Starting phenix.real_space_refine on Thu Mar 21 00:52:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zby_11158/03_2024/6zby_11158.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zby_11158/03_2024/6zby_11158.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zby_11158/03_2024/6zby_11158.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zby_11158/03_2024/6zby_11158.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zby_11158/03_2024/6zby_11158.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zby_11158/03_2024/6zby_11158.pdb" } resolution = 3.1 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 ------------------------------------------------------------------------------- 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= 0.002 sd= 0.014 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: 4 Type Number sf(0) Gaussians S 144 5.16 5 C 18432 2.51 5 N 4944 2.21 5 O 5316 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 39": "OE1" <-> "OE2" Residue "A GLU 48": "OE1" <-> "OE2" Residue "A ARG 72": "NH1" <-> "NH2" Residue "A ASP 75": "OD1" <-> "OD2" Residue "A GLU 143": "OE1" <-> "OE2" Residue "A TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 181": "OE1" <-> "OE2" Residue "A ARG 195": "NH1" <-> "NH2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 231": "OE1" <-> "OE2" Residue "A ASP 278": "OD1" <-> "OD2" Residue "A ASP 280": "OD1" <-> "OD2" Residue "A ASP 301": "OD1" <-> "OD2" Residue "A GLU 310": "OE1" <-> "OE2" Residue "B GLU 48": "OE1" <-> "OE2" Residue "B ASP 61": "OD1" <-> "OD2" Residue "B ARG 72": "NH1" <-> "NH2" Residue "B ASP 75": "OD1" <-> "OD2" Residue "B PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 145": "OD1" <-> "OD2" Residue "B GLU 181": "OE1" <-> "OE2" Residue "B ARG 195": "NH1" <-> "NH2" Residue "B GLU 231": "OE1" <-> "OE2" Residue "B ASP 278": "OD1" <-> "OD2" Residue "B ASP 280": "OD1" <-> "OD2" Residue "B ASP 301": "OD1" <-> "OD2" Residue "B GLU 310": "OE1" <-> "OE2" Residue "C TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 39": "OE1" <-> "OE2" Residue "C GLU 48": "OE1" <-> "OE2" Residue "C ARG 72": "NH1" <-> "NH2" Residue "C ASP 75": "OD1" <-> "OD2" Residue "C GLU 181": "OE1" <-> "OE2" Residue "C ARG 195": "NH1" <-> "NH2" Residue "C PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 231": "OE1" <-> "OE2" Residue "C ASP 278": "OD1" <-> "OD2" Residue "C ASP 280": "OD1" <-> "OD2" Residue "C TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 301": "OD1" <-> "OD2" Residue "C GLU 310": "OE1" <-> "OE2" Residue "D PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 39": "OE1" <-> "OE2" Residue "D GLU 48": "OE1" <-> "OE2" Residue "D ASP 61": "OD1" <-> "OD2" Residue "D ARG 72": "NH1" <-> "NH2" Residue "D ASP 75": "OD1" <-> "OD2" Residue "D PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 86": "OE1" <-> "OE2" Residue "D GLU 181": "OE1" <-> "OE2" Residue "D ARG 195": "NH1" <-> "NH2" Residue "D PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 231": "OE1" <-> "OE2" Residue "D GLU 271": "OE1" <-> "OE2" Residue "D ASP 278": "OD1" <-> "OD2" Residue "D ASP 280": "OD1" <-> "OD2" Residue "D ASP 301": "OD1" <-> "OD2" Residue "D GLU 310": "OE1" <-> "OE2" Residue "E GLU 39": "OE1" <-> "OE2" Residue "E GLU 48": "OE1" <-> "OE2" Residue "E ASP 61": "OD1" <-> "OD2" Residue "E ARG 72": "NH1" <-> "NH2" Residue "E PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 75": "OD1" <-> "OD2" Residue "E GLU 79": "OE1" <-> "OE2" Residue "E GLU 181": "OE1" <-> "OE2" Residue "E ARG 195": "NH1" <-> "NH2" Residue "E PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 231": "OE1" <-> "OE2" Residue "E ASP 238": "OD1" <-> "OD2" Residue "E GLU 244": "OE1" <-> "OE2" Residue "E ASP 278": "OD1" <-> "OD2" Residue "E ASP 280": "OD1" <-> "OD2" Residue "E ASP 301": "OD1" <-> "OD2" Residue "E GLU 310": "OE1" <-> "OE2" Residue "F GLU 48": "OE1" <-> "OE2" Residue "F ASP 61": "OD1" <-> "OD2" Residue "F ARG 72": "NH1" <-> "NH2" Residue "F PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 75": "OD1" <-> "OD2" Residue "F GLU 79": "OE1" <-> "OE2" Residue "F GLU 86": "OE1" <-> "OE2" Residue "F GLU 181": "OE1" <-> "OE2" Residue "F ARG 195": "NH1" <-> "NH2" Residue "F GLU 231": "OE1" <-> "OE2" Residue "F GLU 271": "OE1" <-> "OE2" Residue "F GLU 272": "OE1" <-> "OE2" Residue "F ASP 278": "OD1" <-> "OD2" Residue "F ASP 280": "OD1" <-> "OD2" Residue "F ASP 301": "OD1" <-> "OD2" Residue "F GLU 310": "OE1" <-> "OE2" Residue "G GLU 48": "OE1" <-> "OE2" Residue "G ASP 61": "OD1" <-> "OD2" Residue "G ARG 72": "NH1" <-> "NH2" Residue "G PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 75": "OD1" <-> "OD2" Residue "G PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 181": "OE1" <-> "OE2" Residue "G ARG 195": "NH1" <-> "NH2" Residue "G PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 231": "OE1" <-> "OE2" Residue "G GLU 248": "OE1" <-> "OE2" Residue "G ASP 278": "OD1" <-> "OD2" Residue "G ASP 280": "OD1" <-> "OD2" Residue "G ASP 301": "OD1" <-> "OD2" Residue "G GLU 310": "OE1" <-> "OE2" Residue "H GLU 48": "OE1" <-> "OE2" Residue "H ASP 61": "OD1" <-> "OD2" Residue "H ARG 72": "NH1" <-> "NH2" Residue "H PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 75": "OD1" <-> "OD2" Residue "H PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 145": "OD1" <-> "OD2" Residue "H GLU 181": "OE1" <-> "OE2" Residue "H ARG 195": "NH1" <-> "NH2" Residue "H PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 231": "OE1" <-> "OE2" Residue "H GLU 248": "OE1" <-> "OE2" Residue "H GLU 272": "OE1" <-> "OE2" Residue "H ASP 278": "OD1" <-> "OD2" Residue "H ASP 280": "OD1" <-> "OD2" Residue "H ASP 301": "OD1" <-> "OD2" Residue "H GLU 310": "OE1" <-> "OE2" Residue "I TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 39": "OE1" <-> "OE2" Residue "I GLU 48": "OE1" <-> "OE2" Residue "I ASP 61": "OD1" <-> "OD2" Residue "I ARG 72": "NH1" <-> "NH2" Residue "I PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 75": "OD1" <-> "OD2" Residue "I PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 181": "OE1" <-> "OE2" Residue "I ARG 195": "NH1" <-> "NH2" Residue "I PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 231": "OE1" <-> "OE2" Residue "I GLU 244": "OE1" <-> "OE2" Residue "I PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 272": "OE1" <-> "OE2" Residue "I ASP 278": "OD1" <-> "OD2" Residue "I ASP 280": "OD1" <-> "OD2" Residue "I ASP 301": "OD1" <-> "OD2" Residue "I GLU 310": "OE1" <-> "OE2" Residue "J GLU 39": "OE1" <-> "OE2" Residue "J ASP 61": "OD1" <-> "OD2" Residue "J ARG 72": "NH1" <-> "NH2" Residue "J PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 75": "OD1" <-> "OD2" Residue "J GLU 79": "OE1" <-> "OE2" Residue "J PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 120": "OD1" <-> "OD2" Residue "J GLU 181": "OE1" <-> "OE2" Residue "J ARG 195": "NH1" <-> "NH2" Residue "J PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 231": "OE1" <-> "OE2" Residue "J GLU 235": "OE1" <-> "OE2" Residue "J GLU 244": "OE1" <-> "OE2" Residue "J ASP 278": "OD1" <-> "OD2" Residue "J ASP 280": "OD1" <-> "OD2" Residue "J TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 301": "OD1" <-> "OD2" Residue "J GLU 310": "OE1" <-> "OE2" Residue "K GLU 39": "OE1" <-> "OE2" Residue "K GLU 48": "OE1" <-> "OE2" Residue "K ASP 61": "OD1" <-> "OD2" Residue "K ARG 72": "NH1" <-> "NH2" Residue "K ASP 75": "OD1" <-> "OD2" Residue "K GLU 79": "OE1" <-> "OE2" Residue "K PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 86": "OE1" <-> "OE2" Residue "K ASP 120": "OD1" <-> "OD2" Residue "K ASP 145": "OD1" <-> "OD2" Residue "K GLU 181": "OE1" <-> "OE2" Residue "K ARG 195": "NH1" <-> "NH2" Residue "K PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 231": "OE1" <-> "OE2" Residue "K GLU 271": "OE1" <-> "OE2" Residue "K TYR 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 278": "OD1" <-> "OD2" Residue "K ASP 280": "OD1" <-> "OD2" Residue "K ASP 301": "OD1" <-> "OD2" Residue "K GLU 310": "OE1" <-> "OE2" Residue "L TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 39": "OE1" <-> "OE2" Residue "L GLU 48": "OE1" <-> "OE2" Residue "L ASP 61": "OD1" <-> "OD2" Residue "L ARG 72": "NH1" <-> "NH2" Residue "L ASP 75": "OD1" <-> "OD2" Residue "L GLU 143": "OE1" <-> "OE2" Residue "L TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 181": "OE1" <-> "OE2" Residue "L ARG 195": "NH1" <-> "NH2" Residue "L GLU 231": "OE1" <-> "OE2" Residue "L ASP 278": "OD1" <-> "OD2" Residue "L ASP 280": "OD1" <-> "OD2" Residue "L GLU 310": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 28836 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2403 Classifications: {'peptide': 316} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 297} Chain: "B" Number of atoms: 2403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2403 Classifications: {'peptide': 316} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 297} Chain: "C" Number of atoms: 2403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2403 Classifications: {'peptide': 316} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 297} Chain: "D" Number of atoms: 2403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2403 Classifications: {'peptide': 316} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 297} Chain: "E" Number of atoms: 2403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2403 Classifications: {'peptide': 316} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 297} Chain: "F" Number of atoms: 2403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2403 Classifications: {'peptide': 316} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 297} Chain: "G" Number of atoms: 2403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2403 Classifications: {'peptide': 316} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 297} Chain: "H" Number of atoms: 2403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2403 Classifications: {'peptide': 316} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 297} Chain: "I" Number of atoms: 2403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2403 Classifications: {'peptide': 316} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 297} Chain: "J" Number of atoms: 2403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2403 Classifications: {'peptide': 316} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 297} Chain: "K" Number of atoms: 2403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2403 Classifications: {'peptide': 316} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 297} Chain: "L" Number of atoms: 2403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2403 Classifications: {'peptide': 316} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 297} Time building chain proxies: 14.51, per 1000 atoms: 0.50 Number of scatterers: 28836 At special positions: 0 Unit cell: (143.576, 141.48, 158.248, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 144 16.00 O 5316 8.00 N 4944 7.00 C 18432 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.12 Conformation dependent library (CDL) restraints added in 5.4 seconds 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6936 Finding SS restraints... Secondary structure from input PDB file: 155 helices and 38 sheets defined 37.7% alpha, 24.