Starting phenix.real_space_refine on Tue Mar 12 06:24:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kou_0740/03_2024/6kou_0740.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kou_0740/03_2024/6kou_0740.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kou_0740/03_2024/6kou_0740.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kou_0740/03_2024/6kou_0740.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kou_0740/03_2024/6kou_0740.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kou_0740/03_2024/6kou_0740.pdb" } resolution = 2.43 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= 0.007 sd= 0.380 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mg 24 5.21 5 S 120 5.16 5 C 20004 2.51 5 N 5076 2.21 5 O 5760 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 ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 236": "OE1" <-> "OE2" Residue "D ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 236": "OE1" <-> "OE2" Residue "F ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J GLU 236": "OE1" <-> "OE2" Residue "J ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L GLU 236": "OE1" <-> "OE2" Residue "L ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 62209 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 21.54, per 1000 atoms: 0.35 Number of scatterers: 62209 At special positions: 0 Unit cell: (145.32, 144.48, 143.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 120 16.00 Mg 24 11.99 O 5760 8.00 N 5076 7.00 C 20004 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: 43.76 Conformation dependent library (CDL) restraints added in 5.3 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... Secondary structure from input PDB file: 216 helices and 12 sheets defined 65.9% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.81 Creating SS restraints... Processing helix chain 'A' and resid 24 through 37 removed outlier: 3.504A pdb=" N VAL A 29 " --> pdb=" O ASN A 25 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR A 32 " --> pdb=" O ARG A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 57 removed outlier: 3.508A pdb=" N GLU A 52 " --> pdb=" O ASP A 48 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS A 55 " --> pdb=" O TYR A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 71 removed outlier: 3.580A pdb=" N ARG A 69 " --> pdb=" O ASP A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 90 Processing helix chain 'A' and resid 90 through 97 removed outlier: 3.996A pdb=" N VAL A 94 " --> pdb=" O LYS A 90 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLY A 97 " --> pdb=" O PRO A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 113 Processing helix chain 'A' and resid 133 through 141 removed outlier: 4.042A pdb=" N MET A 137 " --> pdb=" O GLY A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 171 Processing helix chain 'A' and resid 184 through 197 removed outlier: 4.267A pdb=" N LEU A 190 " --> pdb=" O GLU A 186 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU A 195 " --> pdb=" O ASP A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 218 removed outlier: 3.623A pdb=" N ILE A 201 " --> pdb=" O THR A 197 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR A 217 " --> pdb=" O ALA A 213 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY A 218 " --> pdb=" O VAL A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 229 Processing helix chain 'A' and resid 232 through 244 Processing helix chain 'A' and resid 247 through 253 removed outlier: 3.595A pdb=" N VAL A 251 " --> pdb=" O ASN A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 268 Processing helix chain 'A' and resid 268 through 285 removed outlier: 3.937A pdb=" N VAL A 272 " --> pdb=" O TYR A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 299 removed outlier: 3.626A pdb=" N GLN A 297 " --> pdb=" O SER A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 312 Processing helix chain 'A' and resid 313 through 324 Processing helix chain 'B' and resid 24 through 37 removed outlier: 3.870A pdb=" N GLU B 36 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN B 37 " --> pdb=" O ILE B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 57 removed outlier: 3.700A pdb=" N LYS B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 71 removed outlier: 3.680A pdb=" N ARG B 69 " --> pdb=" O ASP B 65 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG B 70 " --> pdb=" O GLU B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 90 Processing helix chain 'B' and resid 90 through 97 removed outlier: 4.204A pdb=" N VAL B 94 " --> pdb=" O LYS B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 113 Processing helix chain 'B' and resid 133 through 141 removed outlier: 3.863A pdb=" N MET B 137 " --> pdb=" O GLY B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 171 Processing helix chain 'B' and resid 184 through 197 removed outlier: 4.160A pdb=" N LEU B 190 " --> pdb=" O GLU B 186 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU B 195 " --> pdb=" O ASP B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 218 removed outlier: 3.659A pdb=" N ILE B 201 " --> pdb=" O THR B 197 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR B 217 " --> pdb=" O ALA B 213 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLY B 218 " --> pdb=" O VAL B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 229 Processing helix chain 'B' and resid 232 through 244 removed outlier: 3.559A pdb=" N GLU B 236 " --> pdb=" O GLY B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 253 Processing helix chain 'B' and resid 254 through 268 Processing helix chain 'B' and resid 268 through 285 removed outlier: 3.937A pdb=" N VAL B 272 " --> pdb=" O TYR B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 299 Processing helix chain 'B' and resid 300 through 312 Processing helix chain 'B' and resid 313 through 324 Processing helix chain 'C' and resid 24 through 37 removed outlier: 3.895A pdb=" N GLU C 36 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN C 37 " --> pdb=" O ILE C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 Processing helix chain 'C' and resid 63 through 71 Processing helix chain 'C' and resid 82 through 90 Processing helix chain 'C' and resid 90 through 97 removed outlier: 4.047A pdb=" N VAL C 94 " --> pdb=" O LYS C 90 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLY C 97 " --> pdb=" O PRO C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 113 Processing helix chain 'C' and resid 133 through 141 removed outlier: 4.035A pdb=" N MET C 137 " --> pdb=" O GLY C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 171 Processing helix chain 'C' and resid 184 through 195 removed outlier: 4.192A pdb=" N LEU C 190 " --> pdb=" O GLU C 186 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU C 195 " --> pdb=" O ASP C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 217 removed outlier: 3.647A pdb=" N ILE C 201 " --> pdb=" O THR C 197 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR C 217 " --> pdb=" O ALA C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 229 Processing helix chain 'C' and resid 232 through 245 Processing helix chain 'C' and resid 247 through 253 Processing helix chain 'C' and resid 254 through 268 Processing helix chain 'C' and resid 268 through 285 removed outlier: 3.939A pdb=" N VAL C 272 " --> pdb=" O TYR C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 299 Processing helix chain 'C' and resid 300 through 312 Processing helix chain 'C' and resid 313 through 324 Processing helix chain 'D' and resid 24 through 37 removed outlier: 3.895A pdb=" N GLU D 36 " --> pdb=" O THR D 32 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN D 37 " --> pdb=" O ILE D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 57 Processing helix chain 'D' and resid 63 through 71 removed outlier: 3.642A pdb=" N ARG D 69 " --> pdb=" O ASP D 65 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG D 70 " --> pdb=" O GLU D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 90 Processing helix chain 'D' and resid 90 through 97 removed outlier: 4.046A pdb=" N VAL D 94 " --> pdb=" O LYS D 90 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLY D 97 " --> pdb=" O PRO D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 113 Processing helix chain 'D' and resid 133 through 141 removed outlier: 3.835A pdb=" N MET D 137 " --> pdb=" O GLY D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 171 Processing helix