252 Processing helix chain 'A' and resid 255 through 267 removed outlier: 3.829A pdb=" N GLY A 260 " --> pdb=" O THR A 256 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG A 264 " --> pdb=" O GLY A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 284 removed outlier: 3.901A pdb=" N ILE A 275 " --> pdb=" O VAL A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 Processing helix chain 'A' and resid 301 through 311 Processing helix chain 'A' and resid 314 through 325 Processing helix chain 'B' and resid 25 through 36 removed outlier: 3.984A pdb=" N VAL B 29 " --> pdb=" O ASN B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 56 removed outlier: 3.638A pdb=" N LEU B 53 " --> pdb=" O LYS B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 68 Processing helix chain 'B' and resid 83 through 89 Processing helix chain 'B' and resid 91 through 97 removed outlier: 3.762A pdb=" N GLY B 97 " --> pdb=" O PRO B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 112 No H-bonds generated for 'chain 'B' and resid 109 through 112' Processing helix chain 'B' and resid 136 through 141 Processing helix chain 'B' and resid 160 through 170 Processing helix chain 'B' and resid 185 through 196 removed outlier: 4.278A pdb=" N LEU B 190 " --> pdb=" O GLU B 186 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLU B 195 " --> pdb=" O ASP B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 217 Processing helix chain 'B' and resid 221 through 228 removed outlier: 3.631A pdb=" N LEU B 225 " --> pdb=" O PRO B 221 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU B 226 " --> pdb=" O GLU B 222 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU B 227 " --> pdb=" O ALA B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 244 Processing helix chain 'B' and resid 248 through 252 Processing helix chain 'B' and resid 255 through 267 removed outlier: 3.828A pdb=" N GLY B 260 " --> pdb=" O THR B 256 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG B 264 " --> pdb=" O GLY B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 284 removed outlier: 3.901A pdb=" N ILE B 275 " --> pdb=" O VAL B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 296 Processing helix chain 'B' and resid 301 through 311 Processing helix chain 'B' and resid 314 through 325 Processing helix chain 'C' and resid 25 through 36 removed outlier: 3.983A pdb=" N VAL C 29 " --> pdb=" O ASN C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 56 removed outlier: 3.637A pdb=" N LEU C 53 " --> pdb=" O LYS C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 68 Processing helix chain 'C' and resid 83 through 89 Processing helix chain 'C' and resid 91 through 97 removed outlier: 3.762A pdb=" N GLY C 97 " --> pdb=" O PRO C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 112 No H-bonds generated for 'chain 'C' and resid 109 through 112' Processing helix chain 'C' and resid 136 through 141 Processing helix chain 'C' and resid 160 through 170 Processing helix chain 'C' and resid 185 through 196 removed outlier: 4.277A pdb=" N LEU C 190 " --> pdb=" O GLU C 186 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU C 195 " --> pdb=" O ASP C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 217 Processing helix chain 'C' and resid 221 through 228 removed outlier: 3.630A pdb=" N LEU C 225 " --> pdb=" O PRO C 221 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU C 226 " --> pdb=" O GLU C 222 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU C 227 " --> pdb=" O ALA C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 244 Processing helix chain 'C' and resid 248 through 252 Processing helix chain 'C' and resid 255 through 267 removed outlier: 3.829A pdb=" N GLY C 260 " --> pdb=" O THR C 256 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG C 264 " --> pdb=" O GLY C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 284 removed outlier: 3.901A pdb=" N ILE C 275 " --> pdb=" O VAL C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 296 Processing helix chain 'C' and resid 301 through 311 Processing helix chain 'C' and resid 314 through 325 Processing helix chain 'D' and resid 25 through 36 removed outlier: 3.983A pdb=" N VAL D 29 " --> pdb=" O ASN D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 56 removed outlier: 3.637A pdb=" N LEU D 53 " --> pdb=" O LYS D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 68 Processing helix chain 'D' and resid 83 through 89 Processing helix chain 'D' and resid 91 through 97 removed outlier: 3.762A pdb=" N GLY D 97 " --> pdb=" O PRO D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 112 No H-bonds generated for 'chain 'D' and resid 109 through 112' Processing helix chain 'D' and resid 136 through 141 Processing helix chain 'D' and resid 160 through 170 Processing helix chain 'D' and resid 185 through 196 removed outlier: 4.278A pdb=" N LEU D 190 " --> pdb=" O GLU D 186 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU D 195 " --> pdb=" O ASP D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 217 Processing helix chain 'D' and resid 221 through 228 removed outlier: 3.630A pdb=" N LEU D 225 " --> pdb=" O PRO D 221 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU D 226 " --> pdb=" O GLU D 222 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU D 227 " --> pdb=" O ALA D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 244 Processing helix chain 'D' and resid 248 through 252 Processing helix chain 'D' and resid 255 through 267 removed outlier: 3.829A pdb=" N GLY D 260 " --> pdb=" O THR D 256 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG D 264 " --> pdb=" O GLY D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 284 removed outlier: 3.902A pdb=" N ILE D 275 " --> pdb=" O VAL D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 296 Processing helix chain 'D' and resid 301 through 311 Processing helix chain 'D' and resid 314 through 325 Processing helix chain 'E' and resid 25 through 36 removed outlier: 3.984A pdb=" N VAL E 29 " --> pdb=" O ASN E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 56 removed outlier: 3.637A pdb=" N LEU E 53 " --> pdb=" O LYS E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 68 Processing helix chain 'E' and resid 83 through 89 Processing helix chain 'E' and resid 91 through 97 removed outlier: 3.762A pdb=" N GLY E 97 " --> pdb=" O PRO E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 112 No H-bonds generated for 'chain 'E' and resid 109 through 112' Processing helix chain 'E' and resid 136 through 141 Processing helix chain 'E' and resid 160 through 170 Processing helix chain 'E' and resid 185 through 196 removed outlier: 4.278A pdb=" N LEU E 190 " --> pdb=" O GLU E 186 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLU E 195 " --> pdb=" O ASP E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 217 Processing helix chain 'E' and resid 221 through 228 removed outlier: 3.631A pdb=" N LEU E 225 " --> pdb=" O PRO E 221 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU E 226 " --> pdb=" O GLU E 222 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU E 227 " --> pdb=" O ALA E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 244 Processing helix chain 'E' and resid 248 through 252 Processing helix chain 'E' and resid 255 through 267 removed outlier: 3.829A pdb=" N GLY E 260 " --> pdb=" O THR E 256 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG E 264 " --> pdb=" O GLY E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 284 removed outlier: 3.901A pdb=" N ILE E 275 " --> pdb=" O VAL E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 296 Processing helix chain 'E' and resid 301 through 311 Processing helix chain 'E' and resid 314 through 325 Processing helix chain 'F' and resid 25 through 36 removed outlier: 3.984A pdb=" N VAL F 29 " --> pdb=" O ASN F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 56 removed outlier: 3.638A pdb=" N LEU F 53 " --> pdb=" O LYS F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 68 Processing helix chain 'F' and resid 83 through 89 Processing helix chain 'F' and resid 91 through 97 removed outlier: 3.762A pdb=" N GLY F 97 " --> pdb=" O PRO F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 112 No H-bonds generated for 'chain 'F' and resid 109 through 112' Processing helix chain 'F' and resid 136 through 141 Processing helix chain 'F' and resid 160 through 170 Processing helix chain 'F' and resid 185 through 196 removed outlier: 4.277A pdb=" N LEU F 190 " --> pdb=" O GLU F 186 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLU F 195 " --> pdb=" O ASP F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 217 Processing helix chain 'F' and resid 221 through 228 removed outlier: 3.631A pdb=" N LEU F 225 " --> pdb=" O PRO F 221 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU F 226 " --> pdb=" O GLU F 222 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU F 227 " --> pdb=" O ALA F 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 244 Processing helix chain 'F' and resid 248 through 252 Processing helix chain 'F' and resid 255 through 267 removed outlier: 3.830A pdb=" N GLY F 260 " --> pdb=" O THR F 256 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG F 264 " --> pdb=" O GLY F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 284 removed outlier: 3.901A pdb=" N ILE F 275 " --> pdb=" O VAL F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 296 Processing helix chain 'F' and resid 301 through 311 Processing helix chain 'F' and resid 314 through 325 Processing helix chain 'G' and resid 25 through 36 removed outlier: 3.983A pdb=" N VAL G 29 " --> pdb=" O ASN G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 56 removed outlier: 3.638A pdb=" N LEU G 53 " --> pdb=" O LYS G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 68 Processing helix chain 'G' and resid 83 through 89 Processing helix chain 'G' and resid 91 through 97 removed outlier: 3.762A pdb=" N GLY G 97 " --> pdb=" O PRO G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 112 No H-bonds generated for 'chain 'G' and resid 109 through 112' Processing helix chain 'G' and resid 136 through 141 Processing helix chain 'G' and resid 160 through 170 Processing helix chain 'G' and resid 185 through 196 removed outlier: 4.278A pdb=" N LEU G 190 " --> pdb=" O GLU G 186 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLU G 195 " --> pdb=" O ASP G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 198 through 217 Processing helix chain 'G' and resid 221 through 228 removed