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.66 Creating SS restraints... Processing helix chain 'A' and resid 21 through 39 Processing helix chain 'A' and resid 56 through 61 removed outlier: 3.679A pdb=" N LEU A 60 " --> pdb=" O TRP A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 76 removed outlier: 4.921A pdb=" N ARG A 68 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N PHE A 69 " --> pdb=" O GLY A 65 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLN A 71 " --> pdb=" O MET A 67 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ARG A 72 " --> pdb=" O ARG A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 94 removed outlier: 4.317A pdb=" N LEU A 88 " --> pdb=" O PRO A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 140 removed outlier: 3.516A pdb=" N ARG A 138 " --> pdb=" O HIS A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 149 Processing helix chain 'A' and resid 165 through 168 Processing helix chain 'A' and resid 169 through 178 Processing helix chain 'A' and resid 198 through 201 removed outlier: 3.584A pdb=" N LEU A 201 " --> pdb=" O ALA A 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 198 through 201' Processing helix chain 'A' and resid 202 through 218 Processing helix chain 'A' and resid 229 through 234 Processing helix chain 'A' and resid 239 through 243 Processing helix chain 'A' and resid 283 through 288 Processing helix chain 'B' and resid 21 through 39 removed outlier: 3.827A pdb=" N ALA B 27 " --> pdb=" O GLU B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'B' and resid 66 through 76 removed outlier: 4.409A pdb=" N GLN B 71 " --> pdb=" O MET B 67 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N ARG B 72 " --> pdb=" O ARG B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 96 removed outlier: 3.564A pdb=" N LEU B 88 " --> pdb=" O PRO B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 139 Processing helix chain 'B' and resid 145 through 149 removed outlier: 3.626A pdb=" N ASP B 148 " --> pdb=" O ASP B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 169 removed outlier: 3.873A pdb=" N GLN B 169 " --> pdb=" O GLU B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 178 removed outlier: 4.444A pdb=" N MET B 176 " --> pdb=" O SER B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 201 Processing helix chain 'B' and resid 202 through 218 removed outlier: 3.584A pdb=" N ASN B 206 " --> pdb=" O SER B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 237 removed outlier: 4.123A pdb=" N GLU B 235 " --> pdb=" O GLU B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 288 Processing helix chain 'C' and resid 21 through 39 Processing helix chain 'C' and resid 56 through 61 removed outlier: 3.600A pdb=" N LEU C 60 " --> pdb=" O TRP C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 77 removed outlier: 5.079A pdb=" N ARG C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N PHE C 69 " --> pdb=" O GLY C 65 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLN C 71 " --> pdb=" O MET C 67 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ARG C 72 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 95 removed outlier: 3.962A pdb=" N LEU C 88 " --> pdb=" O PRO C 84 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA C 91 " --> pdb=" O ARG C 87 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA C 93 " --> pdb=" O CYS C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 140 Processing helix chain 'C' and resid 145 through 149 Processing helix chain 'C' and resid 165 through 168 Processing helix chain 'C' and resid 169 through 178 removed outlier: 3.998A pdb=" N MET C 176 " --> pdb=" O SER C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 201 removed outlier: 3.552A pdb=" N LEU C 201 " --> pdb=" O ALA C 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 198 through 201' Processing helix chain 'C' and resid 202 through 218 Processing helix chain 'C' and resid 229 through 234 removed outlier: 3.512A pdb=" N LEU C 233 " --> pdb=" O SER C 229 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP C 234 " --> pdb=" O LYS C 230 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 229 through 234' Processing helix chain 'C' and resid 239 through 246 removed outlier: 4.877A pdb=" N GLU C 244 " --> pdb=" O ALA C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 288 removed outlier: 4.025A pdb=" N VAL C 286 " --> pdb=" O GLY C 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 39 Processing helix chain 'D' and resid 56 through 61 removed outlier: 3.537A pdb=" N LEU D 60 " --> pdb=" O TRP D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 77 removed outlier: 4.742A pdb=" N ARG D 68 " --> pdb=" O ALA D 64 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N PHE D 69 " --> pdb=" O GLY D 65 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLN D 71 " --> pdb=" O MET D 67 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ARG D 72 " --> pdb=" O ARG D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 96 removed outlier: 4.040A pdb=" N LEU D 88 " --> pdb=" O PRO D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 139 Processing helix chain 'D' and resid 145 through 149 Processing helix chain 'D' and resid 165 through 168 Processing helix chain 'D' and resid 169 through 178 removed outlier: 4.266A pdb=" N MET D 176 " --> pdb=" O SER D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 201 Processing helix chain 'D' and resid 202 through 218 removed outlier: 3.513A pdb=" N ASN D 206 " --> pdb=" O SER D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 234 Processing helix chain 'D' and resid 239 through 244 removed outlier: 4.277A pdb=" N GLU D 244 " --> pdb=" O PRO D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 291 removed outlier: 3.707A pdb=" N ALA D 289 " --> pdb=" O GLY D 285 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ALA D 290 " --> pdb=" O VAL D 286 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR D 291 " --> pdb=" O ALA D 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 39 Processing helix chain 'E' and resid 56 through 61 Processing helix chain 'E' and resid 62 through 76 removed outlier: 5.248A pdb=" N ARG E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N PHE E 69 " --> pdb=" O GLY E 65 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLN E 71 " --> pdb=" O MET E 67 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ARG E 72 " --> pdb=" O ARG E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 96 removed outlier: 3.872A pdb=" N LEU E 88 " --> pdb=" O PRO E 84 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA E 93 " --> pdb=" O CYS E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 139 Processing helix chain 'E' and resid 145 through 149 Processing helix chain 'E' and resid 165 through 168 Processing helix chain 'E' and resid 169 through 178 removed outlier: 3.713A pdb=" N MET E 176 " --> pdb=" O SER E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 201 Processing helix chain 'E' and resid 202 through 218 Processing helix chain 'E' and resid 229 through 237 removed outlier: 4.084A pdb=" N GLU E 235 " --> pdb=" O GLU E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 244 removed outlier: 3.859A pdb=" N GLU E 244 " --> pdb=" O PRO E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 291 removed outlier: 3.509A pdb=" N ALA E 289 " --> pdb=" O GLY E 285 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ALA E 290 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR E 291 " --> pdb=" O ALA E 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 39 Processing helix chain 'F' and resid 56 through 61 Processing helix chain 'F' and resid 62 through 76 removed outlier: 4.877A pdb=" N ARG F 68 " --> pdb=" O ALA F 64 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N PHE F 69 " --> pdb=" O GLY F 65 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL F 70 " --> pdb=" O GLY F 66 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLN F 71 " --> pdb=" O MET F 67 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ARG F 72 " --> pdb=" O ARG F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 95 removed outlier: 3.929A pdb=" N LEU F 88 " --> pdb=" O PRO F 84 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA F 93 " --> pdb=" O CYS F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 139 Processing helix chain 'F' and resid 145 through 149 Processing helix chain 'F' and resid 165 through 168 Processing helix chain 'F' and resid 169 through 178 removed outlier: 3.619A pdb=" N MET F 176 " --> pdb=" O SER F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 201 removed outlier: 3.606A pdb=" N LEU F 201 " --> pdb=" O ALA F 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 198 through 201' Processing helix chain 'F' and resid 202 through 218 Processing helix chain 'F' and resid 229 through 234 Processing helix chain 'F' and resid 239 through 244 removed outlier: 3.506A pdb=" N ALA F 243 " --> pdb=" O SER F 239 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU F 244 " --> pdb=" O PRO F 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 239 through 244' Processing helix chain 'F' and resid 283 through 288 Processing helix chain 'G' and resid 21 through 39 Processing helix chain 'G' and resid 55 through 60 Processing helix chain 'G' and resid 62 through 75 removed outlier: 5.309A pdb=" N ARG G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N PHE G 69 " --> pdb=" O GLY G 65 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLN G 71 " --> pdb=" O MET G 67 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N ARG G 72 " --> pdb=" O ARG G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 96 removed outlier: 3.626A pdb=" N LEU G 88 " --> pdb=" O PRO G 84 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA G 93 " --> pdb=" O CYS G 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 139 Processing helix chain 'G' and resid 145 through 149 Processing helix chain 'G' and resid 165 through 167 No H-bonds generated for 'chain 'G' and resid 165 through 167' Processing helix chain 'G' and resid 169 through 178 removed outlier: 3.854A pdb=" N MET G 176 " --> pdb=" O SER G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 198 through 201 Processing helix chain 'G' and resid 202 through 218 Processing helix chain 'G' and resid 229 through 237 removed outlier: 3.977A pdb=" N GLU G 235 " --> pdb=" O GLU G 231 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU G 236 " --> pdb=" O MET G 232 " (cutoff:3.500A) Processing helix chain 'G' and resid 239 through 243 removed outlier: 3.518A pdb=" N LYS G 242 " --> pdb=" O SER G 239 " (cutoff:3.500A) Processing helix chain 'G' and resid 283 through 291 removed outlier: 4.147A pdb=" N ALA G 290 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR G 291 " --> pdb=" O ALA G 287 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 39 removed outlier: 3.521A pdb=" N GLU H 39 " --> pdb=" O GLN H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 61 Processing helix chain 'H' and resid 62 through 76 removed outlier: 5.286A pdb=" N ARG H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N PHE H 69 " --> pdb=" O GLY H 65 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLN H 71 " --> pdb=" O MET H 67 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N ARG H 72 " --> pdb=" O ARG H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 96 removed outlier: 3.658A pdb=" N LEU H 88 " --> pdb=" O PRO H 84 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA H 93 " --> pdb=" O CYS H 89 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS H 95 " --> pdb=" O ALA H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 134 through 139 Processing helix chain 'H' and resid 145 through 149 Processing helix chain 'H' and resid 165 through 167 No H-bonds generated for 'chain 'H' and resid 165 through 