chain 'D' and resid 184 through 197 removed outlier: 4.157A pdb=" N LEU D 190 " --> pdb=" O GLU D 186 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU D 195 " --> pdb=" O ASP D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 217 removed outlier: 3.656A pdb=" N ILE D 201 " --> pdb=" O THR D 197 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR D 217 " --> pdb=" O ALA D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 229 Processing helix chain 'D' and resid 232 through 245 removed outlier: 3.537A pdb=" N GLU D 236 " --> pdb=" O GLY D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 253 removed outlier: 3.531A pdb=" N VAL D 251 " --> pdb=" O ASN D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 268 Processing helix chain 'D' and resid 268 through 285 removed outlier: 3.941A pdb=" N VAL D 272 " --> pdb=" O TYR D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 299 removed outlier: 3.623A pdb=" N GLN D 297 " --> pdb=" O SER D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 312 Processing helix chain 'D' and resid 313 through 324 Processing helix chain 'E' and resid 24 through 37 removed outlier: 3.793A pdb=" N GLU E 36 " --> pdb=" O THR E 32 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN E 37 " --> pdb=" O ILE E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 57 Processing helix chain 'E' and resid 63 through 71 removed outlier: 3.665A pdb=" N ARG E 69 " --> pdb=" O ASP E 65 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG E 70 " --> pdb=" O GLU E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 90 Processing helix chain 'E' and resid 90 through 97 removed outlier: 3.962A pdb=" N VAL E 94 " --> pdb=" O LYS E 90 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLY E 97 " --> pdb=" O PRO E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 113 Processing helix chain 'E' and resid 133 through 141 removed outlier: 4.032A pdb=" N MET E 137 " --> pdb=" O GLY E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 171 Processing helix chain 'E' and resid 184 through 197 removed outlier: 4.159A pdb=" N LEU E 190 " --> pdb=" O GLU E 186 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU E 195 " --> pdb=" O ASP E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 218 removed outlier: 3.637A pdb=" N ILE E 201 " --> pdb=" O THR E 197 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR E 217 " --> pdb=" O ALA E 213 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY E 218 " --> pdb=" O VAL E 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 229 Processing helix chain 'E' and resid 232 through 244 Processing helix chain 'E' and resid 247 through 253 Processing helix chain 'E' and resid 254 through 268 Processing helix chain 'E' and resid 268 through 285 removed outlier: 3.936A pdb=" N VAL E 272 " --> pdb=" O TYR E 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 299 Processing helix chain 'E' and resid 300 through 312 Processing helix chain 'E' and resid 313 through 324 Processing helix chain 'F' and resid 24 through 37 removed outlier: 3.634A pdb=" N THR F 32 " --> pdb=" O ARG F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 57 Processing helix chain 'F' and resid 63 through 71 removed outlier: 3.623A pdb=" N ARG F 69 " --> pdb=" O ASP F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 90 Processing helix chain 'F' and resid 90 through 97 removed outlier: 4.009A pdb=" N VAL F 94 " --> pdb=" O LYS F 90 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLY F 97 " --> pdb=" O PRO F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 113 Processing helix chain 'F' and resid 133 through 141 removed outlier: 4.260A pdb=" N MET F 137 " --> pdb=" O GLY F 133 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP F 138 " --> pdb=" O GLU F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 171 Processing helix chain 'F' and resid 184 through 197 removed outlier: 4.181A pdb=" N LEU F 190 " --> pdb=" O GLU F 186 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU F 195 " --> pdb=" O ASP F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 217 removed outlier: 3.662A pdb=" N ILE F 201 " --> pdb=" O THR F 197 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR F 217 " --> pdb=" O ALA F 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 229 Processing helix chain 'F' and resid 232 through 245 removed outlier: 3.541A pdb=" N GLU F 236 " --> pdb=" O GLY F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 253 Processing helix chain 'F' and resid 254 through 268 Processing helix chain 'F' and resid 268 through 285 removed outlier: 3.941A pdb=" N VAL F 272 " --> pdb=" O TYR F 268 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 299 removed outlier: 3.627A pdb=" N GLN F 297 " --> pdb=" O SER F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 312 Processing helix chain 'F' and resid 313 through 324 Processing helix chain 'G' and resid 24 through 37 removed outlier: 3.545A pdb=" N VAL G 29 " --> pdb=" O ASN G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 57 removed outlier: 3.682A pdb=" N LYS G 55 " --> pdb=" O TYR G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 71 removed outlier: 3.622A pdb=" N ARG G 69 " --> pdb=" O ASP G 65 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG G 70 " --> pdb=" O GLU G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 90 Processing helix chain 'G' and resid 90 through 97 removed outlier: 4.046A pdb=" N VAL G 94 " --> pdb=" O LYS G 90 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLY G 97 " --> pdb=" O PRO G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 113 Processing helix chain 'G' and resid 133 through 141 removed outlier: 4.029A pdb=" N MET G 137 " --> pdb=" O GLY G 133 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS G 141 " --> pdb=" O MET G 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 171 Processing helix chain 'G' and resid 184 through 197 removed outlier: 4.157A pdb=" N LEU G 190 " --> pdb=" O GLU G 186 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU G 195 " --> pdb=" O ASP G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 217 removed outlier: 3.663A pdb=" N ILE G 201 " --> pdb=" O THR G 197 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR G 217 " --> pdb=" O ALA G 213 " (cutoff:3.500A) Processing helix chain 'G' and resid 220 through 229 Processing helix chain 'G' and resid 232 through 245 Processing helix chain 'G' and resid 247 through 253 Processing helix chain 'G' and resid 254 through 268 Processing helix chain 'G' and resid 268 through 285 removed outlier: 3.934A pdb=" N VAL G 272 " --> pdb=" O TYR G 268 " (cutoff:3.500A) Processing helix chain 'G' and resid 286 through 299 Processing helix chain 'G' and resid 300 through 312 Processing helix chain 'G' and resid 313 through 324 Processing helix chain 'H' and resid 24 through 37 removed outlier: 3.558A pdb=" N VAL H 29 " --> pdb=" O ASN H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 57 Processing helix chain 'H' and resid 63 through 71 Processing helix chain 'H' and resid 82 through 90 Processing helix chain 'H' and resid 90 through 97 removed outlier: 4.150A pdb=" N VAL H 94 " --> pdb=" O LYS H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 113 Processing helix chain 'H' and resid 133 through 141 removed outlier: 4.081A pdb=" N MET H 137 " --> pdb=" O GLY H 133 " (cutoff:3.500A) Processing helix chain 'H' and resid 159 through 171 Processing helix chain 'H' and resid 184 through 197 removed outlier: 4.189A pdb=" N LEU H 190 " --> pdb=" O GLU H 186 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU H 195 " --> pdb=" O ASP H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 197 through 218 removed outlier: 3.632A pdb=" N ILE H 201 " --> pdb=" O THR H 197 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR H 217 " --> pdb=" O ALA H 213 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLY H 218 " --> pdb=" O VAL H 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 220 through 229 Processing helix chain 'H' and resid 232 through 244 Processing helix chain 'H' and resid 247 through 253 removed outlier: 3.576A pdb=" N VAL H 251 " --> pdb=" O ASN H 248 " (cutoff:3.500A) Processing helix chain 'H' and resid 254 through 268 Processing helix chain 'H' and resid 268 through 285 removed outlier: 3.893A pdb=" N VAL H 272 " --> pdb=" O TYR H 268 " (cutoff:3.500A) Processing helix chain 'H' and resid 286 through 299 removed