Starting phenix.real_space_refine on Wed Nov 15 04:18:28 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kou_0740/11_2023/6kou_0740.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kou_0740/11_2023/6kou_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_0740/11_2023/6kou_0740.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kou_0740/11_2023/6kou_0740.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kou_0740/11_2023/6kou_0740.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kou_0740/11_2023/6kou_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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 21.02, per 1000 atoms: 0.34 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: 37.20 Conformation dependent library (CDL) restraints added in 5.2 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: 3.59 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: 22.06 Time building geometry restraints manager: 39.57 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: 22116 14.32 - 28.64: 2141 28.64 - 42.95: 509 42.95 - 57.27: 56 57.27 - 71.59: 15 Dihedral angle restraints: 24837 sinusoidal: 11484 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 24834 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: 2.430 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: 0.670 Extract box with map and model: 10.960 Check model and map are aligned: 0.670 Set scattering table: 0.430 Process input model: 148.510 Find NCS groups from input model: 2.630 Set up NCS constraints: 0.180 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:10.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 177.190 ------------------------------------------------------------------------------- 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 *********************** 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 : 3.695 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 416 average time/residue: 3.3178 time to fit residues: 1576.5736 Evaluate side-chains 244 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 3.690 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.4922 ------------------------------------------------------------------------------- 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: 5.9990 chunk 196 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 300 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 183 optimal weight: 10.0000 chunk 224 optimal weight: 10.0000 chunk 348 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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: 0.8761 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 31596 Z= 0.332 Angle : 0.736 17.012 42660 Z= 0.387 Chirality : 0.130 1.706 4668 Planarity : 0.003 0.030 5424 Dihedral : 4.000 14.019 4284 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.78 % Allowed : 6.99 % Favored : 92.23 % Cbeta Deviations : 0.08 % 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: -2.16 (0.12), residues: 3912 helix: -0.66 (0.10), residues: 2460 sheet: -1.84 (0.20), residues: 504 loop : -2.88 (0.15), residues: 948 *********************** 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 284 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 259 time to evaluate : 3.732 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 outliers start: 25 outliers final: 11 residues processed: 279 average time/residue: 2.9881 time to fit residues: 968.5236 Evaluate side-chains 247 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 236 time to evaluate : 3.742 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 11 residues processed: 3 average time/residue: 0.6403 time to fit residues: 7.8596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 193 optimal weight: 7.9990 chunk 108 optimal weight: 5.9990 chunk 290 optimal weight: 6.9990 chunk 237 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 349 optimal weight: 2.9990 chunk 377 optimal weight: 2.9990 chunk 311 optimal weight: 0.9990 chunk 346 optimal weight: 2.9990 chunk 119 optimal weight: 9.9990 chunk 280 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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: 0.8758 moved from start: 0.2734 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= 0.249 Angle : 0.689 17.320 42660 Z= 0.355 Chirality : 0.129 1.700 4668 Planarity : 0.002 0.026 5424 Dihedral : 3.852 14.054 4284 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.44 % Allowed : 9.11 % Favored : 90.45 % 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: -1.15 (0.13), residues: 3912 helix: 0.03 (0.10), residues: 2460 sheet: -1.26 (0.21), residues: 504 loop : -2.29 (0.17), residues: 948 *********************** 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 247 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 233 time to evaluate : 3.779 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 11 residues processed: 245 average time/residue: 3.0924 time to fit residues: 880.6818 Evaluate side-chains 225 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 214 time to evaluate : 3.662 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 11 residues processed: 0 time to fit residues: 4.5390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 38 optimal weight: 5.9990 chunk 166 optimal weight: 4.9990 chunk 234 optimal weight: 4.9990 chunk 350 optimal weight: 1.9990 chunk 371 optimal weight: 1.9990 chunk 183 optimal weight: 10.0000 chunk 332 