167' Processing helix chain 'H' and resid 169 through 178 Processing helix chain 'H' and resid 198 through 201 removed outlier: 3.617A pdb=" N LEU H 201 " --> pdb=" O ALA H 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 198 through 201' Processing helix chain 'H' and resid 202 through 218 Processing helix chain 'H' and resid 229 through 234 Processing helix chain 'H' and resid 239 through 243 removed outlier: 3.577A pdb=" N LYS H 242 " --> pdb=" O SER H 239 " (cutoff:3.500A) Processing helix chain 'H' and resid 283 through 291 removed outlier: 3.506A pdb=" N ALA H 289 " --> pdb=" O GLY H 285 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ALA H 290 " --> pdb=" O VAL H 286 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR H 291 " --> pdb=" O ALA H 287 " (cutoff:3.500A) Processing helix chain 'I' and resid 21 through 39 Processing helix chain 'I' and resid 56 through 61 Processing helix chain 'I' and resid 62 through 76 removed outlier: 5.297A pdb=" N ARG I 68 " --> pdb=" O ALA I 64 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N PHE I 69 " --> pdb=" O GLY I 65 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N GLN I 71 " --> pdb=" O MET I 67 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ARG I 72 " --> pdb=" O ARG I 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 96 removed outlier: 3.726A pdb=" N LEU I 88 " --> pdb=" O PRO I 84 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA I 93 " --> pdb=" O CYS I 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 136 through 140 Processing helix chain 'I' and resid 145 through 149 Processing helix chain 'I' and resid 165 through 167 No H-bonds generated for 'chain 'I' and resid 165 through 167' Processing helix chain 'I' and resid 169 through 178 removed outlier: 3.689A pdb=" N MET I 176 " --> pdb=" O SER I 172 " (cutoff:3.500A) Processing helix chain 'I' and resid 198 through 201 Processing helix chain 'I' and resid 202 through 218 Processing helix chain 'I' and resid 229 through 234 Processing helix chain 'I' and resid 239 through 244 Processing helix chain 'I' and resid 283 through 291 removed outlier: 3.634A pdb=" N ALA I 289 " --> pdb=" O GLY I 285 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ALA I 290 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR I 291 " --> pdb=" O ALA I 287 " (cutoff:3.500A) Processing helix chain 'J' and resid 21 through 39 Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'J' and resid 62 through 76 removed outlier: 5.076A pdb=" N ARG J 68 " --> pdb=" O ALA J 64 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N PHE J 69 " --> pdb=" O GLY J 65 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL J 70 " --> pdb=" O GLY J 66 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLN J 71 " --> pdb=" O MET J 67 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N ARG J 72 " --> pdb=" O ARG J 68 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 96 removed outlier: 3.761A pdb=" N LEU J 88 " --> pdb=" O PRO J 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 136 through 139 Processing helix chain 'J' and resid 145 through 149 Processing helix chain 'J' and resid 165 through 168 Processing helix chain 'J' and resid 169 through 178 removed outlier: 3.737A pdb=" N MET J 176 " --> pdb=" O SER J 172 " (cutoff:3.500A) Processing helix chain 'J' and resid 198 through 201 removed outlier: 3.652A pdb=" N LEU J 201 " --> pdb=" O ALA J 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 198 through 201' Processing helix chain 'J' and resid 202 through 218 Processing helix chain 'J' and resid 229 through 237 removed outlier: 3.625A pdb=" N GLU J 235 " --> pdb=" O GLU J 231 " (cutoff:3.500A) Processing helix chain 'J' and resid 239 through 244 removed outlier: 3.556A pdb=" N GLU J 244 " --> pdb=" O PRO J 240 " (cutoff:3.500A) Processing helix chain 'J' and resid 283 through 291 removed outlier: 4.075A pdb=" N ALA J 290 " --> pdb=" O VAL J 286 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR J 291 " --> pdb=" O ALA J 287 " (cutoff:3.500A) Processing helix chain 'K' and resid 21 through 40 Processing helix chain 'K' and resid 56 through 61 Processing helix chain 'K' and resid 62 through 76 removed outlier: 5.362A pdb=" N ARG K 68 " --> pdb=" O ALA K 64 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N PHE K 69 " --> pdb=" O GLY K 65 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLN K 71 " --> pdb=" O MET K 67 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ARG K 72 " --> pdb=" O ARG K 68 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 96 removed outlier: 3.639A pdb=" N LEU K 88 " --> pdb=" O PRO K 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 136 through 139 Processing helix chain 'K' and resid 145 through 149 removed outlier: 3.604A pdb=" N LEU K 149 " --> pdb=" O GLY K 146 " (cutoff:3.500A) Processing helix chain 'K' and resid 165 through 168 Processing helix chain 'K' and resid 169 through 178 removed outlier: 3.807A pdb=" N MET K 176 " --> pdb=" O SER K 172 " (cutoff:3.500A) Processing helix chain 'K' and resid 198 through 201 Processing helix chain 'K' and resid 202 through 218 removed outlier: 3.502A pdb=" N ASN K 206 " --> pdb=" O SER K 202 " (cutoff:3.500A) Processing helix chain 'K' and resid 229 through 234 Processing helix chain 'K' and resid 239 through 244 removed outlier: 4.096A pdb=" N GLU K 244 " --> pdb=" O PRO K 240 " (cutoff:3.500A) Processing helix chain 'K' and resid 282 through 288 removed outlier: 4.111A pdb=" N VAL K 286 " --> pdb=" O GLY K 282 " (cutoff:3.500A) Processing helix chain 'L' and resid 21 through 39 Processing helix chain 'L' and resid 56 through 61 removed outlier: 3.639A pdb=" N LEU L 60 " --> pdb=" O TRP L 56 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 76 removed outlier: 4.843A pdb=" N ARG L 68 " --> pdb=" O ALA L 64 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N PHE L 69 " --> pdb=" O GLY L 65 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLN L 71 " --> pdb=" O MET L 67 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ARG L 72 " --> pdb=" O ARG L 68 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 94 removed outlier: 4.036A pdb=" N LEU L 88 " --> pdb=" O PRO L 84 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA L 93 " --> pdb=" O CYS L 89 " (cutoff:3.500A) Processing helix chain 'L' and resid 136 through 140 Processing helix chain 'L' and resid 145 through 149 Processing helix chain 'L' and resid 165 through 168 Processing helix chain 'L' and resid 169 through 178 removed outlier: 3.685A pdb=" N MET L 176 " --> pdb=" O SER L 172 " (cutoff:3.500A) Processing helix chain 'L' and resid 198 through 201 Processing helix chain 'L' and resid 202 through 218 Processing helix chain 'L' and resid 229 through 234 removed outlier: 3.922A pdb=" N ASP L 234 " --> pdb=" O LYS L 230 " (cutoff:3.500A) Processing helix chain 'L' and resid 239 through 246 removed outlier: 5.224A pdb=" N GLU L 244 " --> pdb=" O ALA L 241 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU L 246 " --> pdb=" O ALA L 243 " (cutoff:3.500A) Processing helix chain 'L' and resid 282 through 288 removed outlier: 4.067A pdb=" N VAL L 286 " --> pdb=" O GLY L 282 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 124 through 129 removed outlier: 6.891A pdb=" N ILE A 117 " --> pdb=" O VAL A 125 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N THR A 127 " --> pdb=" O GLN A 115 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N GLN A 115 " --> pdb=" O THR A 127 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ARG A 129 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU A 113 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N SER A 42 " --> pdb=" O GLN A 7 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N LYS A 9 " --> pdb=" O SER A 42 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL A 44 " --> pdb=" O LYS A 9 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ALA A 11 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N CYS A 225 " --> pdb=" O VAL A 13 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA A 15 " --> pdb=" O CYS A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 124 through 129 removed outlier: 6.891A pdb=" N ILE A 117 " --> pdb=" O VAL A 125 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N THR A 127 " --> pdb=" O GLN A 115 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N GLN A 115 " --> pdb=" O THR A 127 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ARG A 129 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU A 113 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N SER A 42 " --> pdb=" O GLN A 7 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N LYS A 9 " --> pdb=" O SER A 42 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL A 44 " --> pdb=" O LYS A 9 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ALA A 11 " --> pdb=" O VAL A 44 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 151 through 154 removed outlier: 6.288A pdb=" N ARG A 158 " --> pdb=" O VAL A 183 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N ILE A 185 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N GLY A 160 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ALA A 187 " --> pdb=" O GLY A 160 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU A 162 " --> pdb=" O ALA A 187 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 315 through 317 removed outlier: 8.444A pdb=" N HIS D 316 " --> pdb=" O LEU B 303 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU B 305 " --> pdb=" O HIS D 316 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 124 through 129 removed outlier: 6.624A pdb=" N LEU B 111 " --> pdb=" O GLY B 142 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 124 through 129 removed outlier: 6.868A pdb=" N VAL B 44 " --> pdb=" O VAL B 100 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N GLY B 102 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU B 43 " --> pdb=" O LYS B 9 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 152 through 154 removed outlier: 6.495A pdb=" N ARG B 158 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N ILE B 185 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N GLY B 160 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N ALA B 187 " --> pdb=" O GLY B 160 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU B 162 " --> pdb=" O ALA B 187 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N HIS B 184 " --> pdb=" O LEU B 222 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 124 through 129 removed outlier: 7.005A pdb=" N ILE C 117 " --> pdb=" O VAL C 125 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N THR C 127 " --> pdb=" O GLN C 115 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLN C 115 " --> pdb=" O THR C 127 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ARG C 129 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU C 113 " --> pdb=" O ARG C 129 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL C 44 " --> pdb=" O VAL C 100 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N GLY C 102 " --> pdb=" O VAL C 44 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU C 43 " --> pdb=" O LYS C 9 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 151 through 154 Processing sheet with id=AB1, first strand: chain 'C' and resid 315 through 317 removed outlier: 6.243A pdb=" N HIS C 316 " --> pdb=" O VAL E 307 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N HIS F 316 " --> pdb=" O LEU D 303 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU D 305 " --> pdb=" O