outlier: 3.516A pdb=" N LYS H 290 " --> pdb=" O GLY H 286 " (cutoff:3.500A) Processing helix chain 'H' and resid 300 through 312 Processing helix chain 'H' and resid 313 through 326 Processing helix chain 'I' and resid 24 through 37 removed outlier: 3.570A pdb=" N VAL I 29 " --> pdb=" O ASN I 25 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 57 Processing helix chain 'I' and resid 63 through 71 removed outlier: 3.581A pdb=" N ARG I 69 " --> pdb=" O ASP I 65 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG I 70 " --> pdb=" O GLU I 66 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 90 Processing helix chain 'I' and resid 90 through 97 removed outlier: 4.042A pdb=" N VAL I 94 " --> pdb=" O LYS I 90 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLY I 97 " --> pdb=" O PRO I 93 " (cutoff:3.500A) Processing helix chain 'I' and resid 108 through 113 Processing helix chain 'I' and resid 133 through 141 removed outlier: 4.180A pdb=" N MET I 137 " --> pdb=" O GLY I 133 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP I 138 " --> pdb=" O GLU I 134 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 171 Processing helix chain 'I' and resid 184 through 197 removed outlier: 4.178A pdb=" N LEU I 190 " --> pdb=" O GLU I 186 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU I 195 " --> pdb=" O ASP I 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 197 through 218 removed outlier: 3.660A pdb=" N ILE I 201 " --> pdb=" O THR I 197 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR I 217 " --> pdb=" O ALA I 213 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY I 218 " --> pdb=" O VAL I 214 " (cutoff:3.500A) Processing helix chain 'I' and resid 220 through 229 Processing helix chain 'I' and resid 232 through 245 removed outlier: 3.549A pdb=" N GLU I 236 " --> pdb=" O GLY I 232 " (cutoff:3.500A) Processing helix chain 'I' and resid 247 through 253 Processing helix chain 'I' and resid 254 through 268 Processing helix chain 'I' and resid 268 through 285 removed outlier: 3.920A pdb=" N VAL I 272 " --> pdb=" O TYR I 268 " (cutoff:3.500A) Processing helix chain 'I' and resid 286 through 299 removed outlier: 3.624A pdb=" N GLN I 297 " --> pdb=" O SER I 293 " (cutoff:3.500A) Processing helix chain 'I' and resid 300 through 312 Processing helix chain 'I' and resid 313 through 324 Processing helix chain 'J' and resid 24 through 37 removed outlier: 3.510A pdb=" N VAL J 29 " --> pdb=" O ASN J 25 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU J 36 " --> pdb=" O THR J 32 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN J 37 " --> pdb=" O ILE J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 48 through 57 Processing helix chain 'J' and resid 63 through 71 removed outlier: 3.585A pdb=" N ARG J 69 " --> pdb=" O ASP J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 90 Processing helix chain 'J' and resid 90 through 97 removed outlier: 4.002A pdb=" N VAL J 94 " --> pdb=" O LYS J 90 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLY J 97 " --> pdb=" O PRO J 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 113 Processing helix chain 'J' and resid 133 through 141 removed outlier: 3.994A pdb=" N MET J 137 " --> pdb=" O GLY J 133 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 171 Processing helix chain 'J' and resid 184 through 197 removed outlier: 4.201A pdb=" N LEU J 190 " --> pdb=" O GLU J 186 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLU J 195 " --> pdb=" O ASP J 191 " (cutoff:3.500A) Processing helix chain 'J' and resid 197 through 217 removed outlier: 3.657A pdb=" N ILE J 201 " --> pdb=" O THR J 197 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR J 217 " --> pdb=" O ALA J 213 " (cutoff:3.500A) Processing helix chain 'J' and resid 220 through 229 Processing helix chain 'J' and resid 232 through 245 Processing helix chain 'J' and resid 247 through 253 Processing helix chain 'J' and resid 254 through 268 Processing helix chain 'J' and resid 268 through 285 removed outlier: 3.937A pdb=" N VAL J 272 " --> pdb=" O TYR J 268 " (cutoff:3.500A) Processing helix chain 'J' and resid 286 through 299 removed outlier: 3.625A pdb=" N GLN J 297 " --> pdb=" O SER J 293 " (cutoff:3.500A) Processing helix chain 'J' and resid 300 through 312 Processing helix chain 'J' and resid 313 through 326 Processing helix chain 'K' and resid 24 through 37 removed outlier: 3.618A pdb=" N VAL K 29 " --> pdb=" O ASN K 25 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR K 32 " --> pdb=" O ARG K 28 " (cutoff:3.500A) Processing helix chain 'K' and resid 48 through 57 removed outlier: 3.540A pdb=" N GLU K 52 " --> pdb=" O ASP K 48 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS K 55 " --> pdb=" O TYR K 51 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 71 removed outlier: 3.702A pdb=" N ARG K 69 " --> pdb=" O ASP K 65 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 90 Processing helix chain 'K' and resid 90 through 97 removed outlier: 4.164A pdb=" N VAL K 94 " --> pdb=" O LYS K 90 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 113 Processing helix chain 'K' and resid 133 through 141 removed outlier: 4.037A pdb=" N MET K 137 " --> pdb=" O GLY K 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 159 through 171 Processing helix chain 'K' and resid 184 through 195 removed outlier: 4.193A pdb=" N LEU K 190 " --> pdb=" O GLU K 186 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU K 195 " --> pdb=" O ASP K 191 " (cutoff:3.500A) Processing helix chain 'K' and resid 197 through 218 removed outlier: 3.645A pdb=" N ILE K 201 " --> pdb=" O THR K 197 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR K 217 " --> pdb=" O ALA K 213 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY K 218 " --> pdb=" O VAL K 214 " (cutoff:3.500A) Processing helix chain 'K' and resid 220 through 229 Processing helix chain 'K' and resid 232 through 245 removed outlier: 3.805A pdb=" N ALA K 242 " --> pdb=" O ALA K 238 " (cutoff:3.500A) Processing helix chain 'K' and resid 247 through 253 removed outlier: 3.572A pdb=" N VAL K 251 " --> pdb=" O ASN K 248 " (cutoff:3.500A) Processing helix chain 'K' and resid 254 through 268 Processing helix chain 'K' and resid 268 through 285 removed outlier: 3.918A pdb=" N VAL K 272 " --> pdb=" O TYR K 268 " (cutoff:3.500A) Processing helix chain 'K' and resid 286 through 299 Processing helix chain 'K' and resid 300 through 312 Processing helix chain 'K' and resid 313 through 326 Processing helix chain 'L' and resid 24 through 37 removed outlier: 3.660A pdb=" N THR L 32 " --> pdb=" O ARG L 28 " (cutoff:3.500A) Processing helix chain 'L' and resid 48 through 57 Processing helix chain 'L' and resid 63 through 71 Processing helix chain 'L' and resid 82 through 90 Processing helix chain 'L' and resid 90 through 97 removed outlier: 4.193A pdb=" N VAL L 94 " --> pdb=" O LYS L 90 " (cutoff:3.500A) Processing helix chain 'L' and resid 108 through 113 Processing helix chain 'L' and resid 133 through 141 removed outlier: 3.994A pdb=" N MET L 137 " --> pdb=" O GLY L 133 " (cutoff:3.500A) Processing helix chain 'L' and resid 159 through 171 Processing helix chain 'L' and resid 184 through 195 removed outlier: 4.170A pdb=" N LEU L 190 " --> pdb=" O GLU L 186 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU L 195 " --> pdb=" O ASP L 191 " (cutoff:3.500A) Processing helix chain 'L' and resid 197 through 217 removed outlier: 3.651A pdb=" N ILE L 201 " --> pdb=" O THR L 197 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR L 217 " --> pdb=" O ALA L 213 " (cutoff:3.500A) Processing helix chain 'L' and resid 220 through 229 Processing helix chain 'L' and resid 232 through 245 removed outlier: 3.522A pdb=" N GLU L 236 " --> pdb=" O GLY L 232 " (cutoff:3.500A) Processing helix chain 'L' and resid 247 through 253 removed outlier: 3.662A pdb=" N VAL L 251 " --> pdb=" O ASN L 248 " (cutoff:3.500A) Processing helix chain 'L' and resid 254 through 268 Processing helix chain 'L' and resid 268 through 285 removed outlier: 3.943A pdb=" N VAL L 272 " --> pdb=" O TYR L 268 " (cutoff:3.500A) Processing helix chain 'L' and resid 286 through 299 removed outlier: 3.531A pdb=" N LYS L 290 " --> pdb=" O GLY L 286 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN L 297 " --> pdb=" O SER L 293 " (cutoff:3.500A) Processing helix chain 'L' and resid 300 through 312 Processing helix chain 'L' and resid 313 through 324 