outlier: 3.631A pdb=" N LEU G 225 " --> pdb=" O PRO G 221 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU G 226 " --> pdb=" O GLU G 222 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU G 227 " --> pdb=" O ALA G 223 " (cutoff:3.500A) Processing helix chain 'G' and resid 233 through 244 Processing helix chain 'G' and resid 248 through 252 Processing helix chain 'G' and resid 255 through 267 removed outlier: 3.828A pdb=" N GLY G 260 " --> pdb=" O THR G 256 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG G 264 " --> pdb=" O GLY G 260 " (cutoff:3.500A) Processing helix chain 'G' and resid 270 through 284 removed outlier: 3.901A pdb=" N ILE G 275 " --> pdb=" O VAL G 271 " (cutoff:3.500A) Processing helix chain 'G' and resid 287 through 296 Processing helix chain 'G' and resid 301 through 311 Processing helix chain 'G' and resid 314 through 325 Processing helix chain 'H' and resid 25 through 36 removed outlier: 3.984A pdb=" N VAL H 29 " --> pdb=" O ASN H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 56 removed outlier: 3.638A pdb=" N LEU H 53 " --> pdb=" O LYS H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 68 Processing helix chain 'H' and resid 83 through 89 Processing helix chain 'H' and resid 91 through 97 removed outlier: 3.762A pdb=" N GLY H 97 " --> pdb=" O PRO H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 109 through 112 No H-bonds generated for 'chain 'H' and resid 109 through 112' Processing helix chain 'H' and resid 136 through 141 Processing helix chain 'H' and resid 160 through 170 Processing helix chain 'H' and resid 185 through 196 removed outlier: 4.279A pdb=" N LEU H 190 " --> pdb=" O GLU H 186 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU H 195 " --> pdb=" O ASP H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 198 through 217 Processing helix chain 'H' and resid 221 through 228 removed outlier: 3.630A pdb=" N LEU H 225 " --> pdb=" O PRO H 221 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU H 226 " --> pdb=" O GLU H 222 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU H 227 " --> pdb=" O ALA H 223 " (cutoff:3.500A) Processing helix chain 'H' and resid 233 through 244 Processing helix chain 'H' and resid 248 through 252 Processing helix chain 'H' and resid 255 through 267 removed outlier: 3.829A pdb=" N GLY H 260 " --> pdb=" O THR H 256 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG H 264 " --> pdb=" O GLY H 260 " (cutoff:3.500A) Processing helix chain 'H' and resid 270 through 284 removed outlier: 3.901A pdb=" N ILE H 275 " --> pdb=" O VAL H 271 " (cutoff:3.500A) Processing helix chain 'H' and resid 287 through 296 Processing helix chain 'H' and resid 301 through 311 Processing helix chain 'H' and resid 314 through 325 Processing helix chain 'I' and resid 25 through 36 removed outlier: 3.984A pdb=" N VAL I 29 " --> pdb=" O ASN I 25 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 56 removed outlier: 3.638A pdb=" N LEU I 53 " --> pdb=" O LYS I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 68 Processing helix chain 'I' and resid 83 through 89 Processing helix chain 'I' and resid 91 through 97 removed outlier: 3.762A pdb=" N GLY I 97 " --> pdb=" O PRO I 93 " (cutoff:3.500A) Processing helix chain 'I' and resid 109 through 112 No H-bonds generated for 'chain 'I' and resid 109 through 112' Processing helix chain 'I' and resid 136 through 141 Processing helix chain 'I' and resid 160 through 170 Processing helix chain 'I' and resid 185 through 196 removed outlier: 4.278A pdb=" N LEU I 190 " --> pdb=" O GLU I 186 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU I 195 " --> pdb=" O ASP I 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 198 through 217 Processing helix chain 'I' and resid 221 through 228 removed outlier: 3.631A pdb=" N LEU I 225 " --> pdb=" O PRO I 221 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU I 226 " --> pdb=" O GLU I 222 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU I 227 " --> pdb=" O ALA I 223 " (cutoff:3.500A) Processing helix chain 'I' and resid 233 through 244 Processing helix chain 'I' and resid 248 through 252 Processing helix chain 'I' and resid 255 through 267 removed outlier: 3.828A pdb=" N GLY I 260 " --> pdb=" O THR I 256 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG I 264 " --> pdb=" O GLY I 260 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 284 removed outlier: 3.901A pdb=" N ILE I 275 " --> pdb=" O VAL I 271 " (cutoff:3.500A) Processing helix chain 'I' and resid 287 through 296 Processing helix chain 'I' and resid 301 through 311 Processing helix chain 'I' and resid 314 through 325 Processing helix chain 'J' and resid 25 through 36 removed outlier: 3.984A pdb=" N VAL J 29 " --> pdb=" O ASN J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 49 through 56 removed outlier: 3.637A pdb=" N LEU J 53 " --> pdb=" O LYS J 49 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 68 Processing helix chain 'J' and resid 83 through 89 Processing helix chain 'J' and resid 91 through 97 removed outlier: 3.762A pdb=" N GLY J 97 " --> pdb=" O PRO J 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 112 No H-bonds generated for 'chain 'J' and resid 109 through 112' Processing helix chain 'J' and resid 136 through 141 Processing helix chain 'J' and resid 160 through 170 Processing helix chain 'J' and resid 185 through 196 removed outlier: 4.277A pdb=" N LEU J 190 " --> pdb=" O GLU J 186 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLU J 195 " --> pdb=" O ASP J 191 " (cutoff:3.500A) Processing helix chain 'J' and resid 198 through 217 Processing helix chain 'J' and resid 221 through 228 removed outlier: 3.631A pdb=" N LEU J 225 " --> pdb=" O PRO J 221 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU J 226 " --> pdb=" O GLU J 222 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU J 227 " --> pdb=" O ALA J 223 " (cutoff:3.500A) Processing helix chain 'J' and resid 233 through 244 Processing helix chain 'J' and resid 248 through 252 Processing helix chain 'J' and resid 255 through 267 removed outlier: 3.829A pdb=" N GLY J 260 " --> pdb=" O THR J 256 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG J 264 " --> pdb=" O GLY J 260 " (cutoff:3.500A) Processing helix chain 'J' and resid 270 through 284 removed outlier: 3.901A pdb=" N ILE J 275 " --> pdb=" O VAL J 271 " (cutoff:3.500A) Processing helix chain 'J' and resid 287 through 296 Processing helix chain 'J' and resid 301 through 311 Processing helix chain 'J' and resid 314 through 325 Processing helix chain 'K' and resid 25 through 36 removed outlier: 3.985A pdb=" N VAL K 29 " --> pdb=" O ASN K 25 " (cutoff:3.500A) Processing helix chain 'K' and resid 49 through 56 removed outlier: 3.638A pdb=" N LEU K 53 " --> pdb=" O LYS K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 64 through 68 Processing helix chain 'K' and resid 83 through 89 Processing helix chain 'K' and resid 91 through 97 removed outlier: 3.762A pdb=" N GLY K 97 " --> pdb=" O PRO K 93 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 112 No H-bonds generated for 'chain 'K' and resid 109 through 112' Processing helix chain 'K' and resid 136 through 141 Processing helix chain 'K' and resid 160 through 170 Processing helix chain 'K' and resid 185 through 196 removed outlier: 4.279A pdb=" N LEU K 190 " --> pdb=" O GLU K 186 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU K 195 " --> pdb=" O ASP K 191 " (cutoff:3.500A) Processing helix chain 'K' and resid 198 through 217 Processing helix chain 'K' and resid 221 through 228 removed outlier: 3.630A pdb=" N LEU K 225 " --> pdb=" O PRO K 221 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU K 226 " --> pdb=" O GLU K 222 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU K 227 " --> pdb=" O ALA K 223 " (cutoff:3.500A) Processing helix chain 'K' and resid 233 through 244 Processing helix chain 'K' and resid 248 through 252 Processing helix chain 'K' and resid 255 through 267 removed outlier: 3.828A pdb=" N GLY K 260 " --> pdb=" O THR K 256 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG K 264 " --> pdb=" O GLY K 260 " (cutoff:3.500A) Processing helix chain 'K' and resid 270 through 284 removed outlier: 3.901A pdb=" N ILE K 275 " --> pdb=" O VAL K 271 " (cutoff:3.500A) Processing helix chain 'K' and resid 287 through 296 Processing helix chain 'K' and resid 301 through 311 Processing helix chain 'K' and resid 314 through 325 Processing helix chain 'L' and resid 25 through 36 removed outlier: 3.984A pdb=" N VAL L 29 " --> pdb=" O ASN L 25 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 56 removed outlier: 3.637A pdb=" N LEU L 53 " --> pdb=" O LYS L 49 " (cutoff:3.500A) Processing helix chain 'L' and resid 64 through 68 Processing helix chain 'L' and resid 83 through 89 Processing helix chain 'L' and resid 91 through 97 removed outlier: 3.762A pdb=" N GLY L 97 " --> pdb=" O PRO L 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 109 through 112 No H-bonds generated for 'chain 'L' and resid 109 through 112' Processing helix chain 'L' and resid 136 through 141 Processing helix chain 'L' and resid 160 through 170 Processing helix chain 'L' and resid 185 through 196 removed outlier: 4.278A pdb=" N LEU L 190 " --> pdb=" O GLU L 186 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU L 195 " --> pdb=" O ASP L 191 " (cutoff:3.500A) Processing helix chain 'L' and resid 198 through 217 Processing helix chain 'L' and resid 221 through 228 removed outlier: 3.632A pdb=" N LEU L 225 " --> pdb=" O PRO L 221 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU L 226 " --> pdb=" O GLU L 222 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU L 227 " --> pdb=" O ALA L 223 " (cutoff:3.500A) Processing helix chain 'L' and resid 233 through 244 Processing helix chain 'L' and resid 248 through 252 Processing helix chain 'L' and resid 255 through 267 removed outlier: 3.828A pdb=" N GLY L 260 " --> pdb=" O THR L 256 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG L 264 " --> pdb=" O GLY L 260 " (cutoff:3.500A) Processing helix chain 'L' and resid 270 through 284 removed outlier: 3.902A pdb=" N ILE L 275 " --> pdb=" O VAL L 271 " (cutoff:3.500A) Processing helix chain 'L' and resid 287 through 296 Processing helix chain 'L' and resid 301 through 311 Processing helix chain 'L' and resid 314 through 325 Processing sheet with id= A, first strand: chain 'A' and resid 42 through 44 removed outlier: 6.174A pdb=" N VAL A 73 " --> pdb=" O GLY A 19 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ILE