HIS F 316 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 124 through 129 removed outlier: 6.613A pdb=" N ILE D 117 " --> pdb=" O VAL D 125 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N THR D 127 " --> pdb=" O GLN D 115 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLN D 115 " --> pdb=" O THR D 127 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ARG D 129 " --> pdb=" O LEU D 113 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LEU D 113 " --> pdb=" O ARG D 129 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N LEU D 111 " --> pdb=" O GLY D 142 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 124 through 129 removed outlier: 6.613A pdb=" N ILE D 117 " --> pdb=" O VAL D 125 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N THR D 127 " --> pdb=" O GLN D 115 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLN D 115 " --> pdb=" O THR D 127 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ARG D 129 " --> pdb=" O LEU D 113 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LEU D 113 " --> pdb=" O ARG D 129 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N SER D 42 " --> pdb=" O TYR D 98 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL D 100 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL D 44 " --> pdb=" O VAL D 100 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N GLY D 102 " --> pdb=" O VAL D 44 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N SER D 42 " --> pdb=" O GLN D 7 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N LYS D 9 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL D 44 " --> pdb=" O LYS D 9 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA D 11 " --> pdb=" O VAL D 44 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 152 through 154 removed outlier: 6.257A pdb=" N ARG D 158 " --> pdb=" O VAL D 183 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N ILE D 185 " --> pdb=" O ARG D 158 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N GLY D 160 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ALA D 187 " --> pdb=" O GLY D 160 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LEU D 162 " --> pdb=" O ALA D 187 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 124 through 129 removed outlier: 7.169A pdb=" N LEU E 111 " --> pdb=" O GLY E 142 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 124 through 129 removed outlier: 3.652A pdb=" N THR E 110 " --> pdb=" O SER E 107 " (cutoff:3.500A) removed outlier: 9.939A pdb=" N ALA E 41 " --> pdb=" O GLN E 7 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LYS E 9 " --> pdb=" O ALA E 41 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU E 43 " --> pdb=" O LYS E 9 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 151 through 154 removed outlier: 6.337A pdb=" N ARG E 158 " --> pdb=" O VAL E 183 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ILE E 185 " --> pdb=" O ARG E 158 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N GLY E 160 " --> pdb=" O ILE E 185 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N ALA E 187 " --> pdb=" O GLY E 160 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU E 162 " --> pdb=" O ALA E 187 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 315 through 317 Processing sheet with id=AB9, first strand: chain 'F' and resid 124 through 129 removed outlier: 7.241A pdb=" N LEU F 111 " --> pdb=" O GLY F 142 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 124 through 129 removed outlier: 8.191A pdb=" N SER F 42 " --> pdb=" O GLN F 7 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N LYS F 9 " --> pdb=" O SER F 42 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL F 44 " --> pdb=" O LYS F 9 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ALA F 11 " --> pdb=" O VAL F 44 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 151 through 154 Processing sheet with id=AC3, first strand: chain 'G' and resid 124 through 129 removed outlier: 6.892A pdb=" N ILE G 117 " --> pdb=" O VAL G 125 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N THR G 127 " --> pdb=" O GLN G 115 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLN G 115 " --> pdb=" O THR G 127 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ARG G 129 " --> pdb=" O LEU G 113 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N LEU G 113 " --> pdb=" O ARG G 129 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N SER G 42 " --> pdb=" O GLN G 7 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N LYS G 9 " --> pdb=" O SER G 42 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL G 44 " --> pdb=" O LYS G 9 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ALA G 11 " --> pdb=" O VAL G 44 " (cutoff:3.500A) removed outlier: 8.829A pdb=" N CYS G 225 " --> pdb=" O ALA G 11 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL G 13 " --> pdb=" O CYS G 225 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 141 through 142 removed outlier: 7.054A pdb=" N LEU G 111 " --> pdb=" O GLY G 142 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N SER G 42 " --> pdb=" O GLN G 7 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N LYS G 9 " --> pdb=" O SER G 42 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL G 44 " --> pdb=" O LYS G 9 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ALA G 11 " --> pdb=" O VAL G 44 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 159 through 163 removed outlier: 7.003A pdb=" N GLY G 160 " --> pdb=" O ILE G 185 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ALA G 187 " --> pdb=" O GLY G 160 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LEU G 162 " --> pdb=" O ALA G 187 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 315 through 317 removed outlier: 6.333A pdb=" N HIS G 316 " --> pdb=" O VAL I 307 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N HIS J 316 " --> pdb=" O LEU H 303 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU H 305 " --> pdb=" O HIS J 316 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 124 through 129 removed outlier: 7.954A pdb=" N SER H 42 " --> pdb=" O GLN H 7 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N LYS H 9 " --> pdb=" O SER H 42 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL H 44 " --> pdb=" O LYS H 9 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ALA H 11 " --> pdb=" O VAL H 44 " (cutoff:3.500A) removed outlier: 8.688A pdb=" N CYS H 225 " --> pdb=" O ALA H 11 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N VAL H 13 " --> pdb=" O CYS H 225 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 141 through 142 removed outlier: 7.118A pdb=" N LEU H 111 " --> pdb=" O GLY H 142 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N SER H 42 " --> pdb=" O GLN H 7 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N LYS H 9 " --> pdb=" O SER H 42 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL H 44 " --> pdb=" O LYS H 9 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ALA H 11 " --> pdb=" O VAL H 44 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 151 through 152 removed outlier: 7.107A pdb=" N GLY H 160 " --> pdb=" O ILE H 185 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ALA H 187 " --> pdb=" O GLY H 160 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LEU H 162 " --> pdb=" O ALA H 187 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 124 through 129 removed outlier: 6.703A pdb=" N SER I 42 " --> pdb=" O TYR I 98 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N VAL I 100 " --> pdb=" O SER I 42 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL I 44 " --> pdb=" O VAL I 100 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N GLY I 102 " --> pdb=" O VAL I 44 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N SER I 42 " --> pdb=" O GLN I 7 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N LYS I 9 " --> pdb=" O SER I 42 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL I 44 " --> pdb=" O LYS I 9 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALA I 11 " --> pdb=" O VAL I 44 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 151 through 152 Processing sheet with id=AD3, first strand: chain 'I' and resid 315 through 317 removed outlier: 8.339A pdb=" N HIS L 316 " --> pdb=" O LEU J 303 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU J 305 " --> pdb=" O HIS L 316 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 124 through 129 removed outlier: 6.722A pdb=" N ILE J 117 " --> pdb=" O VAL J 125 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THR J 127 " --> pdb=" O GLN J 115 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N GLN J 115 " --> pdb=" O THR J 127 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ARG J 129 " --> pdb=" O LEU J 113 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LEU J 113 " --> pdb=" O ARG J 129 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N LEU J 111 " --> pdb=" O GLY J 142 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 124 through 129 removed outlier: 6.722A pdb=" N ILE J 117 " --> pdb=" O VAL J 125 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THR J 127 " --> pdb=" O GLN J 115 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N GLN J 115 " --> pdb=" O THR J 127 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ARG J 129 " --> pdb=" O LEU J 113 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LEU J 113 " --> pdb=" O ARG J 129 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N SER J 42 " --> pdb=" O GLN J 7 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N LYS J 9 " --> pdb=" O SER J 42 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL J 44 " --> pdb=" O LYS J 9 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA J 11 " --> pdb=" O VAL J 44 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 151 through 154 removed outlier: 6.470A pdb=" N ARG J 158 " --> pdb=" O VAL J 183 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N ILE J 185 " --> pdb=" O ARG J 158 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N GLY J 160 " --> pdb=" O ILE J 185 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ALA J 187 " --> pdb=" O GLY J 160 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LEU J 162 " --> pdb=" O ALA J 187 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 124 through 129 removed outlier: 6.717A pdb=" N ILE K 117 " --> pdb=" O VAL K 125 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N THR K 127 " --> pdb=" O GLN K 115 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLN K 115 " --> pdb=" O THR K 127 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ARG K 129 " --> pdb=" O LEU K 113 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU K 113 " --> pdb=" O ARG K 129 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N THR K 110 " --> pdb=" O SER K 107 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N SER K 42 " --> pdb=" O TYR K 98 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N VAL K 100 " --> pdb=" O SER K 42 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL K 44 " --> pdb=" O VAL K 100 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N GLY K 102 " --> pdb=" O VAL K 44 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N SER K 42 " --> pdb=" O GLN K 7 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N LYS K 9 " --> pdb=" O SER K 42 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL K 44 " --> pdb=" O LYS K 9 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA K 11 " --> pdb=" O VAL K 44 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N CYS K 225 " --> pdb=" O ALA K 11 