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 5 removed outlier: 6.558A pdb=" N VAL A 148 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N SER A 182 " --> pdb=" O VAL A 148 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N LEU A 150 " --> pdb=" O SER A 182 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N THR A 124 " --> pdb=" O LYS A 153 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N PHE A 101 " --> pdb=" O ASP A 123 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N ILE A 125 " --> pdb=" O PHE A 101 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU A 103 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N VAL A 127 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N PHE A 105 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE A 18 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N GLY A 44 " --> pdb=" O ILE A 18 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL A 20 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 9.047A pdb=" N TYR A 62 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL A 43 " --> pdb=" O TYR A 62 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 4 through 5 removed outlier: 6.514A pdb=" N VAL B 148 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N SER B 182 " --> pdb=" O VAL B 148 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N LEU B 150 " --> pdb=" O SER B 182 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N THR B 124 " --> pdb=" O LYS B 153 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N PHE B 101 " --> pdb=" O ASP B 123 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N ILE B 125 " --> pdb=" O PHE B 101 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU B 103 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N VAL B 127 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N PHE B 105 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ILE B 18 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N GLY B 44 " --> pdb=" O ILE B 18 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL B 20 " --> pdb=" O GLY B 44 " (cutoff:3.500A) removed outlier: 9.046A pdb=" N TYR B 62 " --> pdb=" O VAL B 41 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL B 43 " --> pdb=" O TYR B 62 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 4 through 5 removed outlier: 6.401A pdb=" N THR C 124 " --> pdb=" O LYS C 153 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N PHE C 101 " --> pdb=" O ASP C 123 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N ILE C 125 " --> pdb=" O PHE C 101 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU C 103 " --> pdb=" O ILE C 125 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N VAL C 127 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N PHE C 105 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ILE C 18 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N GLY C 44 " --> pdb=" O ILE C 18 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL C 20 " --> pdb=" O GLY C 44 " (cutoff:3.500A) removed outlier: 9.039A pdb=" N TYR C 62 " --> pdb=" O VAL C 41 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL C 43 " --> pdb=" O TYR C 62 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 4 through 5 removed outlier: 6.406A pdb=" N THR D 124 " --> pdb=" O LYS D 153 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N PHE D 101 " --> pdb=" O ASP D 123 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N ILE D 125 " --> pdb=" O PHE D 101 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU D 103 " --> pdb=" O ILE D 125 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N VAL D 127 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N PHE D 105 " --> pdb=" O VAL D 127 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ILE D 18 " --> pdb=" O ILE D 42 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N GLY D 44 " --> pdb=" O ILE D 18 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N VAL D 20 " --> pdb=" O GLY D 44 " (cutoff:3.500A) removed outlier: 9.107A pdb=" N TYR D 62 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL D 43 " --> pdb=" O TYR D 62 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 4 through 5 removed outlier: 6.403A pdb=" N THR E 124 " --> pdb=" O LYS E 153 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N PHE E 101 " --> pdb=" O ASP E 123 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N ILE E 125 " --> pdb=" O PHE E 101 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU E 103 " --> pdb=" O ILE E 125 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N VAL E 127 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N PHE E 105 " --> pdb=" O VAL E 127 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ILE E 18 " --> pdb=" O ILE E 42 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N GLY E 44 " --> pdb=" O ILE E 18 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL E 20 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 9.069A pdb=" N TYR E 62 " --> pdb=" O VAL E 41 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL E 43 " --> pdb=" O TYR E 62 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 61 through 62 removed outlier: 9.037A pdb=" N TYR F 62 " --> pdb=" O VAL F 41 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL F 43 " --> pdb=" O TYR F 62 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ILE F 18 " --> pdb=" O ILE F 42 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N GLY F 44 " --> pdb=" O ILE F 18 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL F 20 " --> pdb=" O GLY F 44 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N PHE F 101 " --> pdb=" O ASP F 123 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N ILE F 125 " --> pdb=" O PHE F 101 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU F 103 " --> pdb=" O ILE F 125 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N VAL F 127 " --> pdb=" O LEU F 103 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N PHE F 105 " --> pdb=" O VAL F 127 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N THR F 124 " --> pdb=" O LYS F 153 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 4 through 5 removed outlier: 6.523A pdb=" N VAL G 148 " --> pdb=" O VAL G 180 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N SER G 182 " --> pdb=" O VAL G 148 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N LEU G 150 " --> pdb=" O SER G 182 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N THR G 124 " --> pdb=" O LYS G 153 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N PHE G 101 " --> pdb=" O ASP G 123 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N ILE G 125 " --> pdb=" O PHE G 101 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU G 103 " --> pdb=" O ILE G 125 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N VAL G 127 " --> pdb=" O LEU G 103 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N PHE G 105 " --> pdb=" O VAL G 127 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE G 18 " --> pdb=" O ILE G 42 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N GLY G 44 " --> pdb=" O ILE G 18 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL G 20 " --> pdb=" O GLY G 44 " (cutoff:3.500A) removed outlier: 9.016A pdb=" N TYR G 62 " --> pdb=" O VAL G 41 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL G 43 " --> pdb=" O TYR G 62 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 4 through 5 removed outlier: 6.561A pdb=" N VAL H 148 " --> pdb=" O VAL H 180 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N SER H 182 " --> pdb=" O VAL H 148 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N LEU H 150 " --> pdb=" O SER H 182 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N THR H 124 " --> pdb=" O LYS H 153 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N PHE H 101 " --> pdb=" O ASP H 123 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N ILE H 125 " --> pdb=" O PHE H 101 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU H 103 " --> pdb=" O ILE H 125 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N VAL H 127 " --> pdb=" O LEU H 103 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N PHE H 105 " --> pdb=" O VAL H 127 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ILE H 18 " --> pdb=" O ILE H 42 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N GLY H 44 " --> pdb=" O ILE H 18 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N VAL H 20 " --> pdb=" O GLY H 44 " (cutoff:3.500A) removed outlier: 