A 21 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU A 75 " --> pdb=" O ILE A 21 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL A 102 " --> pdb=" O ALA A 74 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N LEU A 76 " --> pdb=" O VAL A 102 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ASP A 104 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE A 105 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLN A 154 " --> pdb=" O THR A 124 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N MET A 126 " --> pdb=" O VAL A 152 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N VAL A 152 " --> pdb=" O MET A 126 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ALA A 128 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N LEU A 150 " --> pdb=" O ALA A 128 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 41 through 44 removed outlier: 6.376A pdb=" N ILE B 18 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N GLY B 44 " --> pdb=" O ILE B 18 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL B 20 " --> pdb=" O GLY B 44 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N VAL B 73 " --> pdb=" O GLY B 19 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N ILE B 21 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU B 75 " --> pdb=" O ILE B 21 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL B 102 " --> pdb=" O ALA B 74 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N LEU B 76 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ASP B 104 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE B 105 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLN B 154 " --> pdb=" O THR B 124 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N MET B 126 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N VAL B 152 " --> pdb=" O MET B 126 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ALA B 128 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N LEU B 150 " --> pdb=" O ALA B 128 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 41 through 44 removed outlier: 6.376A pdb=" N ILE C 18 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N GLY C 44 " --> pdb=" O ILE C 18 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL C 20 " --> pdb=" O GLY C 44 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N VAL C 73 " --> pdb=" O GLY C 19 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ILE C 21 " --> pdb=" O VAL C 73 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N LEU C 75 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL C 102 " --> pdb=" O ALA C 74 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N LEU C 76 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ASP C 104 " --> pdb=" O LEU C 76 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE C 105 " --> pdb=" O ILE C 125 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLN C 154 " --> pdb=" O THR C 124 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N MET C 126 " --> pdb=" O VAL C 152 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N VAL C 152 " --> pdb=" O MET C 126 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ALA C 128 " --> pdb=" O LEU C 150 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N LEU C 150 " --> pdb=" O ALA C 128 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 41 through 44 removed outlier: 6.377A pdb=" N ILE D 18 " --> pdb=" O ILE D 42 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N GLY D 44 " --> pdb=" O ILE D 18 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL D 20 " --> pdb=" O GLY D 44 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N VAL D 73 " --> pdb=" O GLY D 19 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ILE D 21 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU D 75 " --> pdb=" O ILE D 21 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL D 102 " --> pdb=" O ALA D 74 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N LEU D 76 " --> pdb=" O VAL D 102 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ASP D 104 " --> pdb=" O LEU D 76 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE D 105 " --> pdb=" O ILE D 125 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLN D 154 " --> pdb=" O THR D 124 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N MET D 126 " --> pdb=" O VAL D 152 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL D 152 " --> pdb=" O MET D 126 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ALA D 128 " --> pdb=" O LEU D 150 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LEU D 150 " --> pdb=" O ALA D 128 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 41 through 44 removed outlier: 6.376A pdb=" N ILE E 18 " --> pdb=" O ILE E 42 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N GLY E 44 " --> pdb=" O ILE E 18 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL E 20 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N VAL E 73 " --> pdb=" O GLY E 19 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ILE E 21 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU E 75 " --> pdb=" O ILE E 21 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL E 102 " --> pdb=" O ALA E 74 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N LEU E 76 " --> pdb=" O VAL E 102 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ASP E 104 " --> pdb=" O LEU E 76 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE E 105 " --> pdb=" O ILE E 125 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLN E 154 " --> pdb=" O THR E 124 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N MET E 126 " --> pdb=" O VAL E 152 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N VAL E 152 " --> pdb=" O MET E 126 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ALA E 128 " --> pdb=" O LEU E 150 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N LEU E 150 " --> pdb=" O ALA E 128 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 41 through 44 removed outlier: 6.377A pdb=" N ILE F 18 " --> pdb=" O ILE F 42 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N GLY F 44 " --> pdb=" O ILE F 18 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL F 20 " --> pdb=" O GLY F 44 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N VAL F 73 " --> pdb=" O GLY F 19 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N ILE F 21 " --> pdb=" O VAL F 73 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N LEU F 75 " --> pdb=" O ILE F 21 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL F 102 " --> pdb=" O ALA F 74 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N LEU F 76 " --> pdb=" O VAL F 102 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ASP F 104 " --> pdb=" O LEU F 76 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE F 105 " --> pdb=" O ILE F 125 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLN F 154 " --> pdb=" O THR F 124 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N MET F 126 " --> pdb=" O VAL F 152 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL F 152 " --> pdb=" O MET F 126 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ALA F 128 " --> pdb=" O LEU F 150 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N LEU F 150 " --> pdb=" O ALA F 128 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'G' and resid 41 through 44 removed outlier: 6.376A pdb=" N ILE G 18 " --> pdb=" O ILE G 42 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N GLY G 44 " --> pdb=" O ILE G 18 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL G 20 " --> pdb=" O GLY G 44 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N VAL G 73 " --> pdb=" O GLY G 19 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N ILE G 21 " --> pdb=" O VAL G 73 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N LEU G 75 " --> pdb=" O ILE G 21 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL G 102 " --> pdb=" O ALA G 74 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N LEU G 76 " --> pdb=" O VAL G 102 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ASP G 104 " --> pdb=" O LEU G 76 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE G 105 " --> pdb=" O ILE G 125 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLN G 154 " --> pdb=" O THR G 124 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N MET G 126 " --> pdb=" O VAL G 152 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N VAL G 152 " --> pdb=" O MET G 126 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ALA G 128 " --> pdb=" O LEU G 150 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N LEU G 150 " --> pdb=" O ALA G 128 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'H' and resid 41 through 44 removed outlier: 6.376A pdb=" N ILE H 18 " --> pdb=" O ILE H 42 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N GLY H 44 " --> pdb=" O ILE H 18 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL H 20 " --> pdb=" O GLY H 44 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N VAL H 73 " --> pdb=" O GLY H 19 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ILE H 21 " --> pdb=" O VAL H 73 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N LEU H 75 " --> pdb=" O ILE H 21 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL H 102 " --> pdb=" O ALA H 74 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N LEU H 76 " --> pdb=" O VAL H 102 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ASP H 104 " --> pdb=" O LEU H 76 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE H 105 " --> pdb=" O ILE H 125 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLN H 154 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N MET H 126 " --> pdb=" O VAL H 152 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL H 152 " --> pdb=" O MET H 126 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ALA H 128 " --> pdb=" O LEU H 150 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N LEU H 150 " --> pdb=" O ALA H 128 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'I' and resid 41 through 44 removed outlier: 6.377A pdb=" N ILE I 18 " --> pdb=" O ILE I 42 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N GLY I 44 " --> pdb=" O ILE I 18 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL I 20 " --> pdb=" O GLY I 44 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N VAL I 73 " --> pdb=" O GLY I 19 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ILE I 21 " --> pdb=" O VAL I 73 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N LEU I 75 " --> pdb=" O ILE I 21 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL I 102 " --> pdb=" O ALA I 74 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N LEU I 76 " --> pdb=" O VAL I 102 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ASP I 104 " --> pdb=" O LEU I 76 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE I 105 " --> pdb=" O ILE I 125 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLN I 154 " --> pdb=" O THR I 124 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N MET I 126 " --> pdb=" O VAL I 152 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL I 152 " --> pdb=" O MET I 126 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ALA I 128 " --> pdb=" O LEU I 150 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N LEU I 150 " --> pdb=" O ALA I 128 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'J' and resid 41 through 44 removed outlier: 6.376A pdb=" N ILE J 18 " --> pdb=" O ILE J 42 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N GLY J 44 " --> pdb=" O ILE J 18 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL J 20 " --> pdb=" O GLY J 44 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N VAL J 73 " --> pdb=" O GLY J 19 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N ILE J 21 " --> pdb=" O VAL J 73 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU J 75 " --> pdb=" O ILE J 21 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL J 102 " --> pdb=" O ALA J 74 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N LEU J 76 " --> pdb=" O VAL J 102 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ASP J 104 " --> pdb=" O LEU J 76 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE J 105 " --> pdb=" O ILE J 125 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLN J 154 " --> pdb=" O THR J 124 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N MET J 126 " --> pdb=" O VAL J 152 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL J 152 " --> pdb=" O MET J 126 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ALA J 128 " --> pdb=" O LEU J 150 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LEU J 150 " --> pdb=" O ALA J 128 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'K' and resid 42 through 44 removed outlier: 6.174A pdb=" N VAL K 73 " --> pdb=" O GLY K 19 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ILE K 21 " --> pdb=" O VAL K 73 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N LEU K 75 " --> pdb=" O ILE K 21 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL K 102 " --> pdb=" O ALA K 74 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N LEU K 76 " --> pdb=" O VAL K 102 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ASP K 104 " --> pdb=" O LEU K 76 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE K 105 " --> pdb=" O ILE K 125 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLN K 154 " --> pdb=" O THR K 124 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N MET K 126 " --> pdb=" O VAL K 152 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL K 152 " --> pdb=" O MET K 126 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ALA K 128 " --> pdb=" O LEU K 150 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N LEU K 150 " --> pdb=" O ALA K 128 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'L' and resid 41 through 44 removed outlier: 6.376A pdb=" N ILE L 18 " --> pdb=" O ILE L 42 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N GLY L 44 " --> pdb=" O ILE L 18 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL L 20 " --> pdb=" O GLY L 44 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N VAL L 73 " --> pdb=" O GLY L 19 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ILE L 21 " --> pdb=" O VAL L 73 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N LEU L 75 " --> pdb=" O ILE L 21 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL L 102 " --> pdb=" O ALA L 74 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N LEU L 76 " --> pdb=" O VAL L 102 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ASP L 104 " --> pdb=" O LEU L 76 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE L 105 " --> pdb=" O ILE L 125 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLN L 154 " --> pdb=" O THR L 124 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N MET L 126 " --> pdb=" O VAL L 152 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL L 152 " --> pdb=" O MET L 126 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ALA L 128 " --> pdb=" O LEU L 150 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LEU L 150 " --> pdb=" O ALA L 128 " (cutoff:3.500A) 1218 hydrogen bonds defined for protein. 3576 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 22.72 Time building geometry restraints manager: 43.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.02: 31212 1.02 - 1.22: 25 1.22 - 1.41: 13229 1.41 - 1.61: 18739 1.61 - 1.80: 300 Bond restraints: 63505 Sorted by residual: bond pdb=" C1B NAI E 402 " pdb=" C2B NAI E 402 " ideal model delta sigma weight residual 1.528 1.282 0.246 2.00e-02 2.50e+03 1.51e+02 bond pdb=" C1B NAI I 402 " pdb=" C2B NAI I 402 " ideal model delta sigma weight residual 1.528 1.282 0.246 2.00e-02 2.50e+03 1.51e+02 bond pdb=" C1B NAI K 402 " pdb=" C2B NAI K 402 " ideal model delta sigma weight residual 1.528 1.282 0.246 2.00e-02 2.50e+03 1.51e+02 bond pdb=" C1B NAI L 403 " pdb=" C2B NAI L 403 " ideal model delta sigma weight residual 1.528 1.282 0.246 2.00e-02 2.50e+03 1.51e+02 bond pdb=" C1B NAI J 403 " pdb=" C2B NAI J 403 " ideal model delta sigma weight residual 1.528 1.282 0.246 2.00e-02 2.50e+03 1.51e+02 ... (remaining 63500 not shown) Histogram of bond angle deviations from ideal: 55.61 - 76.56: 184 76.56 - 97.50: 210 97.50 - 118.45: 86853 118.45 - 139.39: 27776 139.39 - 160.34: 7 Bond angle restraints: 115030 Sorted by residual: angle pdb=" CA PHE K 59 " pdb=" N PHE K 59 " pdb=" H PHE K 59 " ideal model delta sigma weight residual 114.44 55.61 58.83 3.00e+00 1.11e-01 3.85e+02 angle pdb=" C GLN L 30 " pdb=" N ALA L 31 " pdb=" H ALA L 31 " ideal model delta sigma weight residual 124.83 66.04 58.78 3.00e+00 1.11e-01 3.84e+02 angle pdb=" C GLY K 58 " pdb=" N PHE K 59 " pdb=" H PHE K 59 " ideal model delta sigma weight residual 124.74 66.09 58.65 3.00e+00 1.11e-01 3.82e+02 angle pdb=" CA ALA L 31 " pdb=" N ALA L 31 " pdb=" H ALA L 31 " ideal model delta sigma weight residual 114.53 55.90 58.63 3.00e+00 1.11e-01 3.82e+02 angle pdb=" C ASP J 48 " pdb=" N LYS J 49 " pdb=" H LYS J 49 " ideal model delta sigma weight residual 124.88 66.85 58.03 3.00e+00 1.11e-01 3.74e+02 ... (remaining 115025 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 26222 17.97 - 35.94: 2843 35.94 - 53.91: 775 53.91 - 71.88: 124 71.88 - 89.85: 25 Dihedral angle restraints: 29989 sinusoidal: 16636 harmonic: 13353 Sorted by residual: dihedral pdb=" CA GLU B 63 " pdb=" C GLU B 63 " pdb=" N ILE B 64 " pdb=" CA ILE B 64 " ideal model delta harmonic sigma weight residual -180.00 -155.22 -24.78 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA GLU A 63 " pdb=" C GLU A 63 " pdb=" N ILE A 64 " pdb=" CA ILE A 64 " ideal model delta harmonic sigma weight residual -180.00 -155.24 -24.76 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA GLU J 63 " pdb=" C GLU J 63 " pdb=" N ILE J 64 " pdb=" CA ILE J 64 " ideal model delta harmonic sigma weight residual -180.00 -155.24 -24.76 0 5.00e+00 4.00e-02 2.45e+01 ... (remaining 29986 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 3872 0.071 - 0.142: 770 0.142 - 0.213: 74 0.213 - 0.283: 24 0.283 - 0.354: 24 Chirality restraints: 4764 Sorted by residual: chirality pdb=" CB VAL K 251 " pdb=" CA VAL K 251 " pdb=" CG1 VAL K 251 " pdb=" CG2 VAL K 251 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.35 2.00e-01 2.50e+01 3.14e+00 chirality pdb=" CB VAL D 251 " pdb=" CA VAL D 251 " pdb=" CG1 VAL D 251 " pdb=" CG2 VAL D 251 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.12e+00 chirality pdb=" CB VAL E 251 " pdb=" CA VAL E 251 " pdb=" CG1 VAL E 251 " pdb=" CG2 VAL E 251 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.11e+00 ... (remaining 4761 not shown) Planarity restraints: 9268 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 198 " -0.009 2.00e-02 2.50e+03 1.28e-02 6.59e+00 pdb=" CG TRP C 198 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 TRP C 198 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP C 198 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 198 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 198 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 198 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 198 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 198 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 198 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 TRP C 198 " 0.020 2.00e-02 2.50e+03 pdb=" HE1 TRP C 198 " -0.039 2.00e-02 2.50e+03 pdb=" HE3 TRP C 198 " -0.003 2.00e-02 2.50e+03 pdb=" HZ2 TRP C 198 " 0.019 2.00e-02 2.50e+03 pdb=" HZ3 TRP C 198 " -0.005 2.00e-02 2.50e+03 pdb=" HH2 TRP C 198 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 302 " 0.005 2.00e-02 2.50e+03 1.09e-02 1.19e+00 pdb=" C VAL D 302 " -0.019 2.00e-02 2.50e+03 pdb=" O VAL D 302 " 0.007 2.00e-02 2.50e+03 pdb=" N PHE D 303 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL I 302 " -0.005 2.00e-02 2.50e+03 1.09e-02 1.19e+00 pdb=" C VAL I 302 " 0.019 2.00e-02 2.50e+03 pdb=" O VAL I 302 " -0.007 2.00e-02 2.50e+03 pdb=" N PHE I 303 " -0.006 2.00e-02 2.50e+03 ... (remaining 9265 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.01: 1039 2.01 - 2.66: 91075 2.66 - 3.30: 178922 3.30 - 3.95: 220885 3.95 - 4.60: 362395 Nonbonded interactions: 854316 Sorted by model distance: nonbonded pdb=" H LYS J 99 " pdb=" HA LYS J 99 " model vdw 1.360 1.816 nonbonded pdb=" H LYS I 99 " pdb=" HA LYS I 99 " model vdw 1.361 1.816 nonbonded pdb=" H ILE K 18 " pdb=" HA ILE K 18 " model vdw 1.367 1.816 nonbonded pdb=" H ILE A 18 " pdb=" HA ILE A 18 " model vdw 1.368 1.816 nonbonded pdb=" O LEU E 192 " pdb=" HD1 HIS E 196 " model vdw 1.478 1.850 ... (remaining 854311 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' and (resid 2 through 195 or (resid 196 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 197 through 329 or resid 401)) selection = (chain 'B' and ((resid 2 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name OD2)) or (resid 3 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name CE or name NZ or name HA or \ name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 \ or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 4 