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N VAL K 13 " --> pdb=" O CYS K 225 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 141 through 142 removed outlier: 7.249A pdb=" N LEU K 111 " --> pdb=" O GLY K 142 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N THR K 110 " --> pdb=" O SER K 107 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N SER K 42 " --> pdb=" O TYR K 98 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N VAL K 100 " --> pdb=" O SER K 42 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL K 44 " --> pdb=" O VAL K 100 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N GLY K 102 " --> pdb=" O VAL K 44 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N SER K 42 " --> pdb=" O GLN K 7 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N LYS K 9 " --> pdb=" O SER K 42 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL K 44 " --> pdb=" O LYS K 9 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA K 11 " --> pdb=" O VAL K 44 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 151 through 154 removed outlier: 6.484A pdb=" N HIS K 184 " --> pdb=" O LEU K 222 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 124 through 129 removed outlier: 6.984A pdb=" N ILE L 117 " --> pdb=" O VAL L 125 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N THR L 127 " --> pdb=" O GLN L 115 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLN L 115 " --> pdb=" O THR L 127 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ARG L 129 " --> pdb=" O LEU L 113 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU L 113 " --> pdb=" O ARG L 129 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU L 43 " --> pdb=" O LYS L 9 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 151 through 154 1232 hydrogen bonds defined for protein. 3282 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.57 Time building geometry restraints manager: 12.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 6222 1.32 - 1.45: 6837 1.45 - 1.58: 16278 1.58 - 1.70: 3 1.70 - 1.83: 204 Bond restraints: 29544 Sorted by residual: bond pdb=" CZ ARG H 309 " pdb=" NH2 ARG H 309 " ideal model delta sigma weight residual 1.330 1.273 0.057 1.30e-02 5.92e+03 1.95e+01 bond pdb=" CB THR K 313 " pdb=" OG1 THR K 313 " ideal model delta sigma weight residual 1.433 1.365 0.068 1.60e-02 3.91e+03 1.83e+01 bond pdb=" CZ ARG A 87 " pdb=" NH2 ARG A 87 " ideal model delta sigma weight residual 1.330 1.279 0.051 1.30e-02 5.92e+03 1.55e+01 bond pdb=" CZ ARG J 314 " pdb=" NH2 ARG J 314 " ideal model delta sigma weight residual 1.330 1.279 0.051 1.30e-02 5.92e+03 1.54e+01 bond pdb=" N ILE E 237 " pdb=" CA ILE E 237 " ideal model delta sigma weight residual 1.456 1.501 -0.044 1.14e-02 7.69e+03 1.51e+01 ... (remaining 29539 not shown) Histogram of bond angle deviations from ideal: 97.22 - 104.87: 651 104.87 - 112.52: 12570 112.52 - 120.17: 14376 120.17 - 127.82: 12307 127.82 - 135.48: 332 Bond angle restraints: 40236 Sorted by residual: angle pdb=" CA ILE E 237 " pdb=" CB ILE E 237 " pdb=" CG1 ILE E 237 " ideal model delta sigma weight residual 110.40 135.11 -24.71 1.70e+00 3.46e-01 2.11e+02 angle pdb=" CA VAL A 124 " pdb=" CB VAL A 124 " pdb=" CG1 VAL A 124 " ideal model delta sigma weight residual 110.40 133.98 -23.58 1.70e+00 3.46e-01 1.92e+02 angle pdb=" CA THR F 265 " pdb=" CB THR F 265 " pdb=" OG1 THR F 265 " ideal model delta sigma weight residual 109.60 128.39 -18.79 1.50e+00 4.44e-01 1.57e+02 angle pdb=" CA VAL L 124 " pdb=" CB VAL L 124 " pdb=" CG1 VAL L 124 " ideal model delta sigma weight residual 110.40 131.69 -21.29 1.70e+00 3.46e-01 1.57e+02 angle pdb=" CA VAL A 80 " pdb=" CB VAL A 80 " pdb=" CG1 VAL A 80 " ideal model delta sigma weight residual 110.40 131.63 -21.23 1.70e+00 3.46e-01 1.56e+02 ... (remaining 40231 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.22: 16078 18.22 - 36.44: 1036 36.44 - 54.66: 258 54.66 - 72.88: 80 72.88 - 91.10: 32 Dihedral angle restraints: 17484 sinusoidal: 6600 harmonic: 10884 Sorted by residual: dihedral pdb=" N PRO I 240 " pdb=" C PRO I 240 " pdb=" CA PRO I 240 " pdb=" CB PRO I 240 " ideal model delta harmonic sigma weight residual 115.10 143.19 -28.09 0 2.50e+00 1.60e-01 1.26e+02 dihedral pdb=" C PRO I 240 " pdb=" N PRO I 240 " pdb=" CA PRO I 240 " pdb=" CB PRO I 240 " ideal model delta harmonic sigma weight residual -120.70 -145.76 25.06 0 2.50e+00 1.60e-01 1.00e+02 dihedral pdb=" C GLN B 319 " pdb=" N GLN B 319 " pdb=" CA GLN B 319 " pdb=" CB GLN B 319 " ideal model delta harmonic sigma weight residual -122.60 -144.48 21.88 0 2.50e+00 1.60e-01 7.66e+01 ... (remaining 17481 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.256: 4295 0.256 - 0.513: 102 0.513 - 0.769: 16 0.769 - 1.025: 12 1.025 - 1.282: 3 Chirality restraints: 4428 Sorted by residual: chirality pdb=" CB VAL L 124 " pdb=" CA VAL L 124 " pdb=" CG1 VAL L 124 " pdb=" CG2 VAL L 124 " both_signs ideal model delta sigma weight residual False -2.63 -1.35 -1.28 2.00e-01 2.50e+01 4.11e+01 chirality pdb=" CA PRO I 240 " pdb=" N PRO I 240 " pdb=" C PRO I 240 " pdb=" CB PRO I 240 " both_signs ideal model delta sigma weight residual False 2.72 1.48 1.23 2.00e-01 2.50e+01 3.81e+01 chirality pdb=" CB VAL A 124 " pdb=" CA VAL A 124 " pdb=" CG1 VAL A 124 " pdb=" CG2 VAL A 124 " both_signs ideal model delta sigma weight residual False -2.63 -1.42 -1.21 2.00e-01 2.50e+01 3.65e+01 ... (remaining 4425 not shown) Planarity restraints: 5268 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 297 " 0.281 2.00e-02 2.50e+03 1.54e-01 4.74e+02 pdb=" CG TYR B 297 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TYR B 297 " -0.150 2.00e-02 2.50e+03 pdb=" CD2 TYR B 297 " -0.137 2.00e-02 2.50e+03 pdb=" CE1 TYR B 297 " -0.071 2.00e-02 2.50e+03 pdb=" CE2 TYR B 297 " -0.097 2.00e-02 2.50e+03 pdb=" CZ TYR B 297 " 0.013 2.00e-02 2.50e+03 pdb=" OH TYR B 297 " 0.225 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR K 297 " 0.237 2.00e-02 2.50e+03 1.37e-01 3.73e+02 pdb=" CG TYR K 297 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR K 297 " -0.136 2.00e-02 2.50e+03 pdb=" CD2 TYR K 297 " -0.097 2.00e-02 2.50e+03 pdb=" CE1 TYR K 297 " -0.065 2.00e-02 2.50e+03 pdb=" CE2 TYR K 297 " -0.109 2.00e-02 2.50e+03 pdb=" CZ TYR K 297 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR K 297 " 0.217 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 297 " -0.234 2.00e-02 2.50e+03 1.34e-01 3.60e+02 pdb=" CG TYR D 297 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR D 297 " 0.123 2.00e-02 2.50e+03 pdb=" CD2 TYR D 297 " 0.116 2.00e-02 2.50e+03 pdb=" CE1 TYR D 297 " 0.079 2.00e-02 2.50e+03 pdb=" CE2 TYR D 297 " 0.090 2.00e-02 2.50e+03 pdb=" CZ TYR D 297 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR D 297 " -0.212 2.00e-02 2.50e+03 ... (remaining 5265 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 13591 2.99 - 3.47: 29215 3.47 - 3.95: 53311 3.95 - 4.42: 62361 4.42 - 4.90: 98577 Nonbonded interactions: 257055 Sorted by model distance: nonbonded pdb=" OD1 ASP J 145 " pdb=" OG SER J 147 " model vdw 2.514 2.440 nonbonded pdb=" OD1 ASP E 145 " pdb=" OG SER E 147 " model vdw 2.532 2.440 nonbonded pdb=" OD1 ASP G 145 " pdb=" OG SER G 147 " model vdw 2.536 2.440 nonbonded pdb=" OD1 ASP D 145 " pdb=" OG SER D 147 " model vdw 2.543 2.440 nonbonded pdb=" OD1 ASP I 145 " pdb=" OG SER I 147 " model vdw 2.544 2.440 ... (remaining 257050 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' 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: 0.210 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: 0.030 Extract box with map and model: 2.370 Check model and map are aligned: 0.420 Set scattering table: 0.240 Process input model: 74.740 Find NCS groups from input model: 2.120 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 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 : 0.013 0.068 29544 Z= 0.827 Angle : 2.021 24.707 40236 Z= 1.336 Chirality : 0.125 1.282 4428 Planarity : 0.017 0.154 5268 Dihedral : 14.555 91.098 10548 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 0.63 Ramachandran Plot: Outliers : 0.56 % Allowed : 4.30 % Favored : 95.14 % Rotamer: Outliers : 1.24 % Allowed : 4.15 % Favored : 94.61 % Cbeta Deviations : 0.55 % Peptide Plane: Cis-proline : 5.56 % 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: -2.34 (0.13), residues: 3768 helix: -2.51 (0.11), residues: 1188 sheet: -1.49 (0.17), residues: 840 loop : -0.62 (0.16), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.138 0.031 TRP I 56 HIS 0.022 0.005 HIS F 135 PHE 0.088 0.020 PHE D 252 TYR 0.281 0.027 TYR B 297 ARG 0.019 0.002 ARG D 138 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 667 time to evaluate : 3.122 Fit side-chains REVERT: A 75 ASP cc_start: 0.7213 (m-30) cc_final: 0.6959 (m-30) REVERT: A 120 ASP cc_start: 0.6325 (m-30) cc_final: 0.6075 (m-30) REVERT: A 131 LEU cc_start: 0.8646 (mp) cc_final: 0.8362 (mt) REVERT: A 143 GLU cc_start: 0.6763 (mt-10) cc_final: 0.6314 (tt0) REVERT: A 148 ASP cc_start: 0.7736 (m-30) cc_final: 0.7434 (m-30) REVERT: A 247 LEU cc_start: 0.7161 (OUTLIER) cc_final: 0.6840 (mt) REVERT: A 312 MET cc_start: 0.7151 (mtt) cc_final: 0.6822 (mtm) REVERT: B 80 VAL cc_start: 0.6819 (t) cc_final: 0.6561 (m) REVERT: B 163 CYS cc_start: 0.7643 (OUTLIER) cc_final: 0.7221 (m) REVERT: B 166 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7673 (mt-10) REVERT: B 206 ASN cc_start: 0.8267 (m-40) cc_final: 0.7873 (m-40) REVERT: C 96 LYS cc_start: 0.7058 (tppt) cc_final: 0.6837 (tptt) REVERT: C 218 GLN cc_start: 0.8215 (mp10) cc_final: 0.7790 (mp10) REVERT: D 21 ASP cc_start: 0.7632 (t0) cc_final: 0.7409 (t0) REVERT: D 50 TRP cc_start: 0.8343 (t60) cc_final: 0.8084 (t60) REVERT: D 76 ASN cc_start: 0.8486 (m110) cc_final: 0.7929 (m110) REVERT: D 79 GLU cc_start: 0.6497 (mt-10) cc_final: 0.6194 (mt-10) REVERT: D 90 ARG cc_start: 0.7379 (mmt90) cc_final: 0.7005 (mmp-170) REVERT: D 182 GLN cc_start: 0.7776 (mt0) cc_final: 0.7485 (mt0) REVERT: D 254 MET cc_start: 0.8414 (mmt) cc_final: 0.8109 (mmp) REVERT: E 71 GLN cc_start: 0.7842 (tt0) cc_final: 0.7329 (tt0) REVERT: E 75 ASP cc_start: 0.7516 (m-30) cc_final: 0.7247 (m-30) REVERT: E 168 ILE cc_start: 0.8445 (mm) cc_final: 0.8126 (mt) REVERT: E 309 ARG cc_start: 0.7416 (mtm180) cc_final: 0.7150 (mmm-85) REVERT: F 76 ASN cc_start: 0.8836 (m110) cc_final: 0.8620 (m110) REVERT: F 135 HIS cc_start: 0.7869 (OUTLIER) cc_final: 0.7290 (p-80) REVERT: F 176 MET cc_start: 0.8799 (mmm) cc_final: 0.8484 (mmm) REVERT: G 135 HIS cc_start: 0.8201 (OUTLIER) cc_final: 0.7536 (p-80) REVERT: H 35 GLN cc_start: 0.8183 (tt0) cc_final: 0.7981 (tt0) REVERT: H 71 GLN cc_start: 0.7525 (tt0) cc_final: 0.7150 (tt0) REVERT: H 96 LYS cc_start: 0.6960 (mmtt) cc_final: 0.6298 (mptt) REVERT: H 176 MET cc_start: 0.8752 (mmm) cc_final: 0.8548 (mmp) REVERT: I 135 HIS cc_start: 0.7926 (OUTLIER) cc_final: 0.7472 (p-80) REVERT: J 309 ARG cc_start: 0.7208 (mtm180) cc_final: 0.6821 (mmm-85) REVERT: K 6 LYS cc_start: 0.8148 (mttp) cc_final: 0.7851 (mttm) REVERT: K 76 ASN cc_start: 0.8313 (m110) cc_final: 0.7938 (m110) REVERT: K 90 ARG cc_start: 0.7297 (mmt90) cc_final: 0.7003 (mmp-170) REVERT: K 254 MET cc_start: 0.8460 (mmt) cc_final: 0.8183 (mmp) REVERT: L 51 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8238 (mt) REVERT: L 304 ARG cc_start: 0.8115 (mtt180) cc_final: 0.6890 (ttt180) REVERT: L 309 ARG cc_start: 0.6222 (mtm180) cc_final: 0.5484 (mtm180) outliers start: 36 outliers final: 9 residues processed: 681 average time/residue: 0.4426 time to fit residues: 461.3231 Evaluate side-chains 467 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 452 time to evaluate : 2.