9.048A pdb=" N TYR H 62 " --> pdb=" O VAL H 41 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL H 43 " --> pdb=" O TYR H 62 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 4 through 5 removed outlier: 6.491A pdb=" N VAL I 148 " --> pdb=" O VAL I 180 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N SER I 182 " --> pdb=" O VAL I 148 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N LEU I 150 " --> pdb=" O SER I 182 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N THR I 124 " --> pdb=" O LYS I 153 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N PHE I 101 " --> pdb=" O ASP I 123 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N ILE I 125 " --> pdb=" O PHE I 101 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU I 103 " --> pdb=" O ILE I 125 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N VAL I 127 " --> pdb=" O LEU I 103 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N PHE I 105 " --> pdb=" O VAL I 127 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ILE I 18 " --> pdb=" O ILE I 42 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N GLY I 44 " --> pdb=" O ILE I 18 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL I 20 " --> pdb=" O GLY I 44 " (cutoff:3.500A) removed outlier: 9.004A pdb=" N TYR I 62 " --> pdb=" O VAL I 41 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL I 43 " --> pdb=" O TYR I 62 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 4 through 5 removed outlier: 6.392A pdb=" N THR J 124 " --> pdb=" O LYS J 153 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N PHE J 101 " --> pdb=" O ASP J 123 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N ILE J 125 " --> pdb=" O PHE J 101 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU J 103 " --> pdb=" O ILE J 125 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N VAL J 127 " --> pdb=" O LEU J 103 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N PHE J 105 " --> pdb=" O VAL J 127 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ILE J 18 " --> pdb=" O ILE J 42 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N GLY J 44 " --> pdb=" O ILE J 18 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL J 20 " --> pdb=" O GLY J 44 " (cutoff:3.500A) removed outlier: 9.088A pdb=" N TYR J 62 " --> pdb=" O VAL J 41 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL J 43 " --> pdb=" O TYR J 62 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 4 through 5 removed outlier: 6.505A pdb=" N VAL K 148 " --> pdb=" O VAL K 180 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N SER K 182 " --> pdb=" O VAL K 148 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N LEU K 150 " --> pdb=" O SER K 182 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N THR K 124 " --> pdb=" O LYS K 153 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N PHE K 101 " --> pdb=" O ASP K 123 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N ILE K 125 " --> pdb=" O PHE K 101 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU K 103 " --> pdb=" O ILE K 125 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N VAL K 127 " --> pdb=" O LEU K 103 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N PHE K 105 " --> pdb=" O VAL K 127 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ILE K 18 " --> pdb=" O ILE K 42 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N GLY K 44 " --> pdb=" O ILE K 18 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VAL K 20 " --> pdb=" O GLY K 44 " (cutoff:3.500A) removed outlier: 9.084A pdb=" N TYR K 62 " --> pdb=" O VAL K 41 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL K 43 " --> pdb=" O TYR K 62 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 4 through 5 removed outlier: 6.462A pdb=" N THR L 124 " --> pdb=" O LYS L 153 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N PHE L 101 " --> pdb=" O ASP L 123 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N ILE L 125 " --> pdb=" O PHE L 101 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU L 103 " --> pdb=" O ILE L 125 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N VAL L 127 " --> pdb=" O LEU L 103 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N PHE L 105 " --> pdb=" O VAL L 127 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ILE L 18 " --> pdb=" O ILE L 42 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N GLY L 44 " --> pdb=" O ILE L 18 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL L 20 " --> pdb=" O GLY L 44 " (cutoff:3.500A) removed outlier: 9.075A pdb=" N TYR L 62 " --> pdb=" O VAL L 41 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL L 43 " --> pdb=" O TYR L 62 " (cutoff:3.500A) 1748 hydrogen bonds defined for protein. 5082 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: 23.63 Time building geometry restraints manager: 46.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 31213 1.03 - 1.22: 12 1.22 - 1.42: 13072 1.42 - 1.61: 18296 1.61 - 1.80: 228 Bond restraints: 62821 Sorted by residual: bond pdb=" N GLY G 232 " pdb=" H GLY G 232 " ideal model delta sigma weight residual 0.860 0.919 -0.059 2.00e-02 2.50e+03 8.73e+00 bond pdb=" N SER G 231 " pdb=" H SER G 231 " ideal model delta sigma weight residual 0.860 0.903 -0.043 2.00e-02 2.50e+03 4.73e+00 bond pdb=" N GLU G 233 " pdb=" CA GLU G 233 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.23e-02 6.61e+03 4.42e+00 bond pdb=" N GLY G 232 " pdb=" CA GLY G 232 " ideal model delta sigma weight residual 1.452 1.480 -0.028 1.42e-02 4.96e+03 3.88e+00 bond pdb=" N SER G 231 " pdb=" CA SER G 231 " ideal model delta sigma weight residual 1.454 1.477 -0.023 1.19e-02 7.06e+03 3.59e+00 ... (remaining 62816 not shown) Histogram of bond angle deviations from ideal: 60.34 - 79.23: 84 79.23 - 98.11: 188 98.11 - 117.00: 83186 117.00 - 135.89: 30525 135.89 - 154.78: 3 Bond angle restraints: 113986 Sorted by residual: angle pdb=" C SER G 231 " pdb=" N GLY G 232 " pdb=" CA GLY G 232 " ideal model delta sigma weight residual 120.74 154.78 -34.04 1.72e+00 3.38e-01 3.92e+02 angle pdb=" C LYS K 55 " pdb=" N LYS K 56 " pdb=" H LYS K 56 " ideal model delta sigma weight residual 124.93 70.60 54.33 3.00e+00 1.11e-01 3.28e+02 angle pdb=" CA LYS K 56 " pdb=" N LYS K 56 " pdb=" H LYS K 56 " ideal model delta sigma weight residual 114.63 60.34 54.29 3.00e+00 1.11e-01 3.28e+02 angle pdb=" C GLN L 30 " pdb=" N ALA L 31 " pdb=" H ALA L 31 " ideal model delta sigma weight residual 124.74 70.76 53.98 3.00e+00 1.11e-01 3.24e+02 angle pdb=" CA ALA L 31 " pdb=" N ALA L 31 " pdb=" H ALA L 31 " ideal model delta sigma weight residual 114.44 60.73 53.71 3.00e+00 1.11e-01 3.20e+02 ... (remaining 113981 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.32: 25698 14.32 - 28.64: 2501 28.64 - 42.95: 688 42.95 - 57.27: 307 57.27 - 71.59: 27 Dihedral angle restraints: 29221 sinusoidal: 15868 harmonic: 13353 Sorted by residual: dihedral pdb=" C ALA I 8 " pdb=" N ALA I 8 " pdb=" CA ALA I 8 " pdb=" CB ALA I 8 " ideal model delta harmonic sigma weight residual -122.60 -133.15 10.55 0 2.50e+00 1.60e-01 1.78e+01 dihedral pdb=" N LYS A 3 " pdb=" C LYS A 3 " pdb=" CA LYS A 3 " pdb=" CB LYS A 3 " ideal model delta harmonic sigma weight residual 122.80 132.77 -9.97 0 2.50e+00 1.60e-01 1.59e+01 dihedral pdb=" C ASP K 65 " pdb=" N ASP K 65 " pdb=" CA ASP K 65 " pdb=" CB ASP K 65 " ideal model delta harmonic sigma weight residual -122.60 -132.33 9.73 0 2.50e+00 1.60e-01 1.52e+01 ... (remaining 29218 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.340: 4625 0.340 - 0.680: 14 0.680 - 1.020: 0 1.020 - 1.360: 2 1.360 - 1.700: 27 Chirality restraints: 4668 Sorted by residual: chirality pdb=" CG LEU C 6 " pdb=" CB LEU C 6 " pdb=" CD1 LEU C 6 " pdb=" CD2 LEU C 6 " both_signs ideal model delta sigma weight residual False -2.59 -0.89 -1.70 2.00e-01 2.50e+01 7.22e+01 chirality pdb=" CG LEU L 13 " pdb=" CB LEU L 13 " pdb=" CD1 LEU L 13 " pdb=" CD2 LEU L 13 " both_signs ideal model delta sigma weight residual False -2.59 -0.89 -1.70 2.00e-01 2.50e+01 7.19e+01 chirality pdb=" CG LEU A 75 " pdb=" CB LEU A 75 " pdb=" CD1 LEU A 75 " pdb=" CD2 LEU A 75 " both_signs ideal model delta sigma weight residual False -2.59 -0.90 -1.69 2.00e-01 2.50e+01 7.11e+01 ... (remaining 4665 not shown) Planarity restraints: 9208 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER G 231 " 0.070 2.00e-02 2.50e+03 7.15e-02 5.11e+01 pdb=" N GLY G 232 " -0.098 2.00e-02 2.50e+03 pdb=" CA GLY G 232 " 0.067 2.00e-02 