through 195 or (re \ sid 196 and (name N or name CA or name C or name O or name CB or name CG or name \ ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or nam \ e HB3 or name HD2 or name HE1 or name HE2)) or resid 197 through 329 or resid 40 \ 1)) selection = (chain 'C' and (resid 2 through 329 or resid 401)) selection = (chain 'D' and (resid 2 through 195 or (resid 196 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 197 through 329 or resid 401)) selection = (chain 'E' and (resid 2 through 195 or (resid 196 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 197 through 329 or resid 401)) selection = (chain 'F' and ((resid 2 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name OD2)) or (resid 3 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name CE or name NZ or name HA or \ name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 \ or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 4 through 195 or (re \ sid 196 and (name N or name CA or name C or name O or name CB or name CG or name \ ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or nam \ e HB3 or name HD2 or name HE1 or name HE2)) or resid 197 through 329 or resid 40 \ 1)) selection = (chain 'G' and ((resid 2 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name OD2)) or (resid 3 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name CE or name NZ or name HA or \ name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 \ or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 4 through 195 or (re \ sid 196 and (name N or name CA or name C or name O or name CB or name CG or name \ ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or nam \ e HB3 or name HD2 or name HE1 or name HE2)) or resid 197 through 329 or resid 40 \ 1)) selection = (chain 'H' and (resid 2 through 195 or (resid 196 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 197 through 329 or resid 401)) selection = (chain 'I' and (resid 2 through 195 or (resid 196 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 197 through 329 or resid 401)) selection = (chain 'J' and (resid 2 through 195 or (resid 196 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 197 through 329 or resid 401)) selection = (chain 'K' and ((resid 2 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name OD2)) or (resid 3 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name CE or name NZ or name HA or \ name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 \ or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 4 through 329 or res \ id 401)) selection = (chain 'L' and (resid 2 through 329 or resid 401)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.890 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: 0.710 Extract box with map and model: 11.360 Check model and map are aligned: 0.700 Set scattering table: 0.480 Process input model: 155.670 Find NCS groups from input model: 2.730 Set up NCS constraints: 0.170 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:8.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 182.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 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 : 0.015 0.246 32280 Z= 0.979 Angle : 0.941 14.265 43704 Z= 0.429 Chirality : 0.060 0.354 4764 Planarity : 0.003 0.027 5484 Dihedral : 14.861 78.791 12504 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.52 (0.11), residues: 3912 helix: -2.82 (0.08), residues: 2244 sheet: -2.08 (0.25), residues: 324 loop : -3.24 (0.15), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 198 HIS 0.003 0.001 HIS C 252 PHE 0.010 0.001 PHE E 228 TYR 0.007 0.001 TYR J 50 ARG 0.002 0.000 ARG L 273 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 562 time to evaluate : 3.872 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: A 9 ASN cc_start: 0.8735 (p0) cc_final: 0.8192 (p0) REVERT: A 319 GLU cc_start: 0.8507 (tt0) cc_final: 0.8195 (tm-30) REVERT: B 9 ASN cc_start: 0.8682 (p0) cc_final: 0.8161 (p0) REVERT: B 319 GLU cc_start: 0.8537 (tt0) cc_final: 0.8187 (tm-30) REVERT: C 9 ASN cc_start: 0.8731 (p0) cc_final: 0.8190 (p0) REVERT: C 319 GLU cc_start: 0.8542 (tt0) cc_final: 0.8159 (tm-30) REVERT: D 9 ASN cc_start: 0.8751 (p0) cc_final: 0.8260 (p0) REVERT: D 319 GLU cc_start: 0.8472 (tt0) cc_final: 0.8147 (tm-30) REVERT: E 9 ASN cc_start: 0.8637 (p0) cc_final: 0.8149 (p0) REVERT: E 186 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7977 (mp0) REVERT: E 319 GLU cc_start: 0.8595 (tt0) cc_final: 0.8305 (tm-30) REVERT: F 9 ASN cc_start: 0.8645 (p0) cc_final: 0.8168 (p0) REVERT: F 186 GLU cc_start: 0.8267 (mt-10) cc_final: 0.8040 (mp0) REVERT: F 319 GLU cc_start: 0.8518 (tt0) cc_final: 0.8108 (tm-30) REVERT: G 9 ASN cc_start: 0.8729 (p0) cc_final: 0.8243 (p0) REVERT: G 186 GLU cc_start: 0.8274 (mt-10) cc_final: 0.8022 (mp0) REVERT: G 319 GLU cc_start: 0.8497 (tt0) cc_final: 0.8179 (tm-30) REVERT: H 9 ASN cc_start: 0.8685 (p0) cc_final: 0.8188 (p0) REVERT: H 319 GLU cc_start: 0.8410 (tt0) cc_final: 0.8110 (tm-30) REVERT: I 9 ASN cc_start: 0.8687 (p0) cc_final: 0.8191 (p0) REVERT: I 319 GLU cc_start: 0.8463 (tt0) cc_final: 0.8198 (tm-30) REVERT: J 9 ASN cc_start: 0.8655 (p0) cc_final: 0.8134 (p0) REVERT: J 319 GLU cc_start: 0.8549 (tt0) cc_final: 0.8267 (tm-30) REVERT: K 9 ASN cc_start: 0.8800 (p0) cc_final: 0.8257 (p0) REVERT: K 186 GLU cc_start: 0.8237 (mt-10) cc_final: 0.8015 (mp0) REVERT: K 319 GLU cc_start: 0.8573 (tt0) cc_final: 0.8268 (tm-30) REVERT: L 9 ASN cc_start: 0.8699 (p0) cc_final: 0.8244 (p0) REVERT: L 186 GLU cc_start: 0.8281 (mt-10) cc_final: 0.7999 (mp0) REVERT: L 319 GLU cc_start: 0.8530 (tt0) cc_final: 0.8198 (tm-30) outliers start: 0 outliers final: 0 residues processed: 562 average time/residue: 3.8590 time to fit residues: 2434.2031 Evaluate side-chains 275 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 275 time to evaluate : 3.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 324 optimal weight: 1.9990 chunk 291 optimal weight: 6.9990 chunk 161 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 196 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 300 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 183 optimal weight: 8.9990 chunk 224 optimal weight: 4.9990 chunk 348 optimal weight: 0.6980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN A 140 HIS A 296 GLN B 96 GLN B 296 GLN B 297 GLN C 96 GLN C 296 GLN D 40 ASN D 96 GLN D 297 GLN E 40 ASN E 96 GLN E 296 GLN E 297 GLN F 96 GLN F 296 GLN F 297 GLN G 96 GLN G 296 GLN G 297 GLN H 40 ASN H 96 GLN H 296 GLN I 96 GLN I 296 GLN J 96 GLN J 296 GLN K 40 ASN K 96 GLN K 140 HIS K 296 GLN K 297 GLN L 96 GLN L 296 GLN L 297 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 32280 Z= 0.224 Angle : 0.754 24.867 43704 Z= 0.368 Chirality : 0.116 1.581 4764 Planarity : 0.004 0.051 5484 Dihedral : 10.746 72.328 5052 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.28 % Allowed : 9.30 % Favored : 90.42 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.12), residues: 3912 helix: -1.47 (0.10), residues: 2256 sheet: -1.51 (0.28), residues: 324 loop : -2.63 (0.16), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 198 HIS 0.004 0.001 HIS I 252 PHE 0.010 0.001 PHE B 303 TYR 0.008 0.001 TYR C 217 ARG 0.015 0.001 ARG F 35 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 314 time to evaluate : 3.869 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: A 9 ASN cc_start: 0.8724 (p0) cc_final: 0.8190 (p0) REVERT: A 131 MET cc_start: 0.8993 (mmm) cc_final: 0.8777 (mmm) REVERT: A 319 GLU cc_start: 0.8498 (tt0) cc_final: 0.8272 (tm-30) REVERT: B 9 ASN cc_start: 0.8680 (p0) cc_final: 0.8152 (p0) REVERT: B 319 GLU cc_start: 0.8546 (tt0) cc_final: 0.8315 (tm-30) REVERT: C 9 ASN cc_start: 0.8692 (p0) cc_final: 0.8143 (p0) REVERT: C 319 GLU cc_start: 0.8527 (tt0) cc_final: 0.8264 (tm-30) REVERT: D 9 ASN cc_start: 0.8739 (p0) cc_final: 0.8243 (p0) REVERT: D 236 GLU cc_start: 0.8918 (mm-30) cc_final: 0.8652 (mm-30) REVERT: E 9 ASN cc_start: 0.8667 (p0) cc_final: 0.8168 (p0) REVERT: E 186 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7958 (mp0) REVERT: F 9 ASN cc_start: 0.8665 (p0) cc_final: 0.8200 (p0) REVERT: F 131 MET cc_start: 0.8856 (mmm) cc_final: 0.8642 (mmm) REVERT: F 186 GLU cc_start: 0.8269 (mt-10) cc_final: 0.8048 (mp0) REVERT: G 9 ASN cc_start: 0.8747 (p0) cc_final: 0.8276 (p0) REVERT: G 88 GLU cc_start: 0.7733 (pp20) cc_final: 0.7491 (pp20) REVERT: G 186 GLU cc_start: 0.8275 (mt-10) cc_final: 0.8015 (mp0) REVERT: H 9 ASN cc_start: 0.8735 (p0) cc_final: 0.8253 (p0) REVERT: H 131 MET cc_start: 0.8970 (mmm) cc_final: 0.8767 (mmm) REVERT: I 9 ASN cc_start: 0.8677 (p0) cc_final: 0.8123 (p0) REVERT: I 236 GLU cc_start: 0.8872 (mm-30) cc_final: 0.8605 (mm-30) REVERT: J 9 ASN cc_start: 0.8638 (p0) cc_final: 0.8094 (p0) REVERT: K 9 ASN cc_start: 0.8803 (p0) cc_final: 0.8264 (p0) REVERT: K 186 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7952 (mp0) REVERT: K 236 GLU cc_start: 0.9023 (mm-30) cc_final: 0.8765 (mm-30) REVERT: L 9 ASN cc_start: 0.8714 (p0) cc_final: 0.8263 (p0) REVERT: L 186 GLU cc_start: 0.8272 (mt-10) cc_final: 0.8007 (mp0) REVERT: L 319 GLU cc_start: 0.8559 (tt0) cc_final: 0.8293 (tm-30) outliers start: 9 outliers final: 0 residues processed: 322 average time/residue: 3.0279 time to fit residues: 1133.3665 Evaluate side-chains 260 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 260 time to evaluate : 3.