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain E residue 237 ILE Chi-restraints excluded: chain F residue 135 HIS Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 313 THR Chi-restraints excluded: chain G residue 135 HIS Chi-restraints excluded: chain I residue 135 HIS Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 124 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 314 optimal weight: 6.9990 chunk 281 optimal weight: 5.9990 chunk 156 optimal weight: 7.9990 chunk 96 optimal weight: 10.0000 chunk 190 optimal weight: 6.9990 chunk 150 optimal weight: 7.9990 chunk 291 optimal weight: 7.9990 chunk 112 optimal weight: 5.9990 chunk 177 optimal weight: 4.9990 chunk 217 optimal weight: 9.9990 chunk 337 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN A 207 ASN B 135 HIS B 179 GLN B 200 GLN C 71 GLN C 115 GLN C 169 GLN D 76 ASN D 115 GLN E 115 GLN E 135 HIS ** E 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 316 HIS F 169 GLN G 71 GLN G 76 ASN G 115 GLN G 135 HIS G 169 GLN G 316 HIS H 316 HIS I 71 GLN I 76 ASN I 207 ASN J 76 ASN J 115 GLN J 135 HIS J 316 HIS K 115 GLN K 135 HIS L 94 GLN L 135 HIS L 204 GLN L 207 ASN L 319 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 29544 Z= 0.319 Angle : 0.673 9.246 40236 Z= 0.354 Chirality : 0.046 0.182 4428 Planarity : 0.005 0.053 5268 Dihedral : 6.387 58.938 4150 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.07 % Favored : 97.58 % Rotamer: Outliers : 1.45 % Allowed : 8.82 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.14), residues: 3768 helix: -0.83 (0.14), residues: 1164 sheet: -1.15 (0.18), residues: 792 loop : -0.02 (0.15), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 50 HIS 0.006 0.001 HIS F 152 PHE 0.014 0.002 PHE G 69 TYR 0.018 0.002 TYR E 317 ARG 0.005 0.001 ARG B 106 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 498 time to evaluate : 3.241 Fit side-chains revert: symmetry clash REVERT: A 312 MET cc_start: 0.7097 (mtt) cc_final: 0.6801 (mtt) REVERT: B 190 SER cc_start: 0.8570 (m) cc_final: 0.8249 (p) REVERT: B 271 GLU cc_start: 0.6621 (tt0) cc_final: 0.6071 (mt-10) REVERT: B 314 ARG cc_start: 0.7724 (mpt180) cc_final: 0.7341 (mmt-90) REVERT: C 96 LYS cc_start: 0.6874 (tppt) cc_final: 0.6665 (tptt) REVERT: C 304 ARG cc_start: 0.8255 (mtt180) cc_final: 0.8053 (mtt180) REVERT: D 50 TRP cc_start: 0.8396 (t60) cc_final: 0.8114 (t60) REVERT: D 76 ASN cc_start: 0.8576 (m-40) cc_final: 0.8080 (m110) REVERT: D 79 GLU cc_start: 0.6757 (mt-10) cc_final: 0.6528 (mt-10) REVERT: D 90 ARG cc_start: 0.7305 (mmt90) cc_final: 0.6869 (mmp-170) REVERT: D 94 GLN cc_start: 0.7237 (tt0) cc_final: 0.7017 (mt0) REVERT: D 254 MET cc_start: 0.8311 (mmt) cc_final: 0.7997 (mmp) REVERT: E 90 ARG cc_start: 0.6568 (mmp-170) cc_final: 0.6032 (mtm110) REVERT: E 168 ILE cc_start: 0.8433 (mm) cc_final: 0.8179 (mm) REVERT: E 309 ARG cc_start: 0.7755 (mtm180) cc_final: 0.7109 (mtp180) REVERT: G 6 LYS cc_start: 0.7383 (mttp) cc_final: 0.7142 (mtmt) REVERT: G 96 LYS cc_start: 0.7322 (mmtt) cc_final: 0.6773 (mptt) REVERT: G 248 GLU cc_start: 0.7794 (tp30) cc_final: 0.7445 (tp30) REVERT: H 96 LYS cc_start: 0.7331 (mmtt) cc_final: 0.6777 (mptt) REVERT: H 123 ARG cc_start: 0.7412 (ptt180) cc_final: 0.7025 (ptp90) REVERT: H 176 MET cc_start: 0.8759 (mmm) cc_final: 0.8332 (mmt) REVERT: I 271 GLU cc_start: 0.6901 (tp30) cc_final: 0.6644 (mm-30) REVERT: J 76 ASN cc_start: 0.8521 (OUTLIER) cc_final: 0.8224 (m110) REVERT: J 309 ARG cc_start: 0.7614 (mtm180) cc_final: 0.6995 (mmm-85) REVERT: K 6 LYS cc_start: 0.8057 (mttp) cc_final: 0.7763 (mttm) REVERT: K 76 ASN cc_start: 0.8630 (m110) cc_final: 0.8032 (m110) REVERT: K 90 ARG cc_start: 0.7199 (mmt90) cc_final: 0.6890 (mmp-170) REVERT: K 254 MET cc_start: 0.8269 (mmt) cc_final: 0.7981 (mmp) REVERT: K 317 TYR cc_start: 0.8147 (m-80) cc_final: 0.7519 (m-80) REVERT: L 169 GLN cc_start: 0.7690 (mm-40) cc_final: 0.7297 (mm-40) REVERT: L 304 ARG cc_start: 0.8149 (mtt180) cc_final: 0.7073 (ttt180) REVERT: L 309 ARG cc_start: 0.6425 (mtm180) cc_final: 0.5839 (mtm180) outliers start: 42 outliers final: 23 residues processed: 517 average time/residue: 0.4413 time to fit residues: 350.9982 Evaluate side-chains 457 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 433 time to evaluate : 3.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 313 THR Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 313 THR Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain J residue 190 SER Chi-restraints excluded: chain J residue 227 THR Chi-restraints excluded: chain K residue 190 SER Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 313 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 187 optimal weight: 20.0000 chunk 104 optimal weight: 30.0000 chunk 281 optimal weight: 20.0000 chunk 230 optimal weight: 0.9980 chunk 93 optimal weight: 30.0000 chunk 338 optimal weight: 0.9980 chunk 365 optimal weight: 30.0000 chunk 301 optimal weight: 5.9990 chunk 335 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 chunk 271 optimal weight: 5.9990 overall best weight: 4.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN B 76 ASN C 71 GLN C 169 GLN D 14 GLN F 73 ASN G 135 HIS G 169 GLN H 206 ASN I 169 GLN K 169 GLN L 71 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 29544 Z= 0.239 Angle : 0.589 8.346 40236 Z= 0.306 Chirality : 0.044 0.179 4428 Planarity : 0.004 0.045 5268 Dihedral : 5.445 38.717 4133 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.32 % Allowed : 2.39 % Favored : 97.29 % Rotamer: Outliers : 1.90 % Allowed : 10.41 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.01 (0.14), residues: 3768 helix: -0.77 (0.14), residues: 1308 sheet: -1.21 (0.18), residues: 780 loop : -0.04 (0.16), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 50 HIS 0.005 0.001 HIS I 167 PHE 0.014 0.002 PHE A 69 TYR 0.012 0.001 TYR E 317 ARG 0.005 0.000 ARG J 123 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 503 time to evaluate : 3.284 Fit side-chains revert: symmetry clash REVERT: A 112 TYR cc_start: 0.8207 (m-80) cc_final: 0.8003 (m-80) REVERT: A 148 ASP cc_start: 0.7260 (m-30) cc_final: 0.6922 (m-30) REVERT: A 169 GLN cc_start: 0.6548 (mp10) cc_final: 0.5842 (mp10) REVERT: A 312 MET cc_start: 0.7077 (mtt) cc_final: 0.6830 (mtt) REVERT: B 190 SER cc_start: 0.8678 (m) cc_final: 0.8461 (p) REVERT: B 271 GLU cc_start: 0.6699 (tt0) cc_final: 0.6218 (mt-10) REVERT: C 96 LYS cc_start: 0.6746 (tppt) cc_final: 0.6403 (tptm) REVERT: C 123 ARG cc_start: 0.6412 (OUTLIER) cc_final: 0.6009 (ptp-170) REVERT: D 50 TRP cc_start: 0.8314 (t60) cc_final: 0.7995 (t60) REVERT: D 76 ASN cc_start: 0.8394 (m-40) cc_final: 0.7854 (m110) REVERT: D 79 GLU cc_start: 0.6804 (mt-10) cc_final: 0.6551 (mt-10) REVERT: D 90 ARG cc_start: 0.7171 (mmt90) cc_final: 0.6744 (mmp-170) REVERT: D 94 GLN cc_start: 0.7411 (tt0) cc_final: 0.7141 (mt0) REVERT: D 310 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7464 (mm-30) REVERT: E 90 ARG cc_start: 0.6530 (mmp-170) cc_final: 0.5950 (mtt90) REVERT: E 123 ARG cc_start: 0.7086 (ptt-90) cc_final: 0.6782 (ptt-90) REVERT: E 227 THR cc_start: 0.8380 (OUTLIER) cc_final: 0.8066 (p) REVERT: E 297 TYR cc_start: 0.8526 (OUTLIER) cc_final: 0.8245 (t80) REVERT: E 309 ARG cc_start: 0.7674 (mtm180) cc_final: 0.7068 (mtp180) REVERT: G 6 LYS cc_start: 0.7363 (mttp) cc_final: 0.7154 (mtmt) REVERT: G 176 MET cc_start: 0.8791 (mmm) cc_final: 0.8489 (mmm) REVERT: H 123 ARG cc_start: 0.7335 (ptt180) cc_final: 0.6913 (ptp90) REVERT: J 270 THR cc_start: 0.8779 (m) cc_final: 0.8557 (m) REVERT: J 271 GLU cc_start: 0.7240 (tp30) cc_final: 0.7012 (mm-30) REVERT: J 309 ARG cc_start: 0.7577 (mtm180) cc_final: 0.6970 (mmm-85) REVERT: K 6 LYS cc_start: 0.8060 (mttp) cc_final: 0.7800 (mttm) REVERT: K 90 ARG cc_start: 0.7062 (mmt90) cc_final: 0.6712 (mmp-170) REVERT: K 317 TYR cc_start: 0.8153 (m-80) cc_final: 0.7522 (m-80) REVERT: L 169 GLN cc_start: 0.7994 (mm-40) cc_final: 0.7632 (mm-40) REVERT: L 304 ARG cc_start: 0.8136 (mtt180) cc_final: 0.7071 (ttt180) REVERT: L 309 ARG cc_start: 0.6620 (mtm180) cc_final: 0.5697 (mtm-85) outliers start: 55 outliers final: 29 residues processed: 531 average time/residue: 0.4426 time to fit residues: 364.1175 Evaluate side-chains 489 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 457 time to evaluate : 2.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 301 ASP Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 123 ARG Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain E residue 297 TYR Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain H residue 153 ASP Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain J residue 190 SER Chi-restraints excluded: chain J residue 227 THR Chi-restraints excluded: chain K residue 190 SER Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 313 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 334 optimal weight: 9.9990 chunk 254 optimal weight: 20.0000 chunk 175 optimal weight: 1.9990 chunk 37 optimal weight: 30.0000 chunk 161 optimal weight: 9.9990 chunk 227 optimal weight: 6.9990 chunk 339 optimal weight: 8.9990 chunk 359 optimal weight: 6.9990 chunk 177 optimal weight: 5.9990 chunk 321 optimal weight: 30.0000 chunk 96 optimal weight: 30.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 204 GLN A 206 ASN B 76 ASN C 71 GLN D 135 HIS F 73 ASN I 71 GLN I 73 ASN I 76 ASN J 169 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 29544 Z= 0.319 Angle : 0.614 9.193 40236 Z= 0.317 Chirality : 0.045 0.171 4428 Planarity : 0.004 0.050 5268 Dihedral : 5.400 28.245 4129 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.32 % Allowed : 2.47 % Favored : 97.21 % Rotamer: Outliers : 2.52 % Allowed : 11.69 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.14), residues: 3768 helix: -0.40 (0.15), residues: 1236 sheet: -1.25 (0.18), residues: 780 loop : 0.09 (0.15), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 50 HIS 0.005 0.002 HIS C 135 PHE 0.013 0.002 PHE A 69 TYR 0.018 0.002 TYR I 297 ARG 0.004 0.001 ARG E 128 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 469 time to evaluate : 3.386 Fit side-chains revert: symmetry clash REVERT: A 148 ASP cc_start: 0.7285 (m-30) cc_final: 0.6947 (m-30) REVERT: A 169 GLN cc_start: 0.6643 (mp10) cc_final: 0.5804 (mp10) REVERT: A 236 LEU cc_start: 0.6805 (tp) cc_final: 0.6532 (mt) REVERT: A 312 MET cc_start: 0.7050 (mtt) cc_final: 0.6825 (mtt) REVERT: B 134 THR cc_start: 0.7928 (OUTLIER) cc_final: 0.7607 (p) REVERT: C 96 LYS cc_start: 0.6880 (tppt) cc_final: 0.6472 (tptt) REVERT: C 123 ARG cc_start: 0.6503 (OUTLIER) cc_final: 0.6135 (ptp-170) REVERT: D 50 TRP cc_start: 0.8322 (t60) cc_final: 0.7978 (t60) REVERT: D 76 ASN cc_start: 0.8426 (m-40) cc_final: 0.7923 (m110) REVERT: D 79 GLU cc_start: 0.6959 (mt-10) cc_final: 0.6596 (mt-10) REVERT: D 90 ARG cc_start: 0.7267 (mmt90) cc_final: 0.6836 (mmp-170) REVERT: D 94 GLN cc_start: 0.7260 (tt0) cc_final: 0.7008 (mt0) REVERT: D 254 MET cc_start: 0.8414 (mmt) cc_final: 0.8169 (mmp) REVERT: D 310 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7424 (mm-30) REVERT: E 90 ARG cc_start: 0.6519 (mmp-170) cc_final: 0.5924 (mtt90) REVERT: E 123 ARG cc_start: 0.7135 (ptt-90) cc_final: 0.6842 (ptt-90) REVERT: E 227 THR cc_start: 0.8373 (OUTLIER) cc_final: 0.8058 (p) REVERT: E 297 TYR cc_start: 0.8550 (t80) cc_final: 0.8255 (t80) REVERT: G 6 LYS cc_start: 0.7342 (mttp) cc_final: 0.7123 (mttp) REVERT: H 71 GLN cc_start: 0.7976 (tp40) cc_final: 0.7753 (tp40) REVERT: H 123 ARG cc_start: 0.7356 (ptt180) cc_final: 0.6959 (ptp90) REVERT: J 270 THR cc_start: 0.8933 (OUTLIER) cc_final: 0.8683 (m) REVERT: K 6 LYS cc_start: 0.8087 (mttp) cc_final: 0.7810 (mttm) REVERT: K 90 ARG cc_start: 0.7092 (mmt90) cc_final: 0.6732 (mmp-170) REVERT: K 123 ARG cc_start: 0.7118 (ptp-170) cc_final: 0.6873 (ptp90) REVERT: K 254 MET cc_start: 0.8366 (mmt) cc_final: 0.8104 (mmp) REVERT: K 310 GLU cc_start: 0.7644 (mm-30) cc_final: 0.7321 (mm-30) REVERT: K 317 TYR cc_start: 0.8145 (m-80) cc_final: 0.7635 (m-80) REVERT: L 143 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7242 (mt-10) REVERT: L 148 ASP cc_start: 0.7845 (m-30) cc_final: 0.7616 (m-30) REVERT: L 169 GLN cc_start: 0.8042 (mm-40) cc_final: 0.7675 (mm-40) REVERT: L 218 GLN cc_start: 0.8140 (mp10) cc_final: 0.7660 (mp10) REVERT: L 304 ARG cc_start: 0.8170 (mtt180) cc_final: 0.7097 (ttt180) REVERT: L 309 ARG cc_start: 0.6558 (mtm180) cc_final: 0.5602 (mtm180) outliers start: 73 outliers final: 50 residues processed: 508 average time/residue: 0.4225 time to fit residues: 334.4991 Evaluate side-chains 500 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 446 time to evaluate : 3.