2.50e+03 pdb=" H GLY G 232 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY G 232 " -0.011 2.00e-02 2.50e+03 2.19e-02 4.79e+00 pdb=" C GLY G 232 " 0.038 2.00e-02 2.50e+03 pdb=" O GLY G 232 " -0.014 2.00e-02 2.50e+03 pdb=" N GLU G 233 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU G 233 " -0.006 2.00e-02 2.50e+03 1.29e-02 1.66e+00 pdb=" C GLU G 233 " 0.022 2.00e-02 2.50e+03 pdb=" O GLU G 233 " -0.008 2.00e-02 2.50e+03 pdb=" N LEU G 234 " -0.008 2.00e-02 2.50e+03 ... (remaining 9205 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.09: 1222 2.09 - 2.72: 105986 2.72 - 3.35: 171958 3.35 - 3.97: 219398 3.97 - 4.60: 362319 Nonbonded interactions: 860883 Sorted by model distance: nonbonded pdb=" H PHE K 59 " pdb=" HA PHE K 59 " model vdw 1.467 1.816 nonbonded pdb=" O PRO B 119 " pdb="HE22 GLN B 154 " model vdw 1.515 1.850 nonbonded pdb=" O PRO H 119 " pdb="HE22 GLN H 154 " model vdw 1.526 1.850 nonbonded pdb=" O PRO A 119 " pdb="HE22 GLN A 154 " model vdw 1.532 1.850 nonbonded pdb=" O PRO I 119 " pdb="HE22 GLN I 154 " model vdw 1.539 1.850 ... (remaining 860878 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 through 402)) 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 through 402)) selection = chain 'C' 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 through 402)) 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 through 402)) 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 through 402)) 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 through 402)) 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 through 402)) 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 through 402)) 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 through 402)) 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 through 402)) selection = chain 'L' } 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: 2.290 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: 0.990 Extract box with map and model: 12.460 Check model and map are aligned: 0.720 Set scattering table: 0.460 Process input model: 162.250 Find NCS groups from input model: 3.030 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:10.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 192.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 31596 Z= 0.274 Angle : 0.668 34.038 42660 Z= 0.366 Chirality : 0.126 1.700 4668 Planarity : 0.003 0.027 5424 Dihedral : 11.880 71.591 11736 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % 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: -4.12 (0.11), residues: 3912 helix: -2.21 (0.09), residues: 2376 sheet: -2.71 (0.18), residues: 504 loop : -3.44 (0.14), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 198 HIS 0.006 0.001 HIS J 196 PHE 0.008 0.001 PHE A 288 TYR 0.009 0.001 TYR E 304 ARG 0.003 0.000 ARG D 69 *********************** 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 416 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 416 time to evaluate : 4.245 Fit side-chains revert: symmetry clash REVERT: A 215 LYS cc_start: 0.9007 (mttt) cc_final: 0.8750 (mppt) REVERT: A 274 ARG cc_start: 0.7997 (ttm-80) cc_final: 0.7787 (mtm-85) REVERT: B 215 LYS cc_start: 0.9013 (mttt) cc_final: 0.8736 (mppt) REVERT: B 274 ARG cc_start: 0.8003 (ttm-80) cc_final: 0.7793 (mtm-85) REVERT: C 215 LYS cc_start: 0.9010 (mttt) cc_final: 0.8749 (mppt) REVERT: C 274 ARG cc_start: 0.8019 (ttm-80) cc_final: 0.7819 (mtm-85) REVERT: D 215 LYS cc_start: 0.9006 (mttt) cc_final: 0.8765 (mppt) REVERT: E 215 LYS cc_start: 0.9018 (mttt) cc_final: 0.8773 (mppt) REVERT: E 274 ARG cc_start: 0.7986 (ttm-80) cc_final: 0.7771 (mtm-85) REVERT: F 215 LYS cc_start: 0.9008 (mttt) cc_final: 0.8756 (mppt) REVERT: F 274 ARG cc_start: 0.8013 (ttm-80) cc_final: 0.7812 (mtm-85) REVERT: G 215 LYS cc_start: 0.9013 (mttt) cc_final: 0.8756 (mppt) REVERT: G 243 GLU cc_start: 0.8507 (tp30) cc_final: 0.8036 (tp30) REVERT: G 274 ARG cc_start: 0.8010 (ttm-80) cc_final: 0.7798 (mtm-85) REVERT: H 3 LYS cc_start: 0.9177 (mttt) cc_final: 0.8931 (mppt) REVERT: H 215 LYS cc_start: 0.9011 (mttt) cc_final: 0.8739 (mppt) REVERT: H 274 ARG cc_start: 0.8002 (ttm-80) cc_final: 0.7784 (mtm-85) REVERT: I 215 LYS cc_start: 0.9017 (mttt) cc_final: 0.8766 (mppt) REVERT: I 274 ARG cc_start: 0.8002 (ttm-80) cc_final: 0.7787 (mtm-85) REVERT: J 215 LYS cc_start: 0.9017 (mttt) cc_final: 0.8759 (mppt) REVERT: J 274 ARG cc_start: 0.8008 (ttm-80) cc_final: 0.7796 (mtm-85) REVERT: K 215 LYS cc_start: 0.9020 (mttt) cc_final: 0.8751 (mppt) REVERT: K 274 ARG cc_start: 0.7984 (ttm-80) cc_final: 0.7767 (mtm-85) REVERT: L 3 LYS cc_start: 0.9131 (mttt) cc_final: 0.8917 (mppt) REVERT: L 215 LYS cc_start: 0.9006 (mttt) cc_final: 0.8776 (mppt) outliers start: 0 outliers final: 0 residues processed: 416 average time/residue: 3.3106 time to fit residues: 1572.4131 Evaluate side-chains 260 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 260 time to evaluate : 4.023 ------------------------------------------------------------------------------- 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: 7.9990 chunk 291 optimal weight: 6.9990 chunk 161 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 196 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 300 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 183 optimal weight: 10.0000 chunk 224 optimal weight: 6.9990 chunk 348 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN A 96 GLN A 154 GLN A 278 ASN B 26 GLN B 154 GLN B 278 ASN C 26 GLN C 96 GLN C 278 ASN D 26 GLN D 96 GLN D 278 ASN E 26 GLN E 278 ASN F 26 GLN F 96 GLN F 278 ASN G 26 GLN G 96 GLN G 154 GLN G 278 ASN H 26 GLN H 154 GLN H 278 ASN I 26 GLN I 96 GLN I 154 GLN I 278 ASN J 26 GLN J 96 GLN J 278 ASN K 26 GLN K 278 ASN L 26 GLN L 278 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 31596 Z= 0.347 Angle : 0.731 16.926 42660 Z= 0.385 Chirality : 0.130 1.700 4668 Planarity : 0.003 0.032 5424 Dihedral : 3.990 14.001 4284 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.97 % Allowed : 6.30 % Favored : 92.73 % Cbeta Deviations : 0.06 % 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: -2.29 (0.12), residues: 3912 helix: -0.77 (0.10), residues: 2460 sheet: -1.90 (0.20), residues: 504 loop : -2.90 (0.15), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 198 HIS 0.005 0.001 HIS I 196 PHE 0.013 0.002 PHE B 288 TYR 0.009 0.001 TYR H 300 ARG 0.003 0.000 ARG J 28 *********************** 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 306 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 275 time to evaluate : 4.015 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: B 96 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.8140 (mp10) REVERT: G 243 GLU cc_start: 0.8570 (tp30) cc_final: 0.8020 (tp30) REVERT: H 3 LYS cc_start: 0.9223 (mttt) cc_final: 0.8977 (mppt) REVERT: H 96 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.8037 (mp10) REVERT: K 96 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.8080 (mp10) REVERT: L 96 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.8130 (mp10) outliers start: 31 outliers final: 9 residues processed: 301 average time/residue: 3.2010 time to fit residues: 1106.5069 Evaluate side-chains 257 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 244 time to evaluate : 3.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 GLN Chi-restraints excluded: chain C residue 30 GLN Chi-restraints excluded: chain D residue 30 GLN Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 96 GLN Chi-restraints excluded: chain J residue 321 GLU Chi-restraints excluded: chain K residue 95 LEU Chi-restraints excluded: chain K residue 96 GLN Chi-restraints excluded: chain K residue 243 GLU Chi-restraints excluded: chain K residue 321 GLU Chi-restraints excluded: chain L residue 25 ASN Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain L residue 96 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 193 optimal weight: 7.9990 chunk 108 optimal weight: 3.9990 chunk 290 optimal weight: 6.9990 chunk 237 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 349 optimal weight: 3.9990 chunk 377 optimal weight: 3.9990 chunk 311 optimal weight: 9.9990 chunk 346 optimal weight: 3.9990 chunk 119 optimal weight: 9.9990 chunk 280 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 96 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 31596 Z= 0.348 Angle : 0.719 17.239 42660 Z= 0.375 Chirality : 0.130 1.706 4668 Planarity : 0.003 0.038 5424 Dihedral : 3.974 14.442 4284 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.94 % Allowed : 8.55 % Favored : 90.51 % 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: -1.20 (0.13), residues: 3912 helix: -0.06 (0.10), residues: 2460 sheet: -1.32 (0.21), residues: 516 loop : -2.15 (0.17), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 198 HIS 0.008 0.002 HIS B 196 PHE 0.015 0.002 PHE E 288 TYR 0.008 0.001 TYR C 300 ARG 0.009 0.001 ARG H 274 *********************** 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 271 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 241 time to evaluate : 4.079 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: H 3 LYS cc_start: 0.9226 (mttt) cc_final: 0.8978 (mppt) REVERT: H 96 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.8012 (mp10) outliers start: 30 outliers final: 6 residues processed: 265 average time/residue: 3.2937 time to fit residues: 1004.7922 Evaluate side-chains 234 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 227 time to evaluate : 3.