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 193 optimal weight: 6.9990 chunk 108 optimal weight: 5.9990 chunk 290 optimal weight: 7.9990 chunk 237 optimal weight: 2.9990 chunk 96 optimal weight: 8.9990 chunk 349 optimal weight: 3.9990 chunk 377 optimal weight: 4.9990 chunk 311 optimal weight: 10.0000 chunk 346 optimal weight: 2.9990 chunk 119 optimal weight: 10.0000 chunk 280 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN B 96 GLN B 278 ASN C 96 GLN C 278 ASN D 96 GLN D 278 ASN E 96 GLN E 278 ASN E 297 GLN F 96 GLN F 278 ASN G 96 GLN H 96 GLN I 96 GLN I 278 ASN J 96 GLN J 278 ASN K 96 GLN K 278 ASN L 96 GLN L 278 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 32280 Z= 0.386 Angle : 0.815 26.459 43704 Z= 0.403 Chirality : 0.129 1.764 4764 Planarity : 0.004 0.066 5484 Dihedral : 10.017 61.669 5052 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.72 % Allowed : 10.02 % Favored : 88.26 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 9.09 % 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: -1.41 (0.13), residues: 3912 helix: -0.39 (0.11), residues: 2256 sheet: -0.43 (0.29), residues: 324 loop : -1.84 (0.18), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP J 198 HIS 0.004 0.001 HIS C 196 PHE 0.027 0.002 PHE G 228 TYR 0.016 0.002 TYR D 217 ARG 0.006 0.001 ARG J 70 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 279 time to evaluate : 3.822 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: A 9 ASN cc_start: 0.8699 (p0) cc_final: 0.8118 (p0) REVERT: A 186 GLU cc_start: 0.8364 (mp0) cc_final: 0.8093 (mp0) REVERT: B 9 ASN cc_start: 0.8681 (p0) cc_final: 0.8097 (p0) REVERT: B 249 GLN cc_start: 0.9508 (OUTLIER) cc_final: 0.9286 (pp30) REVERT: C 9 ASN cc_start: 0.8693 (p0) cc_final: 0.8118 (p0) REVERT: C 319 GLU cc_start: 0.8635 (tt0) cc_final: 0.8425 (tm-30) REVERT: D 9 ASN cc_start: 0.8791 (p0) cc_final: 0.8244 (p0) REVERT: E 9 ASN cc_start: 0.8750 (p0) cc_final: 0.8218 (p0) REVERT: E 186 GLU cc_start: 0.8448 (mt-10) cc_final: 0.8062 (mt-10) REVERT: E 319 GLU cc_start: 0.8817 (tm-30) cc_final: 0.8187 (tm-30) REVERT: F 9 ASN cc_start: 0.8688 (p0) cc_final: 0.8169 (p0) REVERT: F 186 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8179 (mp0) REVERT: G 9 ASN cc_start: 0.8746 (p0) cc_final: 0.8207 (p0) REVERT: G 186 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8180 (mp0) REVERT: G 319 GLU cc_start: 0.8809 (tm-30) cc_final: 0.8187 (tm-30) REVERT: H 9 ASN cc_start: 0.8768 (p0) cc_final: 0.8223 (p0) REVERT: I 9 ASN cc_start: 0.8685 (p0) cc_final: 0.8085 (p0) REVERT: I 236 GLU cc_start: 0.9046 (mm-30) cc_final: 0.8794 (mm-30) REVERT: I 319 GLU cc_start: 0.8831 (tm-30) cc_final: 0.8241 (tm-30) REVERT: J 9 ASN cc_start: 0.8651 (p0) cc_final: 0.8077 (p0) REVERT: J 319 GLU cc_start: 0.8851 (tm-30) cc_final: 0.8232 (tm-30) REVERT: K 9 ASN cc_start: 0.8760 (p0) cc_final: 0.8168 (p0) REVERT: K 186 GLU cc_start: 0.8428 (mt-10) cc_final: 0.8108 (mp0) REVERT: K 319 GLU cc_start: 0.8889 (tm-30) cc_final: 0.8244 (tm-30) REVERT: L 9 ASN cc_start: 0.8767 (p0) cc_final: 0.8267 (p0) REVERT: L 186 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8164 (mp0) outliers start: 55 outliers final: 2 residues processed: 313 average time/residue: 2.9318 time to fit residues: 1073.7735 Evaluate side-chains 250 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 247 time to evaluate : 3.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 249 GLN Chi-restraints excluded: chain F residue 194 SER Chi-restraints excluded: chain I residue 95 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 345 optimal weight: 3.9990 chunk 262 optimal weight: 5.9990 chunk 181 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 166 optimal weight: 4.9990 chunk 234 optimal weight: 4.9990 chunk 350 optimal weight: 2.9990 chunk 371 optimal weight: 0.9980 chunk 183 optimal weight: 10.0000 chunk 332 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN B 96 GLN C 96 GLN D 96 GLN E 96 GLN F 96 GLN G 96 GLN H 96 GLN I 96 GLN J 96 GLN K 96 GLN L 96 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 32280 Z= 0.285 Angle : 0.740 25.863 43704 Z= 0.357 Chirality : 0.127 1.782 4764 Planarity : 0.003 0.036 5484 Dihedral : 9.720 67.778 5052 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.40 % Allowed : 11.36 % Favored : 87.23 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 9.09 % 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: -0.62 (0.14), residues: 3912 helix: 0.27 (0.11), residues: 2244 sheet: -0.13 (0.28), residues: 324 loop : -1.53 (0.18), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP I 198 HIS 0.003 0.001 HIS C 140 PHE 0.022 0.002 PHE E 228 TYR 0.011 0.001 TYR I 217 ARG 0.006 0.001 ARG C 28 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 271 time to evaluate : 3.814 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: A 9 ASN cc_start: 0.8660 (p0) cc_final: 0.8221 (p0) REVERT: A 319 GLU cc_start: 0.8538 (tm-30) cc_final: 0.8068 (tm-30) REVERT: B 9 ASN cc_start: 0.8666 (p0) cc_final: 0.8222 (p0) REVERT: B 85 GLU cc_start: 0.7910 (tm-30) cc_final: 0.7502 (tm-30) REVERT: B 249 GLN cc_start: 0.9534 (OUTLIER) cc_final: 0.9318 (pp30) REVERT: B 319 GLU cc_start: 0.8540 (tm-30) cc_final: 0.8074 (tm-30) REVERT: C 9 ASN cc_start: 0.8660 (p0) cc_final: 0.8236 (p0) REVERT: D 9 ASN cc_start: 0.8740 (p0) cc_final: 0.8268 (p0) REVERT: D 11 ASP cc_start: 0.8496 (OUTLIER) cc_final: 0.8227 (m-30) REVERT: E 9 ASN cc_start: 0.8694 (p0) cc_final: 0.8245 (p0) REVERT: E 11 ASP cc_start: 0.8528 (OUTLIER) cc_final: 0.8262 (m-30) REVERT: E 85 GLU cc_start: 0.8129 (tm-30) cc_final: 0.7926 (tm-30) REVERT: E 186 GLU cc_start: 0.8425 (mt-10) cc_final: 0.7999 (mp0) REVERT: E 319 GLU cc_start: 0.8740 (tm-30) cc_final: 0.8098 (tm-30) REVERT: F 9 ASN cc_start: 0.8680 (p0) cc_final: 0.8231 (p0) REVERT: F 11 ASP cc_start: 0.8537 (OUTLIER) cc_final: 0.8295 (m-30) REVERT: F 186 GLU cc_start: 0.8392 (mt-10) cc_final: 0.8025 (mp0) REVERT: G 9 ASN cc_start: 0.8712 (p0) cc_final: 0.8296 (p0) REVERT: G 11 ASP cc_start: 0.8537 (OUTLIER) cc_final: 0.8257 (m-30) REVERT: G 186 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8001 (mp0) REVERT: G 319 GLU cc_start: 0.8680 (tm-30) cc_final: 0.8305 (tm-30) REVERT: H 9 ASN cc_start: 0.8752 (p0) cc_final: 0.8272 (p0) REVERT: H 11 ASP cc_start: 0.8473 (OUTLIER) cc_final: 0.8220 (m-30) REVERT: I 9 ASN cc_start: 0.8649 (p0) cc_final: 0.8162 (p0) REVERT: I 11 ASP cc_start: 0.8494 (OUTLIER) cc_final: 0.8266 (m-30) REVERT: I 319 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8116 (tm-30) REVERT: J 9 ASN cc_start: 0.8610 (p0) cc_final: 0.8151 (p0) REVERT: J 11 ASP cc_start: 0.8477 (OUTLIER) cc_final: 0.8265 (m-30) REVERT: J 85 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7646 (tm-30) REVERT: J 319 GLU cc_start: 0.8707 (tm-30) cc_final: 0.8322 (tm-30) REVERT: K 9 ASN cc_start: 0.8733 (p0) cc_final: 0.8271 (p0) REVERT: K 11 ASP cc_start: 0.8501 (OUTLIER) cc_final: 0.8266 (m-30) REVERT: K 142 GLN cc_start: 0.9359 (OUTLIER) cc_final: 0.9088 (mp10) REVERT: K 186 GLU cc_start: 0.8381 (mt-10) cc_final: 0.8099 (mp0) REVERT: K 319 GLU cc_start: 0.8727 (tm-30) cc_final: 0.8315 (tm-30) REVERT: L 9 ASN cc_start: 0.8739 (p0) cc_final: 0.8341 (p0) REVERT: L 11 ASP cc_start: 0.8464 (OUTLIER) cc_final: 0.8214 (m-30) REVERT: L 186 GLU cc_start: 0.8419 (mt-10) cc_final: 0.7995 (mp0) REVERT: L 319 GLU cc_start: 0.8544 (tm-30) cc_final: 0.8063 (tm-30) outliers start: 45 outliers final: 5 residues processed: 313 average time/residue: 2.4225 time to fit residues: 908.8500 Evaluate side-chains 274 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 258 time to evaluate : 3.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 249 GLN Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain F residue 11 ASP Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain I residue 11 ASP Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain J residue 11 ASP Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 142 GLN Chi-restraints excluded: chain L residue 11 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 309 optimal weight: 4.9990 chunk 210 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 276 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 316 optimal weight: 2.9990 chunk 256 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 189 optimal weight: 1.9990 chunk 333 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN A 278 ASN B 96 GLN D 96 GLN E 25 ASN E 96 GLN F 96 GLN G 25 ASN G 96 GLN G 278 ASN H 96 GLN H 278 ASN I 96 GLN K 25 ASN K 96 GLN L 96 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.4493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 32280 Z= 0.333 Angle : 0.747 25.939 43704 Z= 0.362 Chirality : 0.128 1.741 4764 Planarity : 0.003 0.030 5484 Dihedral : 9.750 73.236 5052 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.47 % Allowed : 11.95 % Favored : 86.58 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 9.09 % 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: -0.17 (0.14), residues: 3912 helix: 0.48 (0.11), residues: 2268 sheet: 0.49 (0.26), residues: 420 loop : -1.31 (0.19), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 198 HIS 0.005 0.001 HIS C 196 PHE 0.029 0.002 PHE L 228 TYR 0.012 0.001 TYR C 217 ARG 0.005 0.000 ARG I 28 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 271 time to evaluate : 3.892 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: A 9 ASN cc_start: 0.8892 (p0) cc_final: 0.8387 (p0) REVERT: A 319 GLU cc_start: 0.8520 (tm-30) cc_final: 0.8202 (tm-30) REVERT: B 9 ASN cc_start: 0.8885 (p0) cc_final: 0.8388 (p0) REVERT: B 249 GLN cc_start: 0.9571 (OUTLIER) cc_final: 0.9357 (pp30) REVERT: B 319 GLU cc_start: 0.8519 (tm-30) cc_final: 0.8064 (tm-30) REVERT: C 9 ASN cc_start: 0.8888 (p0) cc_final: 0.8412 (p0) REVERT: C 319 GLU cc_start: 0.8640 (tm-30) cc_final: 0.8150 (tm-30) REVERT: D 9 ASN cc_start: 0.8740 (p0) cc_final: 0.8263 (p0) REVERT: D 11 ASP cc_start: 0.8548 (OUTLIER) cc_final: 0.8309 (m-30) REVERT: D 249 GLN cc_start: 0.9559 (OUTLIER) cc_final: 0.9323 (pp30) REVERT: E 9 ASN cc_start: 0.8719 (p0) cc_final: 0.8244 (p0) REVERT: E 11 ASP cc_start: 0.8518 (OUTLIER) cc_final: 0.8265 (m-30) REVERT: E 186 GLU cc_start: 0.8427 (mt-10) cc_final: 0.8076 (mt-10) REVERT: E 319 GLU cc_start: 0.8856 (tm-30) cc_final: 0.8187 (tm-30) REVERT: F 9 ASN cc_start: 0.8664 (p0) cc_final: 0.8205 (p0) REVERT: F 11 ASP cc_start: 0.8587 (OUTLIER) cc_final: 0.8361 (m-30) REVERT: F 186 GLU cc_start: 0.8401 (mt-10) cc_final: 0.7999 (mp0) REVERT: G 9 ASN cc_start: 0.8681 (p0) cc_final: 0.8256 (p0) REVERT: G 11 ASP cc_start: 0.8548 (OUTLIER) cc_final: 0.8277 (m-30) REVERT: G 186 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8129 (mm-30) REVERT: G 319 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8327 (tm-30) REVERT: H 9 ASN cc_start: 0.8727 (p0) cc_final: 0.8231 (p0) REVERT: H 11 ASP cc_start: 0.8515 (OUTLIER) cc_final: 0.8283 (m-30) REVERT: I 9 ASN cc_start: 0.8671 (p0) cc_final: 0.8180 (p0) REVERT: I 11 ASP cc_start: 0.8504 (OUTLIER) cc_final: 0.8289 (m-30) REVERT: I 249 GLN cc_start: 0.9571 (OUTLIER) cc_final: 0.9325 (pp30) REVERT: I 319 GLU cc_start: 0.8748 (tm-30) cc_final: 0.8320 (tm-30) REVERT: J 9 ASN cc_start: 0.8659 (p0) cc_final: 0.8168 (p0) REVERT: J 11 ASP cc_start: 0.8508 (OUTLIER) cc_final: 0.8286 (m-30) REVERT: J 249 GLN cc_start: 0.9592 (OUTLIER) cc_final: 0.9356 (pp30) REVERT: J 319 GLU cc_start: 0.8781 (tm-30) cc_final: 0.8352 (tm-30) REVERT: K 9 ASN cc_start: 0.8756 (p0) cc_final: 0.8275 (p0) REVERT: K 11 ASP cc_start: 0.8534 (OUTLIER) cc_final: 0.8307 (m-30) REVERT: K 186 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8100 (mp0) REVERT: K 319 GLU cc_start: 0.8788 (tm-30) cc_final: 0.8179 (tm-30) REVERT: L 9 ASN cc_start: 0.8705 (p0) cc_final: 0.8247 (p0) REVERT: L 11 ASP cc_start: 0.8540 (OUTLIER) cc_final: 0.8280 (m-30) REVERT: L 186 GLU cc_start: 0.8405 (mt-10) cc_final: 0.8003 (mp0) outliers start: 47 outliers final: 4 residues processed: 299 average time/residue: 2.5329 time to fit residues: 912.0408 Evaluate side-chains 260 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 243 time to evaluate : 3.