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 D 96 GLN F 96 GLN G 96 GLN H 96 GLN I 96 GLN J 96 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 31596 Z= 0.319 Angle : 0.709 16.859 42660 Z= 0.368 Chirality : 0.129 1.700 4668 Planarity : 0.002 0.024 5424 Dihedral : 3.863 14.452 4284 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.87 % Allowed : 8.93 % Favored : 90.20 % 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: -0.59 (0.13), residues: 3912 helix: 0.34 (0.10), residues: 2472 sheet: -0.90 (0.22), residues: 516 loop : -1.82 (0.18), residues: 924 *********************** 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 254 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 226 time to evaluate : 3.704 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 8 residues processed: 247 average time/residue: 3.0038 time to fit residues: 863.7051 Evaluate side-chains 222 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 214 time to evaluate : 3.670 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 4.5760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 309 optimal weight: 2.9990 chunk 210 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 chunk 276 optimal weight: 3.9990 chunk 153 optimal weight: 4.9990 chunk 316 optimal weight: 0.7980 chunk 256 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 189 optimal weight: 0.6980 chunk 333 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 96 GLN E 96 GLN K 96 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.3382 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= 0.236 Angle : 0.681 16.973 42660 Z= 0.349 Chirality : 0.129 1.696 4668 Planarity : 0.002 0.024 5424 Dihedral : 3.775 13.780 4284 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.59 % Allowed : 9.43 % Favored : 89.98 % 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: -0.15 (0.13), residues: 3912 helix: 0.68 (0.10), residues: 2460 sheet: -0.71 (0.22), residues: 516 loop : -1.62 (0.19), residues: 936 *********************** 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 246 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 227 time to evaluate : 3.853 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 11 residues processed: 237 average time/residue: 3.0707 time to fit residues: 844.4623 Evaluate side-chains 227 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 216 time to evaluate : 3.663 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 8 residues processed: 3 average time/residue: 0.5721 time to fit residues: 7.6055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 73 optimal weight: 0.3980 chunk 217 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 371 optimal weight: 2.9990 chunk 308 optimal weight: 3.9990 chunk 172 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 195 optimal weight: 5.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- 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: 0.8775 moved from start: 0.3520 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= 0.273 Angle : 0.690 16.787 42660 Z= 0.354 Chirality : 0.128 1.696 4668 Planarity : 0.002 0.024 5424 Dihedral : 3.762 14.527 4284 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.47 % Allowed : 10.33 % Favored : 89.20 % 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: 0.07 (0.13), residues: 3912 helix: 0.81 (0.10), residues: 2460 sheet: -0.56 (0.22), residues: 516 loop : -1.45 (0.19), residues: 936 *********************** 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 245 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 230 time to evaluate : 3.702 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 8 residues processed: 239 average time/residue: 3.1478 time to fit residues: 872.8351 Evaluate side-chains 228 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 220 time to evaluate : 3.698 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 4.5231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 358 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 211 optimal weight: 0.8980 chunk 271 optimal weight: 7.9990 chunk 210 optimal weight: 0.6980 chunk 312 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 370 optimal weight: 4.9990 chunk 231 optimal weight: 2.9990 chunk 225 optimal weight: 0.9980 chunk 170 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 26 GLN H 26 GLN I 26 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 31596 Z= 0.162 Angle : 0.663 16.969 42660 Z= 0.334 Chirality : 0.128 1.702 4668 Planarity : 0.002 0.055 5424 Dihedral : 3.612 13.231 4284 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.41 % Allowed : 10.42 % Favored : 89.17 % 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: 0.56 (0.13), residues: 3912 helix: 1.25 (0.10), residues: 2424 sheet: -0.40 (0.23), residues: 516 loop : -1.33 (0.19), residues: 972 *********************** 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 259 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 246 time to evaluate : 3.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 252 average time/residue: 3.0605 time to fit residues: 900.1649 Evaluate side-chains 229 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 223 time to evaluate : 3.810 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 4.7179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 228 optimal weight: 4.9990 chunk 147 optimal weight: 1.9990 chunk 221 optimal weight: 2.9990 chunk 111 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 235 optimal weight: 0.8980 chunk 252 optimal weight: 3.9990 chunk 182 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 290 optimal weight: 10.