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain H residue 96 GLN Chi-restraints excluded: chain H residue 99 LYS Chi-restraints excluded: chain J residue 321 GLU Chi-restraints excluded: chain K residue 99 LYS Chi-restraints excluded: chain K residue 321 GLU Chi-restraints excluded: chain L residue 99 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 345 optimal weight: 4.9990 chunk 262 optimal weight: 5.9990 chunk 181 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 166 optimal weight: 4.9990 chunk 234 optimal weight: 5.9990 chunk 350 optimal weight: 0.8980 chunk 371 optimal weight: 1.9990 chunk 183 optimal weight: 10.0000 chunk 332 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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 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: 0.8784 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 31596 Z= 0.308 Angle : 0.700 16.811 42660 Z= 0.364 Chirality : 0.129 1.695 4668 Planarity : 0.003 0.042 5424 Dihedral : 3.908 14.994 4284 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.87 % Allowed : 9.02 % Favored : 90.11 % Cbeta Deviations : 0.06 % 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: -0.60 (0.13), residues: 3912 helix: 0.35 (0.10), residues: 2460 sheet: -0.91 (0.22), residues: 516 loop : -1.81 (0.18), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 198 HIS 0.007 0.001 HIS E 196 PHE 0.015 0.002 PHE G 288 TYR 0.009 0.001 TYR K 304 ARG 0.007 0.000 ARG E 274 *********************** 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 268 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 240 time to evaluate : 4.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 2 ASP cc_start: 0.6887 (OUTLIER) cc_final: 0.6607 (p0) REVERT: H 3 LYS cc_start: 0.9202 (mttt) cc_final: 0.8974 (mppt) REVERT: K 96 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.8038 (mp10) REVERT: L 96 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.8028 (mp10) outliers start: 28 outliers final: 2 residues processed: 260 average time/residue: 3.2457 time to fit residues: 974.5954 Evaluate side-chains 241 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 236 time to evaluate : 3.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain J residue 321 GLU Chi-restraints excluded: chain K residue 96 GLN Chi-restraints excluded: chain K residue 321 GLU Chi-restraints excluded: chain L residue 96 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 309 optimal weight: 3.9990 chunk 210 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 276 optimal weight: 3.9990 chunk 153 optimal weight: 4.9990 chunk 316 optimal weight: 3.9990 chunk 256 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 189 optimal weight: 0.9980 chunk 333 optimal weight: 7.9990 chunk 93 optimal weight: 2.9990 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 C 96 GLN E 96 GLN H 96 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 31596 Z= 0.313 Angle : 0.700 16.790 42660 Z= 0.362 Chirality : 0.129 1.696 4668 Planarity : 0.003 0.047 5424 Dihedral : 3.892 14.394 4284 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.97 % Allowed : 9.33 % Favored : 89.70 % Cbeta Deviations : 0.06 % 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: -0.25 (0.13), residues: 3912 helix: 0.56 (0.10), residues: 2460 sheet: -0.77 (0.22), residues: 516 loop : -1.51 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 198 HIS 0.007 0.001 HIS B 196 PHE 0.015 0.002 PHE E 288 TYR 0.009 0.001 TYR K 304 ARG 0.009 0.001 ARG E 274 *********************** 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 278 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 247 time to evaluate : 4.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 2 ASP cc_start: 0.7027 (OUTLIER) cc_final: 0.6721 (p0) REVERT: H 3 LYS cc_start: 0.9214 (mttt) cc_final: 0.8983 (mppt) REVERT: I 243 GLU cc_start: 0.8409 (tp30) cc_final: 0.8187 (tp30) REVERT: J 243 GLU cc_start: 0.8444 (tp30) cc_final: 0.8220 (tp30) outliers start: 31 outliers final: 2 residues processed: 262 average time/residue: 3.2313 time to fit residues: 971.1599 Evaluate side-chains 231 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 228 time to evaluate : 3.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain J residue 321 GLU Chi-restraints excluded: chain K residue 321 GLU 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: 2.9990 chunk 73 optimal weight: 4.9990 chunk 217 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 371 optimal weight: 0.6980 chunk 308 optimal weight: 3.9990 chunk 172 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 195 optimal weight: 2.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 31596 Z= 0.256 Angle : 0.690 16.838 42660 Z= 0.354 Chirality : 0.129 1.697 4668 Planarity : 0.003 0.053 5424 Dihedral : 3.829 14.841 4284 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.37 % Allowed : 10.83 % Favored : 88.80 % Cbeta Deviations : 0.06 % 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: 0.10 (0.13), residues: 3912 helix: 0.80 (0.10), residues: 2460 sheet: -0.58 (0.23), residues: 516 loop : -1.30 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 198 HIS 0.005 0.001 HIS B 196 PHE 0.013 0.002 PHE G 288 TYR 0.008 0.001 TYR K 304 ARG 0.009 0.000 ARG C 274 *********************** 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 240 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 228 time to evaluate : 4.031 Fit side-chains revert: symmetry clash REVERT: E 2 ASP cc_start: 0.7222 (OUTLIER) cc_final: 0.6900 (p0) REVERT: H 3 LYS cc_start: 0.9202 (mttt) cc_final: 0.8983 (mppt) REVERT: I 243 GLU cc_start: 0.8435 (tp30) cc_final: 0.8208 (tp30) REVERT: J 243 GLU cc_start: 0.8470 (tp30) cc_final: 0.8257 (tp30) outliers start: 12 outliers final: 5 residues processed: 233 average time/residue: 3.2491 time to fit residues: 870.6842 Evaluate side-chains 233 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 227 time to evaluate : 3.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain J residue 321 GLU Chi-restraints excluded: chain K residue 95 LEU Chi-restraints excluded: chain K residue 321 GLU Chi-restraints excluded: chain L residue 95 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 358 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 211 optimal weight: 0.9990 chunk 271 optimal weight: 6.9990 chunk 210 optimal weight: 4.9990 chunk 312 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 370 optimal weight: 4.9990 chunk 231 optimal weight: 5.9990 chunk 225 optimal weight: 4.9990 chunk 170 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 31596 Z= 0.296 Angle : 0.700 16.676 42660 Z= 0.361 Chirality : 0.129 1.696 4668 Planarity : 0.004 0.056 5424 Dihedral : 3.835 14.307 4284 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.41 % Allowed : 10.71 % Favored : 88.89 % Cbeta Deviations : 0.06 % 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: 0.29 (0.13), residues: 3912 helix: 0.92 (0.10), residues: 2460 sheet: -0.49 (0.23), residues: 516 loop : -1.14 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 198 HIS 0.006 0.001 HIS F 196 PHE 0.014 0.002 PHE G 288 TYR 0.009 0.001 TYR K 304 ARG 0.012 0.001 ARG L 274 *********************** 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 245 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 232 time to evaluate : 3.971 Fit side-chains revert: symmetry clash REVERT: B 243 GLU cc_start: 0.8381 (tp30) cc_final: 0.8109 (tp30) REVERT: E 2 ASP cc_start: 0.7281 (OUTLIER) cc_final: 0.6971 (p0) REVERT: H 3 LYS cc_start: 0.9213 (mttt) cc_final: 0.8983 (mppt) REVERT: I 243 GLU cc_start: 0.8448 (tp30) cc_final: 0.8220 (tp30) REVERT: J 243 GLU cc_start: 0.8485 (tp30) cc_final: 0.8274 (tp30) REVERT: L 243 GLU cc_start: 0.8428 (tp30) cc_final: 0.8220 (tp30) outliers start: 13 outliers final: 5 residues processed: 238 average time/residue: 3.3149 time to fit residues: 909.9997 Evaluate side-chains 236 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 230 time to evaluate : 4.