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 249 GLN Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 249 GLN Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain F residue 11 ASP Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain I residue 11 ASP Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 249 GLN Chi-restraints excluded: chain J residue 11 ASP Chi-restraints excluded: chain J residue 249 GLN Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain L residue 11 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 124 optimal weight: 3.9990 chunk 334 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 217 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 371 optimal weight: 1.9990 chunk 308 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 195 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN B 96 GLN C 96 GLN D 25 ASN D 96 GLN E 96 GLN F 25 ASN F 96 GLN G 96 GLN I 96 GLN J 96 GLN K 96 GLN L 96 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.4705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 32280 Z= 0.255 Angle : 0.724 25.841 43704 Z= 0.347 Chirality : 0.127 1.716 4764 Planarity : 0.003 0.027 5484 Dihedral : 9.648 78.496 5052 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.15 % Allowed : 12.83 % Favored : 86.02 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 9.09 % 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: 0.24 (0.14), residues: 3912 helix: 0.89 (0.11), residues: 2196 sheet: 0.61 (0.26), residues: 420 loop : -1.18 (0.18), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 198 HIS 0.003 0.001 HIS C 196 PHE 0.022 0.002 PHE E 228 TYR 0.010 0.001 TYR K 217 ARG 0.002 0.000 ARG H 28 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 257 time to evaluate : 3.868 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 9 ASN cc_start: 0.8880 (p0) cc_final: 0.8367 (p0) REVERT: A 319 GLU cc_start: 0.8560 (tm-30) cc_final: 0.8034 (tm-30) REVERT: B 9 ASN cc_start: 0.8860 (p0) cc_final: 0.8361 (p0) REVERT: B 249 GLN cc_start: 0.9570 (OUTLIER) cc_final: 0.9355 (pp30) REVERT: B 319 GLU cc_start: 0.8541 (tm-30) cc_final: 0.8019 (tm-30) REVERT: C 9 ASN cc_start: 0.8888 (p0) cc_final: 0.8397 (p0) REVERT: C 319 GLU cc_start: 0.8550 (tm-30) cc_final: 0.8017 (tm-30) REVERT: D 9 ASN cc_start: 0.8725 (p0) cc_final: 0.8245 (p0) REVERT: D 11 ASP cc_start: 0.8567 (OUTLIER) cc_final: 0.8318 (m-30) REVERT: D 85 GLU cc_start: 0.8032 (tm-30) cc_final: 0.7722 (tm-30) REVERT: D 249 GLN cc_start: 0.9579 (OUTLIER) cc_final: 0.9344 (pp30) REVERT: E 9 ASN cc_start: 0.8698 (p0) cc_final: 0.8205 (p0) REVERT: E 11 ASP cc_start: 0.8582 (OUTLIER) cc_final: 0.8343 (m-30) REVERT: E 186 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8026 (mt-10) REVERT: E 319 GLU cc_start: 0.8836 (tm-30) cc_final: 0.8119 (tm-30) REVERT: F 9 ASN cc_start: 0.8656 (p0) cc_final: 0.8202 (p0) REVERT: F 186 GLU cc_start: 0.8390 (mt-10) cc_final: 0.7995 (mp0) REVERT: G 9 ASN cc_start: 0.8689 (p0) cc_final: 0.8244 (p0) REVERT: G 11 ASP cc_start: 0.8597 (OUTLIER) cc_final: 0.8328 (m-30) REVERT: G 85 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7648 (tm-30) REVERT: G 319 GLU cc_start: 0.8777 (tm-30) cc_final: 0.8306 (tm-30) REVERT: H 9 ASN cc_start: 0.8711 (p0) cc_final: 0.8212 (p0) REVERT: H 11 ASP cc_start: 0.8553 (OUTLIER) cc_final: 0.8317 (m-30) REVERT: I 9 ASN cc_start: 0.8677 (p0) cc_final: 0.8168 (p0) REVERT: I 249 GLN cc_start: 0.9578 (OUTLIER) cc_final: 0.9331 (pp30) REVERT: I 319 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8292 (tm-30) REVERT: J 9 ASN cc_start: 0.8648 (p0) cc_final: 0.8156 (p0) REVERT: J 85 GLU cc_start: 0.8087 (tm-30) cc_final: 0.7750 (tm-30) REVERT: J 319 GLU cc_start: 0.8786 (tm-30) cc_final: 0.8315 (tm-30) REVERT: K 9 ASN cc_start: 0.8758 (p0) cc_final: 0.8227 (p0) REVERT: K 186 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8104 (mp0) REVERT: K 319 GLU cc_start: 0.8801 (tm-30) cc_final: 0.8317 (tm-30) REVERT: L 9 ASN cc_start: 0.8690 (p0) cc_final: 0.8242 (p0) REVERT: L 11 ASP cc_start: 0.8579 (OUTLIER) cc_final: 0.8361 (m-30) REVERT: L 186 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8177 (mm-30) REVERT: L 319 GLU cc_start: 0.8645 (tm-30) cc_final: 0.8134 (tm-30) outliers start: 37 outliers final: 0 residues processed: 278 average time/residue: 2.6471 time to fit residues: 885.9435 Evaluate side-chains 256 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 248 time to evaluate : 3.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 249 GLN Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain D residue 249 GLN Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain I residue 249 GLN Chi-restraints excluded: chain L residue 11 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 358 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 211 optimal weight: 1.9990 chunk 271 optimal weight: 8.9990 chunk 210 optimal weight: 4.9990 chunk 312 optimal weight: 5.9990 chunk 207 optimal weight: 0.7980 chunk 370 optimal weight: 5.9990 chunk 231 optimal weight: 5.9990 chunk 225 optimal weight: 0.9980 chunk 170 optimal weight: 6.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 ASN A 96 GLN D 96 GLN E 96 GLN H 25 ASN H 96 GLN I 25 ASN J 25 ASN K 96 GLN L 25 ASN L 96 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.4880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 32280 Z= 0.232 Angle : 0.722 25.880 43704 Z= 0.344 Chirality : 0.127 1.715 4764 Planarity : 0.003 0.029 5484 Dihedral : 9.547 83.755 5052 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.15 % Allowed : 13.11 % Favored : 85.74 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 9.09 % 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: 0.47 (0.14), residues: 3912 helix: 1.08 (0.11), residues: 2196 sheet: 0.68 (0.26), residues: 420 loop : -1.09 (0.18), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 198 HIS 0.003 0.001 HIS C 196 PHE 0.023 0.002 PHE F 228 TYR 0.010 0.001 TYR C 217 ARG 0.002 0.000 ARG I 28 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 265 time to evaluate : 3.837 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 9 ASN cc_start: 0.8877 (p0) cc_final: 0.8368 (p0) REVERT: A 319 GLU cc_start: 0.8555 (tm-30) cc_final: 0.7991 (tm-30) REVERT: B 9 ASN cc_start: 0.8850 (p0) cc_final: 0.8367 (p0) REVERT: B 319 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8004 (tm-30) REVERT: C 9 ASN cc_start: 0.8884 (p0) cc_final: 0.8394 (p0) REVERT: C 154 GLN cc_start: 0.8883 (tt0) cc_final: 0.8616 (tt0) REVERT: C 319 GLU cc_start: 0.8593 (tm-30) cc_final: 0.8009 (tm-30) REVERT: D 9 ASN cc_start: 0.8690 (p0) cc_final: 0.8192 (p0) REVERT: D 11 ASP cc_start: 0.8578 (OUTLIER) cc_final: 0.8352 (m-30) REVERT: E 9 ASN cc_start: 0.8702 (p0) cc_final: 0.8236 (p0) REVERT: E 186 GLU cc_start: 0.8398 (mt-10) cc_final: 0.8197 (mm-30) REVERT: E 319 GLU cc_start: 0.8844 (tm-30) cc_final: 0.8113 (tm-30) REVERT: F 9 ASN cc_start: 0.8854 (p0) cc_final: 0.8408 (p0) REVERT: F 186 GLU cc_start: 0.8380 (mt-10) cc_final: 0.7974 (mp0) REVERT: G 9 ASN cc_start: 0.8705 (p0) cc_final: 0.8225 (p0) REVERT: G 11 ASP cc_start: 0.8616 (OUTLIER) cc_final: 0.8394 (m-30) REVERT: G 319 GLU cc_start: 0.8788 (tm-30) cc_final: 0.8283 (tm-30) REVERT: H 9 ASN cc_start: 0.8700 (p0) cc_final: 0.8202 (p0) REVERT: H 11 ASP cc_start: 0.8563 (OUTLIER) cc_final: 0.8342 (m-30) REVERT: I 9 ASN cc_start: 0.8886 (p0) cc_final: 0.8417 (p0) REVERT: I 319 GLU cc_start: 0.8746 (tm-30) cc_final: 0.8267 (tm-30) REVERT: J 9 ASN cc_start: 0.8849 (p0) cc_final: 0.8351 (p0) REVERT: J 319 GLU cc_start: 0.8796 (tm-30) cc_final: 0.8302 (tm-30) REVERT: K 9 ASN cc_start: 0.8948 (p0) cc_final: 0.8457 (p0) REVERT: K 186 GLU cc_start: 0.8363 (mt-10) cc_final: 0.8045 (mp0) REVERT: K 319 GLU cc_start: 0.8811 (tm-30) cc_final: 0.8080 (tm-30) REVERT: L 9 ASN cc_start: 0.8686 (p0) cc_final: 0.8213 (p0) REVERT: L 11 ASP cc_start: 0.8621 (OUTLIER) cc_final: 0.8406 (m-30) REVERT: L 186 GLU cc_start: 0.8365 (mt-10) cc_final: 0.8152 (mm-30) REVERT: L 319 GLU cc_start: 0.8700 (tm-30) cc_final: 0.8178 (tm-30) outliers start: 37 outliers final: 0 residues processed: 279 average time/residue: 2.7285 time to fit residues: 900.7769 Evaluate side-chains 256 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 252 time to evaluate : 3.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain L residue 11 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 228 optimal weight: 6.9990 chunk 147 optimal weight: 1.9990 chunk 221 optimal weight: 4.9990 chunk 111 optimal weight: 0.0980 chunk 72 optimal weight: 0.7980 chunk 71 optimal weight: 6.9990 chunk 235 optimal weight: 2.9990 chunk 252 optimal weight: 0.0070 chunk 182 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 290 optimal weight: 7.9990 overall best weight: 1.