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 301 ASP Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 123 ARG Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain G residue 232 MET Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 153 ASP Chi-restraints excluded: chain H residue 307 VAL Chi-restraints excluded: chain H residue 313 THR Chi-restraints excluded: chain I residue 101 LEU Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 267 LEU Chi-restraints excluded: chain J residue 79 GLU Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain J residue 153 ASP Chi-restraints excluded: chain J residue 190 SER Chi-restraints excluded: chain J residue 227 THR Chi-restraints excluded: chain J residue 267 LEU Chi-restraints excluded: chain J residue 270 THR Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 190 SER Chi-restraints excluded: chain K residue 227 THR Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 313 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 299 optimal weight: 7.9990 chunk 204 optimal weight: 9.9990 chunk 5 optimal weight: 20.0000 chunk 267 optimal weight: 5.9990 chunk 148 optimal weight: 20.0000 chunk 306 optimal weight: 7.9990 chunk 248 optimal weight: 20.0000 chunk 0 optimal weight: 50.0000 chunk 183 optimal weight: 6.9990 chunk 322 optimal weight: 0.9990 chunk 90 optimal weight: 30.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN B 76 ASN C 71 GLN F 71 GLN F 73 ASN F 115 GLN I 71 GLN I 73 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 29544 Z= 0.310 Angle : 0.601 9.362 40236 Z= 0.310 Chirality : 0.044 0.174 4428 Planarity : 0.004 0.048 5268 Dihedral : 5.312 26.552 4129 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.32 % Allowed : 2.63 % Favored : 97.05 % Rotamer: Outliers : 2.84 % Allowed : 12.17 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.63 (0.14), residues: 3768 helix: -0.31 (0.15), residues: 1236 sheet: -1.19 (0.18), residues: 804 loop : 0.14 (0.16), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 50 HIS 0.005 0.001 HIS G 167 PHE 0.013 0.002 PHE A 69 TYR 0.015 0.002 TYR E 297 ARG 0.004 0.000 ARG E 128 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 480 time to evaluate : 3.010 Fit side-chains REVERT: A 148 ASP cc_start: 0.7291 (m-30) cc_final: 0.6935 (m-30) REVERT: A 169 GLN cc_start: 0.6654 (mp10) cc_final: 0.5776 (mp10) REVERT: A 180 HIS cc_start: 0.7610 (m-70) cc_final: 0.7385 (m170) REVERT: A 236 LEU cc_start: 0.6789 (tp) cc_final: 0.6533 (mt) REVERT: A 312 MET cc_start: 0.6989 (mtt) cc_final: 0.6781 (mtt) REVERT: B 134 THR cc_start: 0.8003 (OUTLIER) cc_final: 0.6913 (p) REVERT: B 137 GLU cc_start: 0.7388 (mt-10) cc_final: 0.6988 (mt-10) REVERT: C 96 LYS cc_start: 0.6780 (tppt) cc_final: 0.6361 (tptt) REVERT: C 123 ARG cc_start: 0.6558 (ptp-170) cc_final: 0.6283 (ptp90) REVERT: D 76 ASN cc_start: 0.8462 (m-40) cc_final: 0.7960 (m110) REVERT: D 79 GLU cc_start: 0.6944 (mt-10) cc_final: 0.6594 (mt-10) REVERT: D 90 ARG cc_start: 0.7225 (mmt90) cc_final: 0.6815 (mmp-170) REVERT: D 94 GLN cc_start: 0.7197 (tt0) cc_final: 0.6969 (mt0) REVERT: D 254 MET cc_start: 0.8407 (mmt) cc_final: 0.8177 (mmp) REVERT: D 310 GLU cc_start: 0.7587 (mm-30) cc_final: 0.7291 (mm-30) REVERT: E 123 ARG cc_start: 0.7065 (ptt-90) cc_final: 0.6775 (ptt-90) REVERT: E 227 THR cc_start: 0.8389 (OUTLIER) cc_final: 0.8079 (p) REVERT: G 176 MET cc_start: 0.8664 (mmm) cc_final: 0.8448 (mmm) REVERT: H 123 ARG cc_start: 0.7378 (ptt180) cc_final: 0.7007 (ptp90) REVERT: J 94 GLN cc_start: 0.7628 (tm-30) cc_final: 0.7426 (mt0) REVERT: J 227 THR cc_start: 0.8368 (OUTLIER) cc_final: 0.8143 (p) REVERT: K 6 LYS cc_start: 0.8069 (mttp) cc_final: 0.7759 (mttm) REVERT: K 90 ARG cc_start: 0.7110 (mmt90) cc_final: 0.6718 (mmp-170) REVERT: K 123 ARG cc_start: 0.7059 (ptp-170) cc_final: 0.6843 (ptp90) REVERT: K 254 MET cc_start: 0.8354 (mmt) cc_final: 0.7902 (mmp) REVERT: K 310 GLU cc_start: 0.7617 (mm-30) cc_final: 0.7284 (mm-30) REVERT: K 317 TYR cc_start: 0.8138 (m-80) cc_final: 0.7864 (m-80) REVERT: L 5 LYS cc_start: 0.7104 (ttmt) cc_final: 0.6789 (mtpt) REVERT: L 169 GLN cc_start: 0.8056 (mm-40) cc_final: 0.7678 (mm-40) REVERT: L 218 GLN cc_start: 0.8063 (mp10) cc_final: 0.7609 (mp10) REVERT: L 304 ARG cc_start: 0.8168 (mtt180) cc_final: 0.7090 (ttt180) REVERT: L 309 ARG cc_start: 0.6572 (mtm180) cc_final: 0.6318 (mtt90) outliers start: 82 outliers final: 62 residues processed: 523 average time/residue: 0.4170 time to fit residues: 339.7422 Evaluate side-chains 513 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 448 time to evaluate : 3.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 248 GLU Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 301 ASP Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 297 TYR Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain G residue 306 LEU Chi-restraints excluded: chain G residue 313 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 153 ASP Chi-restraints excluded: chain H residue 232 MET Chi-restraints excluded: chain H residue 279 ILE Chi-restraints excluded: chain H residue 306 LEU Chi-restraints excluded: chain H residue 307 VAL Chi-restraints excluded: chain H residue 313 THR Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 267 LEU Chi-restraints excluded: chain J residue 79 GLU Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain J residue 153 ASP Chi-restraints excluded: chain J residue 190 SER Chi-restraints excluded: chain J residue 227 THR Chi-restraints excluded: chain J residue 267 LEU Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 190 SER Chi-restraints excluded: chain K residue 227 THR Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain L residue 131 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 120 optimal weight: 7.9990 chunk 323 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 211 optimal weight: 5.9990 chunk 88 optimal weight: 7.9990 chunk 359 optimal weight: 10.0000 chunk 298 optimal weight: 10.0000 chunk 166 optimal weight: 10.0000 chunk 29 optimal weight: 30.0000 chunk 119 optimal weight: 8.9990 chunk 188 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN B 76 ASN C 71 GLN C 206 ASN F 73 ASN H 76 ASN H 115 GLN I 71 GLN I 73 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 29544 Z= 0.335 Angle : 0.612 9.558 40236 Z= 0.316 Chirality : 0.045 0.168 4428 Planarity : 0.004 0.050 5268 Dihedral : 5.331 21.806 4128 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.32 % Allowed : 2.55 % Favored : 97.13 % Rotamer: Outliers : 3.04 % Allowed : 12.97 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.14), residues: 3768 helix: -0.29 (0.15), residues: 1236 sheet: -1.25 (0.17), residues: 876 loop : 0.11 (0.16), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 50 HIS 0.004 0.001 HIS F 152 PHE 0.013 0.002 PHE A 69 TYR 0.018 0.002 TYR E 297 ARG 0.004 0.000 ARG E 128 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 450 time to evaluate : 2.931 Fit side-chains REVERT: A 113 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.7973 (tt) REVERT: A 148 ASP cc_start: 0.7410 (m-30) cc_final: 0.7012 (m-30) REVERT: A 169 GLN cc_start: 0.6671 (mp10) cc_final: 0.5772 (mp10) REVERT: A 185 ILE cc_start: 0.8175 (OUTLIER) cc_final: 0.7933 (mp) REVERT: A 236 LEU cc_start: 0.6689 (tp) cc_final: 0.6481 (mt) REVERT: B 134 THR cc_start: 0.8150 (OUTLIER) cc_final: 0.7077 (p) REVERT: B 137 GLU cc_start: 0.7432 (mt-10) cc_final: 0.7054 (mt-10) REVERT: C 96 LYS cc_start: 0.6709 (tppt) cc_final: 0.6284 (tptt) REVERT: C 123 ARG cc_start: 0.6537 (ptp-170) cc_final: 0.6239 (ptp90) REVERT: D 50 TRP cc_start: 0.8360 (t60) cc_final: 0.8026 (t60) REVERT: D 76 ASN cc_start: 0.8473 (m-40) cc_final: 0.7980 (m110) REVERT: D 79 GLU cc_start: 0.6953 (mt-10) cc_final: 0.6656 (mt-10) REVERT: D 90 ARG cc_start: 0.7147 (mmt90) cc_final: 0.6729 (mmp-170) REVERT: D 94 GLN cc_start: 0.7224 (tt0) cc_final: 0.6934 (mt0) REVERT: D 254 MET cc_start: 0.8403 (mmt) cc_final: 0.7925 (mmp) REVERT: D 310 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7283 (mm-30) REVERT: E 123 ARG cc_start: 0.7132 (ptt-90) cc_final: 0.6839 (ptt-90) REVERT: E 227 THR cc_start: 0.8414 (OUTLIER) cc_final: 0.8109 (p) REVERT: H 123 ARG cc_start: 0.7419 (OUTLIER) cc_final: 0.7045 (ptp90) REVERT: J 227 THR cc_start: 0.8324 (OUTLIER) cc_final: 0.8117 (p) REVERT: K 6 LYS cc_start: 0.8053 (mttp) cc_final: 0.7748 (mttm) REVERT: K 90 ARG cc_start: 0.7115 (mmt90) cc_final: 0.6725 (mmp-170) REVERT: K 123 ARG cc_start: 0.7043 (ptp-170) cc_final: 0.6826 (ptp90) REVERT: K 254 MET cc_start: 0.8352 (mmt) cc_final: 0.7895 (mmp) REVERT: K 310 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7274 (mm-30) REVERT: K 317 TYR cc_start: 0.8130 (m-80) cc_final: 0.7801 (m-80) REVERT: L 5 LYS cc_start: 0.7119 (ttmt) cc_final: 0.6870 (mtpt) REVERT: L 169 GLN cc_start: 0.8063 (mm-40) cc_final: 0.7678 (mm-40) REVERT: L 218 GLN cc_start: 0.8043 (mp10) cc_final: 0.7626 (mp10) REVERT: L 304 ARG cc_start: 0.8183 (mtt180) cc_final: 0.7095 (ttt180) REVERT: L 309 ARG cc_start: 0.6572 (mtm180) cc_final: 0.6306 (mtt90) outliers start: 88 outliers final: 66 residues processed: 499 average time/residue: 0.4237 time to fit residues: 329.0731 Evaluate side-chains 515 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 443 time to evaluate : 3.