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain J residue 321 GLU Chi-restraints excluded: chain K residue 95 LEU Chi-restraints excluded: chain K residue 321 GLU Chi-restraints excluded: chain L residue 95 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 228 optimal weight: 8.9990 chunk 147 optimal weight: 0.9980 chunk 221 optimal weight: 2.9990 chunk 111 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 71 optimal weight: 0.3980 chunk 235 optimal weight: 0.7980 chunk 252 optimal weight: 3.9990 chunk 182 optimal weight: 0.7980 chunk 34 optimal weight: 6.9990 chunk 290 optimal weight: 10.0000 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 31596 Z= 0.173 Angle : 0.678 16.899 42660 Z= 0.342 Chirality : 0.128 1.701 4668 Planarity : 0.004 0.059 5424 Dihedral : 3.692 14.325 4284 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.22 % Allowed : 10.96 % Favored : 88.83 % Cbeta Deviations : 0.06 % 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: 0.75 (0.14), residues: 3912 helix: 1.37 (0.10), residues: 2424 sheet: -0.36 (0.23), residues: 516 loop : -1.14 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 198 HIS 0.002 0.000 HIS E 196 PHE 0.009 0.001 PHE K 288 TYR 0.008 0.001 TYR J 51 ARG 0.009 0.000 ARG B 274 *********************** 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 246 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 239 time to evaluate : 4.896 Fit side-chains revert: symmetry clash REVERT: B 243 GLU cc_start: 0.8384 (tp30) cc_final: 0.8107 (tp30) REVERT: E 2 ASP cc_start: 0.7330 (OUTLIER) cc_final: 0.7018 (p0) REVERT: H 3 LYS cc_start: 0.9232 (mttt) cc_final: 0.8979 (mppt) REVERT: I 243 GLU cc_start: 0.8479 (tp30) cc_final: 0.8237 (tp30) REVERT: J 243 GLU cc_start: 0.8518 (tp30) cc_final: 0.8303 (tp30) REVERT: L 243 GLU cc_start: 0.8447 (tp30) cc_final: 0.8229 (tp30) outliers start: 7 outliers final: 6 residues processed: 242 average time/residue: 3.1755 time to fit residues: 884.3925 Evaluate side-chains 240 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 233 time to evaluate : 3.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain J residue 321 GLU Chi-restraints excluded: chain K residue 95 LEU Chi-restraints excluded: chain K residue 321 GLU Chi-restraints excluded: chain L residue 95 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 336 optimal weight: 0.3980 chunk 354 optimal weight: 6.9990 chunk 323 optimal weight: 6.9990 chunk 344 optimal weight: 5.9990 chunk 207 optimal weight: 7.9990 chunk 150 optimal weight: 4.9990 chunk 270 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 311 optimal weight: 8.9990 chunk 326 optimal weight: 4.9990 chunk 343 optimal weight: 7.9990 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 31596 Z= 0.357 Angle : 0.717 16.616 42660 Z= 0.369 Chirality : 0.129 1.702 4668 Planarity : 0.004 0.060 5424 Dihedral : 3.791 14.500 4284 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.28 % Allowed : 11.58 % Favored : 88.14 % Cbeta Deviations : 0.06 % 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: 1.18 (0.10), residues: 2460 sheet: -0.39 (0.23), residues: 516 loop : -1.00 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 198 HIS 0.006 0.001 HIS D 196 PHE 0.016 0.002 PHE A 288 TYR 0.010 0.001 TYR I 300 ARG 0.010 0.001 ARG L 274 *********************** 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 241 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 232 time to evaluate : 4.037 Fit side-chains revert: symmetry clash REVERT: B 243 GLU cc_start: 0.8383 (tp30) cc_final: 0.8151 (tp30) REVERT: E 2 ASP cc_start: 0.7413 (OUTLIER) cc_final: 0.7094 (p0) REVERT: H 3 LYS cc_start: 0.9249 (mttt) cc_final: 0.8976 (mppt) REVERT: I 243 GLU cc_start: 0.8479 (tp30) cc_final: 0.8241 (tp30) REVERT: J 243 GLU cc_start: 0.8529 (tp30) cc_final: 0.8307 (tp30) REVERT: L 243 GLU cc_start: 0.8453 (tp30) cc_final: 0.8229 (tp30) outliers start: 9 outliers final: 6 residues processed: 238 average time/residue: 3.3479 time to fit residues: 917.9235 Evaluate side-chains 239 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 232 time to evaluate : 3.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain J residue 321 GLU Chi-restraints excluded: chain K residue 95 LEU Chi-restraints excluded: chain K residue 321 GLU Chi-restraints excluded: chain L residue 95 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 226 optimal weight: 8.9990 chunk 364 optimal weight: 0.6980 chunk 222 optimal weight: 2.9990 chunk 173 optimal weight: 9.9990 chunk 253 optimal weight: 2.9990 chunk 382 optimal weight: 1.9990 chunk 352 optimal weight: 8.9990 chunk 304 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 235 optimal weight: 0.7980 chunk 186 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 31596 Z= 0.217 Angle : 0.694 16.826 42660 Z= 0.352 Chirality : 0.128 1.699 4668 Planarity : 0.004 0.067 5424 Dihedral : 3.729 14.436 4284 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.25 % Allowed : 11.61 % Favored : 88.14 % Cbeta Deviations : 0.06 % 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: 0.77 (0.14), residues: 3912 helix: 1.28 (0.10), residues: 2460 sheet: -0.30 (0.23), residues: 516 loop : -0.93 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 198 HIS 0.003 0.001 HIS F 196 PHE 0.011 0.001 PHE C 288 TYR 0.008 0.001 TYR J 51 ARG 0.013 0.001 ARG D 274 ********************** 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 244 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 236 time to evaluate : 4.085 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 243 GLU cc_start: 0.8389 (tp30) cc_final: 0.8119 (tp30) REVERT: E 2 ASP cc_start: 0.7465 (OUTLIER) cc_final: 0.7109 (p0) REVERT: H 3 LYS cc_start: 0.9255 (mttt) cc_final: 0.8972 (mppt) REVERT: I 243 GLU cc_start: 0.8500 (tp30) cc_final: 0.8262 (tp30) REVERT: J 243 GLU cc_start: 0.8536 (tp30) cc_final: 0.8318 (tp30) REVERT: L 243 GLU cc_start: 0.8480 (tp30) cc_final: 0.8256 (tp30) outliers start: 8 outliers final: 7 residues processed: 240 average time/residue: 3.3703 time to fit residues: 934.1381 Evaluate side-chains 243 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 235 time to evaluate : 4.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 99 LYS Chi-restraints excluded: chain J residue 321 GLU Chi-restraints excluded: chain K residue 95 LEU Chi-restraints excluded: chain K residue 321 GLU Chi-restraints excluded: chain L residue 95 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 241 optimal weight: 4.9990 chunk 324 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 280 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 305 optimal weight: 0.6980 chunk 127 optimal weight: 2.9990 chunk 313 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.075815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.053563 restraints weight = 210082.149| |-----------------------------------------------------------------------------| r_work (start): 0.2664 rms_B_bonded: 3.04 r_work: 0.2507 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2376 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 31596 Z= 0.231 Angle : 0.692 16.793 42660 Z= 0.352 Chirality : 0.128 1.699 4668 Planarity : 0.004 0.064 5424 Dihedral : 3.702 14.325 4284 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.34 % Allowed : 11.55 % Favored : 88.11 % Cbeta Deviations : 0.06 % 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: 0.83 (0.14), residues: 3912 helix: 1.33 (0.10), residues: 2460 sheet: -0.26 (0.23), residues: 516 loop : -0.90 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 198 HIS 0.004 0.001 HIS F 196 PHE 0.012 0.001 PHE C 288 TYR 0.008 0.001 TYR D 229 ARG 0.010 0.001 ARG D 274 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16645.34 seconds wall clock time: 286 minutes 38.21 seconds (17198.21 seconds total)