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 GLN C 96 GLN F 96 GLN G 96 GLN I 96 GLN J 96 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.4987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 32280 Z= 0.170 Angle : 0.712 25.927 43704 Z= 0.336 Chirality : 0.127 1.715 4764 Planarity : 0.003 0.026 5484 Dihedral : 9.361 89.492 5052 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.78 % Allowed : 13.45 % Favored : 85.77 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 9.09 % 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: 0.80 (0.14), residues: 3912 helix: 1.37 (0.11), residues: 2196 sheet: 0.67 (0.26), residues: 420 loop : -0.94 (0.19), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 198 HIS 0.002 0.001 HIS L 196 PHE 0.017 0.001 PHE D 228 TYR 0.009 0.001 TYR H 217 ARG 0.003 0.000 ARG J 28 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 280 time to evaluate : 3.808 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 9 ASN cc_start: 0.8846 (p0) cc_final: 0.8353 (p0) REVERT: A 319 GLU cc_start: 0.8545 (tm-30) cc_final: 0.7946 (tm-30) REVERT: B 9 ASN cc_start: 0.8826 (p0) cc_final: 0.8365 (p0) REVERT: B 154 GLN cc_start: 0.8887 (tt0) cc_final: 0.8620 (tt0) REVERT: B 319 GLU cc_start: 0.8536 (tm-30) cc_final: 0.7949 (tm-30) REVERT: C 9 ASN cc_start: 0.8868 (p0) cc_final: 0.8399 (p0) REVERT: C 154 GLN cc_start: 0.8859 (tt0) cc_final: 0.8611 (tt0) REVERT: C 319 GLU cc_start: 0.8574 (tm-30) cc_final: 0.7930 (tm-30) REVERT: D 9 ASN cc_start: 0.8678 (p0) cc_final: 0.8205 (p0) REVERT: D 215 LYS cc_start: 0.8821 (mttp) cc_final: 0.8594 (mttp) REVERT: E 9 ASN cc_start: 0.8873 (p0) cc_final: 0.8450 (p0) REVERT: E 319 GLU cc_start: 0.8799 (tm-30) cc_final: 0.8235 (tm-30) REVERT: F 9 ASN cc_start: 0.8845 (p0) cc_final: 0.8414 (p0) REVERT: F 186 GLU cc_start: 0.8361 (mt-10) cc_final: 0.7969 (mp0) REVERT: G 9 ASN cc_start: 0.8688 (p0) cc_final: 0.8111 (p0) REVERT: G 319 GLU cc_start: 0.8733 (tm-30) cc_final: 0.8222 (tm-30) REVERT: H 9 ASN cc_start: 0.8681 (p0) cc_final: 0.8217 (p0) REVERT: I 9 ASN cc_start: 0.8865 (p0) cc_final: 0.8404 (p0) REVERT: I 319 GLU cc_start: 0.8741 (tm-30) cc_final: 0.8237 (tm-30) REVERT: J 9 ASN cc_start: 0.8826 (p0) cc_final: 0.8324 (p0) REVERT: J 85 GLU cc_start: 0.8071 (tm-30) cc_final: 0.7773 (tm-30) REVERT: J 319 GLU cc_start: 0.8761 (tm-30) cc_final: 0.7994 (tm-30) REVERT: K 9 ASN cc_start: 0.8925 (p0) cc_final: 0.8441 (p0) REVERT: K 186 GLU cc_start: 0.8360 (mt-10) cc_final: 0.7994 (mp0) REVERT: K 319 GLU cc_start: 0.8792 (tm-30) cc_final: 0.8040 (tm-30) REVERT: L 9 ASN cc_start: 0.8718 (p0) cc_final: 0.8188 (p0) REVERT: L 319 GLU cc_start: 0.8664 (tm-30) cc_final: 0.8037 (tm-30) outliers start: 25 outliers final: 0 residues processed: 290 average time/residue: 2.7877 time to fit residues: 952.3502 Evaluate side-chains 258 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 258 time to evaluate : 3.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 336 optimal weight: 4.9990 chunk 354 optimal weight: 7.9990 chunk 323 optimal weight: 10.0000 chunk 344 optimal weight: 5.9990 chunk 207 optimal weight: 8.9990 chunk 150 optimal weight: 5.9990 chunk 270 optimal weight: 3.9990 chunk 105 optimal weight: 0.4980 chunk 311 optimal weight: 10.0000 chunk 326 optimal weight: 4.9990 chunk 343 optimal weight: 5.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN D 96 GLN E 96 GLN H 96 GLN K 96 GLN L 96 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.5192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 32280 Z= 0.376 Angle : 0.768 25.531 43704 Z= 0.372 Chirality : 0.128 1.719 4764 Planarity : 0.003 0.025 5484 Dihedral : 9.596 89.840 5052 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.09 % Allowed : 13.30 % Favored : 85.61 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 9.09 % 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: 0.36 (0.14), residues: 3912 helix: 0.95 (0.11), residues: 2268 sheet: 0.73 (0.25), residues: 420 loop : -1.22 (0.19), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 198 HIS 0.006 0.002 HIS K 140 PHE 0.031 0.002 PHE C 228 TYR 0.013 0.001 TYR A 217 ARG 0.002 0.000 ARG J 28 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 248 time to evaluate : 3.836 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 9 ASN cc_start: 0.8869 (p0) cc_final: 0.8363 (p0) REVERT: B 9 ASN cc_start: 0.8839 (p0) cc_final: 0.8354 (p0) REVERT: B 154 GLN cc_start: 0.8923 (tt0) cc_final: 0.8646 (tt0) REVERT: B 186 GLU cc_start: 0.8429 (tt0) cc_final: 0.8226 (tt0) REVERT: B 319 GLU cc_start: 0.8548 (tm-30) cc_final: 0.7933 (tm-30) REVERT: C 9 ASN cc_start: 0.8873 (p0) cc_final: 0.8385 (p0) REVERT: C 154 GLN cc_start: 0.8926 (tt0) cc_final: 0.8659 (tt0) REVERT: C 319 GLU cc_start: 0.8578 (tm-30) cc_final: 0.8078 (tm-30) REVERT: D 9 ASN cc_start: 0.8899 (p0) cc_final: 0.8409 (p0) REVERT: D 319 GLU cc_start: 0.9062 (OUTLIER) cc_final: 0.8210 (tm-30) REVERT: E 9 ASN cc_start: 0.8867 (p0) cc_final: 0.8402 (p0) REVERT: E 319 GLU cc_start: 0.8812 (tm-30) cc_final: 0.8149 (tm-30) REVERT: F 9 ASN cc_start: 0.8859 (p0) cc_final: 0.8413 (p0) REVERT: F 186 GLU cc_start: 0.8397 (mt-10) cc_final: 0.7992 (mp0) REVERT: F 319 GLU cc_start: 0.9080 (OUTLIER) cc_final: 0.8060 (tm-30) REVERT: G 9 ASN cc_start: 0.8702 (p0) cc_final: 0.8193 (p0) REVERT: G 11 ASP cc_start: 0.8648 (OUTLIER) cc_final: 0.8415 (m-30) REVERT: G 154 GLN cc_start: 0.9000 (tt0) cc_final: 0.8702 (tt0) REVERT: G 319 GLU cc_start: 0.8775 (tm-30) cc_final: 0.8088 (tm-30) REVERT: H 9 ASN cc_start: 0.8908 (p0) cc_final: 0.8413 (p0) REVERT: I 9 ASN cc_start: 0.8887 (p0) cc_final: 0.8408 (p0) REVERT: I 319 GLU cc_start: 0.8758 (tm-30) cc_final: 0.8086 (tm-30) REVERT: J 9 ASN cc_start: 0.8875 (p0) cc_final: 0.8367 (p0) REVERT: J 85 GLU cc_start: 0.8020 (tm-30) cc_final: 0.7761 (tm-30) REVERT: J 186 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7711 (mt-10) REVERT: J 319 GLU cc_start: 0.8784 (tm-30) cc_final: 0.8097 (tm-30) REVERT: K 9 ASN cc_start: 0.8947 (p0) cc_final: 0.8470 (p0) REVERT: K 186 GLU cc_start: 0.8398 (mt-10) cc_final: 0.8047 (mt-10) REVERT: K 319 GLU cc_start: 0.8786 (tm-30) cc_final: 0.8102 (tm-30) REVERT: L 9 ASN cc_start: 0.8699 (p0) cc_final: 0.8225 (p0) REVERT: L 319 GLU cc_start: 0.8692 (tm-30) cc_final: 0.8130 (tm-30) outliers start: 35 outliers final: 3 residues processed: 264 average time/residue: 2.7754 time to fit residues: 861.6515 Evaluate side-chains 246 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 240 time to evaluate : 3.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 85 GLU Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain K residue 142 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 226 optimal weight: 6.9990 chunk 364 optimal weight: 4.9990 chunk 222 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 chunk 253 optimal weight: 4.9990 chunk 382 optimal weight: 1.9990 chunk 352 optimal weight: 8.9990 chunk 304 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 235 optimal weight: 0.9980 chunk 186 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 GLN C 25 ASN C 96 GLN F 96 GLN G 96 GLN J 96 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.5279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 32280 Z= 0.208 Angle : 0.733 26.045 43704 Z= 0.348 Chirality : 0.127 1.722 4764 Planarity : 0.003 0.027 5484 Dihedral : 9.006 89.168 5052 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.53 % Allowed : 14.08 % Favored : 85.39 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 9.09 % 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: 0.71 (0.14), residues: 3912 helix: 1.22 (0.11), residues: 2340 sheet: 0.73 (0.26), residues: 420 loop : -1.13 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 198 HIS 0.003 0.001 HIS L 196 PHE 0.020 0.001 PHE D 228 TYR 0.009 0.001 TYR K 217 ARG 0.002 0.000 ARG I 28 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 259 time to evaluate : 4.728 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 9 ASN cc_start: 0.8844 (p0) cc_final: 0.8348 (p0) REVERT: A 186 GLU cc_start: 0.8246 (mt-10) cc_final: 0.8017 (tt0) REVERT: A 319 GLU cc_start: 0.8723 (tm-30) cc_final: 0.8223 (tm-30) REVERT: B 9 ASN cc_start: 0.8823 (p0) cc_final: 0.8348 (p0) REVERT: B 154 GLN cc_start: 0.8914 (tt0) cc_final: 0.8650 (tt0) REVERT: B 319 GLU cc_start: 0.8594 (tm-30) cc_final: 0.7938 (tm-30) REVERT: C 9 ASN cc_start: 0.8844 (p0) cc_final: 0.8369 (p0) REVERT: C 154 GLN cc_start: 0.8871 (tt0) cc_final: 0.8626 (tt0) REVERT: C 319 GLU cc_start: 0.8603 (tm-30) cc_final: 0.7892 (tm-30) REVERT: D 9 ASN cc_start: 0.8880 (p0) cc_final: 0.8396 (p0) REVERT: D 319 GLU cc_start: 0.9013 (OUTLIER) cc_final: 0.8043 (tm-30) REVERT: E 9 ASN cc_start: 0.8863 (p0) cc_final: 0.8409 (p0) REVERT: E 319 GLU cc_start: 0.8806 (tm-30) cc_final: 0.8013 (tm-30) REVERT: F 9 ASN cc_start: 0.8826 (p0) cc_final: 0.8378 (p0) REVERT: F 186 GLU cc_start: 0.8358 (mt-10) cc_final: 0.7964 (mp0) REVERT: F 319 GLU cc_start: 0.9055 (OUTLIER) cc_final: 0.8089 (tm-30) REVERT: G 9 ASN cc_start: 0.8681 (p0) cc_final: 0.8176 (p0) REVERT: G 154 GLN cc_start: 0.8938 (tt0) cc_final: 0.8695 (tt0) REVERT: G 319 GLU cc_start: 0.8782 (tm-30) cc_final: 0.7975 (tm-30) REVERT: H 9 ASN cc_start: 0.8878 (p0) cc_final: 0.8396 (p0) REVERT: I 9 ASN cc_start: 0.8871 (p0) cc_final: 0.8396 (p0) REVERT: I 154 GLN cc_start: 0.8986 (tt0) cc_final: 0.8732 (tt0) REVERT: I 319 GLU cc_start: 0.8763 (tm-30) cc_final: 0.7961 (tm-30) REVERT: J 9 ASN cc_start: 0.8850 (p0) cc_final: 0.8348 (p0) REVERT: J 154 GLN cc_start: 0.8981 (tt0) cc_final: 0.8724 (tt0) REVERT: J 319 GLU cc_start: 0.8800 (tm-30) cc_final: 0.8012 (tm-30) REVERT: K 9 ASN cc_start: 0.8916 (p0) cc_final: 0.8441 (p0) REVERT: K 186 GLU cc_start: 0.8367 (mt-10) cc_final: 0.7999 (mp0) REVERT: K 319 GLU cc_start: 0.8805 (tm-30) cc_final: 0.8019 (tm-30) REVERT: L 9 ASN cc_start: 0.8847 (p0) cc_final: 0.8385 (p0) REVERT: L 319 GLU cc_start: 0.8697 (tm-30) cc_final: 0.8062 (tm-30) outliers start: 17 outliers final: 0 residues processed: 269 average time/residue: 2.8421 time to fit residues: 899.2744 Evaluate side-chains 245 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 243 time to evaluate : 4.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain F residue 319 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 241 optimal weight: 5.9990 chunk 324 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 280 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 305 optimal weight: 0.9980 chunk 127 optimal weight: 0.9980 chunk 313 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN D 96 GLN E 96 GLN K 96 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.064965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.046995 restraints weight = 271212.001| |-----------------------------------------------------------------------------| r_work (start): 0.2619 rms_B_bonded: 3.40 r_work: 0.2465 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9005 moved from start: 0.5413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 32280 Z= 0.274 Angle : 0.742 25.603 43704 Z= 0.358 Chirality : 0.127 1.717 4764 Planarity : 0.003 0.032 5484 Dihedral : 8.711 83.867 5052 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.31 % Allowed : 14.42 % Favored : 85.27 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 9.09 % 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: 0.64 (0.14), residues: 3912 helix: 1.13 (0.11), residues: 2340 sheet: 0.74 (0.25), residues: 420 loop : -1.08 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 198 HIS 0.006 0.001 HIS C 196 PHE 0.027 0.002 PHE F 228 TYR 0.013 0.001 TYR D 217 ARG 0.002 0.000 ARG I 28 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16652.79 seconds wall clock time: 291 minutes 57.81 seconds (17517.81 seconds total)