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 GLN J 26 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.3698 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= 0.254 Angle : 0.690 16.724 42660 Z= 0.351 Chirality : 0.129 1.771 4668 Planarity : 0.002 0.057 5424 Dihedral : 3.616 14.130 4284 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.28 % Allowed : 11.17 % Favored : 88.55 % 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: 0.65 (0.14), residues: 3912 helix: 1.24 (0.10), residues: 2460 sheet: -0.35 (0.23), residues: 516 loop : -1.16 (0.20), residues: 936 *********************** 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 236 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 227 time to evaluate : 3.807 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 9 residues processed: 233 average time/residue: 3.1710 time to fit residues: 854.6308 Evaluate side-chains 228 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 219 time to evaluate : 3.679 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 6 residues processed: 3 average time/residue: 0.5726 time to fit residues: 7.6832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 336 optimal weight: 4.9990 chunk 354 optimal weight: 6.9990 chunk 323 optimal weight: 8.9990 chunk 344 optimal weight: 6.9990 chunk 207 optimal weight: 6.9990 chunk 150 optimal weight: 3.9990 chunk 270 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 311 optimal weight: 8.9990 chunk 326 optimal weight: 4.9990 chunk 343 optimal weight: 3.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- 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: 0.8781 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 31596 Z= 0.308 Angle : 0.707 16.686 42660 Z= 0.363 Chirality : 0.130 1.764 4668 Planarity : 0.003 0.069 5424 Dihedral : 3.719 13.726 4284 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.31 % Allowed : 11.30 % Favored : 88.39 % 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: 0.64 (0.13), residues: 3912 helix: 1.22 (0.10), residues: 2460 sheet: -0.34 (0.23), residues: 516 loop : -1.11 (0.20), residues: 936 *********************** 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 233 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 223 time to evaluate : 3.750 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 230 average time/residue: 3.2880 time to fit residues: 875.0348 Evaluate side-chains 229 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 223 time to evaluate : 3.674 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 4.5554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 226 optimal weight: 6.9990 chunk 364 optimal weight: 5.9990 chunk 222 optimal weight: 0.7980 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: 3.9990 chunk 31 optimal weight: 4.9990 chunk 235 optimal weight: 0.7980 chunk 186 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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: 0.8754 moved from start: 0.3815 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= 0.204 Angle : 0.690 16.835 42660 Z= 0.348 Chirality : 0.129 1.746 4668 Planarity : 0.003 0.068 5424 Dihedral : 3.649 14.343 4284 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.19 % Allowed : 11.42 % Favored : 88.39 % 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 (0.13), residues: 3912 helix: 1.37 (0.10), residues: 2460 sheet: -0.26 (0.23), residues: 516 loop : -1.05 (0.20), residues: 936 ********************** 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 233 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 227 time to evaluate : 3.733 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 233 average time/residue: 3.2692 time to fit residues: 884.9560 Evaluate side-chains 232 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 226 time to evaluate : 3.694 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 4.5962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 241 optimal weight: 5.9990 chunk 324 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 280 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 305 optimal weight: 0.9980 chunk 127 optimal weight: 3.9990 chunk 313 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 GLN G 26 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.076263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.054087 restraints weight = 210124.772| |-----------------------------------------------------------------------------| r_work (start): 0.2676 rms_B_bonded: 3.03 r_work: 0.2522 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2391 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.3866 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= 0.219 Angle : 0.688 16.814 42660 Z= 0.348 Chirality : 0.129 1.759 4668 Planarity : 0.003 0.064 5424 Dihedral : 3.606 13.618 4284 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.19 % Allowed : 11.55 % Favored : 88.26 % 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: 0.93 (0.14), residues: 3912 helix: 1.43 (0.10), residues: 2460 sheet: -0.19 (0.23), residues: 516 loop : -0.98 (0.21), residues: 936 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16131.36 seconds wall clock time: 278 minutes 10.77 seconds (16690.77 seconds total)