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 248 GLU Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 301 ASP Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 297 TYR Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain G residue 232 MET Chi-restraints excluded: chain G residue 306 LEU Chi-restraints excluded: chain G residue 313 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 123 ARG Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 153 ASP Chi-restraints excluded: chain H residue 232 MET Chi-restraints excluded: chain H residue 279 ILE Chi-restraints excluded: chain H residue 306 LEU Chi-restraints excluded: chain H residue 307 VAL Chi-restraints excluded: chain H residue 313 THR Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 267 LEU Chi-restraints excluded: chain J residue 79 GLU Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain J residue 153 ASP Chi-restraints excluded: chain J residue 168 ILE Chi-restraints excluded: chain J residue 190 SER Chi-restraints excluded: chain J residue 227 THR Chi-restraints excluded: chain J residue 267 LEU Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 190 SER Chi-restraints excluded: chain K residue 227 THR Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 272 GLU Chi-restraints excluded: chain L residue 313 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 347 optimal weight: 20.0000 chunk 40 optimal weight: 20.0000 chunk 205 optimal weight: 10.0000 chunk 262 optimal weight: 9.9990 chunk 203 optimal weight: 0.9990 chunk 302 optimal weight: 3.9990 chunk 200 optimal weight: 1.9990 chunk 358 optimal weight: 10.0000 chunk 224 optimal weight: 10.0000 chunk 218 optimal weight: 9.9990 chunk 165 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN B 76 ASN C 71 GLN F 73 ASN I 71 GLN I 73 ASN K 76 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 29544 Z= 0.256 Angle : 0.571 9.734 40236 Z= 0.295 Chirality : 0.043 0.166 4428 Planarity : 0.004 0.041 5268 Dihedral : 5.107 20.550 4128 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.29 % Allowed : 2.60 % Favored : 97.11 % Rotamer: Outliers : 2.84 % Allowed : 13.42 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.58 (0.14), residues: 3768 helix: -0.05 (0.15), residues: 1224 sheet: -1.24 (0.17), residues: 840 loop : 0.06 (0.16), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 50 HIS 0.004 0.001 HIS F 152 PHE 0.012 0.001 PHE A 69 TYR 0.013 0.001 TYR E 297 ARG 0.003 0.000 ARG E 128 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 471 time to evaluate : 3.099 Fit side-chains REVERT: A 113 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.7958 (tt) REVERT: A 148 ASP cc_start: 0.7397 (m-30) cc_final: 0.7000 (m-30) REVERT: A 169 GLN cc_start: 0.6710 (mp10) cc_final: 0.5838 (mp10) REVERT: A 185 ILE cc_start: 0.8135 (OUTLIER) cc_final: 0.7903 (mp) REVERT: B 134 THR cc_start: 0.8157 (OUTLIER) cc_final: 0.6985 (p) REVERT: B 137 GLU cc_start: 0.7389 (mt-10) cc_final: 0.6990 (mt-10) REVERT: C 96 LYS cc_start: 0.6694 (tppt) cc_final: 0.6279 (tptt) REVERT: C 123 ARG cc_start: 0.6500 (ptp-170) cc_final: 0.6232 (ptp90) REVERT: D 50 TRP cc_start: 0.8322 (t60) cc_final: 0.7994 (t60) REVERT: D 76 ASN cc_start: 0.8443 (m-40) cc_final: 0.7946 (m110) REVERT: D 79 GLU cc_start: 0.6994 (mt-10) cc_final: 0.6676 (mt-10) REVERT: D 90 ARG cc_start: 0.7047 (mmt90) cc_final: 0.6664 (mmp-170) REVERT: D 94 GLN cc_start: 0.7220 (tt0) cc_final: 0.7001 (mt0) REVERT: D 254 MET cc_start: 0.8378 (mmt) cc_final: 0.8169 (mmp) REVERT: D 310 GLU cc_start: 0.7581 (mm-30) cc_final: 0.7291 (mm-30) REVERT: E 123 ARG cc_start: 0.7119 (ptt-90) cc_final: 0.6768 (ptt-90) REVERT: E 227 THR cc_start: 0.8382 (OUTLIER) cc_final: 0.8106 (p) REVERT: F 6 LYS cc_start: 0.7694 (mttp) cc_final: 0.7339 (mtpt) REVERT: G 206 ASN cc_start: 0.8496 (m-40) cc_final: 0.8147 (m-40) REVERT: H 123 ARG cc_start: 0.7388 (OUTLIER) cc_final: 0.7033 (ptp90) REVERT: K 6 LYS cc_start: 0.8042 (mttp) cc_final: 0.7729 (mttm) REVERT: K 90 ARG cc_start: 0.7070 (mmt90) cc_final: 0.6697 (mmp-170) REVERT: K 123 ARG cc_start: 0.7079 (ptp-170) cc_final: 0.6795 (ptp90) REVERT: K 254 MET cc_start: 0.8312 (mmt) cc_final: 0.7857 (mmp) REVERT: K 310 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7274 (mm-30) REVERT: L 169 GLN cc_start: 0.8040 (mm-40) cc_final: 0.7662 (mm-40) REVERT: L 218 GLN cc_start: 0.8003 (mp10) cc_final: 0.7631 (mp10) REVERT: L 254 MET cc_start: 0.8365 (mmp) cc_final: 0.7970 (tpt) REVERT: L 304 ARG cc_start: 0.8168 (mtt180) cc_final: 0.7097 (ttt180) REVERT: L 309 ARG cc_start: 0.6554 (mtm180) cc_final: 0.6282 (mtt90) outliers start: 82 outliers final: 63 residues processed: 518 average time/residue: 0.4284 time to fit residues: 344.7771 Evaluate side-chains 521 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 453 time to evaluate : 2.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 248 GLU Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 301 ASP Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 297 TYR Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain G residue 238 ASP Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain G residue 306 LEU Chi-restraints excluded: chain G residue 313 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 123 ARG Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 153 ASP Chi-restraints excluded: chain H residue 232 MET Chi-restraints excluded: chain H residue 279 ILE Chi-restraints excluded: chain H residue 306 LEU Chi-restraints excluded: chain H residue 313 THR Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 267 LEU Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain J residue 153 ASP Chi-restraints excluded: chain J residue 190 SER Chi-restraints excluded: chain J residue 267 LEU Chi-restraints excluded: chain J residue 307 VAL Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 190 SER Chi-restraints excluded: chain K residue 227 THR Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain L residue 272 GLU Chi-restraints excluded: chain L residue 313 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 221 optimal weight: 0.1980 chunk 143 optimal weight: 9.9990 chunk 214 optimal weight: 2.9990 chunk 108 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 227 optimal weight: 10.0000 chunk 244 optimal weight: 7.9990 chunk 177 optimal weight: 8.9990 chunk 33 optimal weight: 40.0000 chunk 281 optimal weight: 9.9990 overall best weight: 3.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN B 200 GLN C 71 GLN F 73 ASN I 71 GLN I 73 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 29544 Z= 0.221 Angle : 0.552 10.043 40236 Z= 0.286 Chirality : 0.043 0.181 4428 Planarity : 0.004 0.041 5268 Dihedral : 4.931 20.083 4128 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.44 % Favored : 97.32 % Rotamer: Outliers : 2.87 % Allowed : 13.55 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.14), residues: 3768 helix: -0.01 (0.15), residues: 1224 sheet: -1.17 (0.18), residues: 816 loop : -0.07 (0.15), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 50 HIS 0.004 0.001 HIS F 152 PHE 0.010 0.001 PHE D 69 TYR 0.012 0.001 TYR B 141 ARG 0.003 0.000 ARG E 128 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 488 time to evaluate : 3.395 Fit side-chains REVERT: A 113 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8016 (tt) REVERT: A 148 ASP cc_start: 0.7375 (m-30) cc_final: 0.6986 (m-30) REVERT: A 169 GLN cc_start: 0.6705 (mp10) cc_final: 0.5869 (mp10) REVERT: B 106 ARG cc_start: 0.7088 (ptt-90) cc_final: 0.6862 (ptt-90) REVERT: B 134 THR cc_start: 0.8075 (OUTLIER) cc_final: 0.6952 (p) REVERT: B 137 GLU cc_start: 0.7348 (mt-10) cc_final: 0.6957 (mt-10) REVERT: C 5 LYS cc_start: 0.7149 (ttmt) cc_final: 0.6923 (mtpt) REVERT: C 123 ARG cc_start: 0.6474 (OUTLIER) cc_final: 0.6211 (ptp90) REVERT: D 50 TRP cc_start: 0.8286 (t60) cc_final: 0.7951 (t60) REVERT: D 76 ASN cc_start: 0.8406 (m-40) cc_final: 0.7852 (m110) REVERT: D 79 GLU cc_start: 0.6964 (mt-10) cc_final: 0.6625 (mt-10) REVERT: D 90 ARG cc_start: 0.7072 (mmt90) cc_final: 0.6649 (mmp-170) REVERT: D 94 GLN cc_start: 0.7160 (tt0) cc_final: 0.6921 (mt0) REVERT: D 254 MET cc_start: 0.8374 (mmt) cc_final: 0.8165 (mmp) REVERT: D 310 GLU cc_start: 0.7562 (mm-30) cc_final: 0.7272 (mm-30) REVERT: E 123 ARG cc_start: 0.7117 (ptt-90) cc_final: 0.6916 (ptt-90) REVERT: E 227 THR cc_start: 0.8347 (OUTLIER) cc_final: 0.8066 (p) REVERT: F 6 LYS cc_start: 0.7624 (mttp) cc_final: 0.7292 (mtpt) REVERT: G 206 ASN cc_start: 0.8435 (m-40) cc_final: 0.8074 (m-40) REVERT: G 310 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7074 (mm-30) REVERT: H 123 ARG cc_start: 0.7360 (ptt180) cc_final: 0.7019 (ptp90) REVERT: K 6 LYS cc_start: 0.8063 (mttp) cc_final: 0.7759 (mttm) REVERT: K 76 ASN cc_start: 0.8645 (m110) cc_final: 0.8195 (m110) REVERT: K 90 ARG cc_start: 0.7139 (mmt90) cc_final: 0.6631 (mmp-170) REVERT: K 94 GLN cc_start: 0.7221 (tt0) cc_final: 0.6725 (mt0) REVERT: K 310 GLU cc_start: 0.7591 (mm-30) cc_final: 0.7267 (mm-30) REVERT: L 169 GLN cc_start: 0.8022 (mm-40) cc_final: 0.7625 (mm-40) REVERT: L 218 GLN cc_start: 0.7961 (mp10) cc_final: 0.7598 (mp10) REVERT: L 304 ARG cc_start: 0.8152 (mtt180) cc_final: 0.7078 (ttt180) REVERT: L 309 ARG cc_start: 0.6589 (mtm180) cc_final: 0.5941 (mtm180) outliers start: 83 outliers final: 69 residues processed: 534 average time/residue: 0.4270 time to fit residues: 352.3729 Evaluate side-chains 538 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 465 time to evaluate : 3.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 132 LYS Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 248 GLU Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 301 ASP Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 123 ARG Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 297 TYR Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain G residue 238 ASP Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain G residue 306 LEU Chi-restraints excluded: chain G residue 313 THR Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 153 ASP Chi-restraints excluded: chain H residue 232 MET Chi-restraints excluded: chain H residue 279 ILE Chi-restraints excluded: chain H residue 297 TYR Chi-restraints excluded: chain H residue 306 LEU Chi-restraints excluded: chain H residue 313 THR Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 267 LEU Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain J residue 153 ASP Chi-restraints excluded: chain J residue 190 SER Chi-restraints excluded: chain J residue 307 VAL Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 190 SER Chi-restraints excluded: chain K residue 227 THR Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 134 THR Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain L residue 272 GLU Chi-restraints excluded: chain L residue 313 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 326 optimal weight: 9.9990 chunk 343 optimal weight: 2.9990 chunk 313 optimal weight: 20.0000 chunk 334 optimal weight: 9.9990 chunk 201 optimal weight: 7.9990 chunk 145 optimal weight: 9.9990 chunk 262 optimal weight: 9.9990 chunk 102 optimal weight: 9.9990 chunk 301 optimal weight: 0.9990 chunk 316 optimal weight: 6.9990 chunk 332 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN C 71 GLN D 200 GLN I 73 ASN K 200 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 29544 Z= 0.282 Angle : 0.590 9.926 40236 Z= 0.303 Chirality : 0.044 0.178 4428 Planarity : 0.004 0.043 5268 Dihedral : 5.061 20.754 4128 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.63 % Favored : 97.16 % Rotamer: Outliers : 2.66 % Allowed : 14.25 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.14), residues: 3768 helix: 0.28 (0.15), residues: 1152 sheet: -1.17 (0.17), residues: 876 loop : -0.04 (0.16), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 56 HIS 0.004 0.001 HIS G 167 PHE 0.010 0.001 PHE F 69 TYR 0.013 0.001 TYR K 297 ARG 0.004 0.000 ARG E 128 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 468 time to evaluate : 3.346 Fit side-chains REVERT: A 21 ASP cc_start: 0.6486 (t0) cc_final: 0.6152 (m-30) REVERT: A 113 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7974 (tt) REVERT: A 148 ASP cc_start: 0.7395 (m-30) cc_final: 0.6991 (m-30) REVERT: A 169 GLN cc_start: 0.6711 (mp10) cc_final: 0.5841 (mp10) REVERT: B 106 ARG cc_start: 0.7124 (ptt-90) cc_final: 0.6876 (ptt-90) REVERT: B 134 THR cc_start: 0.8122 (OUTLIER) cc_final: 0.6981 (p) REVERT: B 137 GLU cc_start: 0.7389 (mt-10) cc_final: 0.6980 (mt-10) REVERT: C 123 ARG cc_start: 0.6479 (OUTLIER) cc_final: 0.6218 (ptp90) REVERT: D 50 TRP cc_start: 0.8294 (t60) cc_final: 0.7973 (t60) REVERT: D 76 ASN cc_start: 0.8452 (m-40) cc_final: 0.7939 (m110) REVERT: D 79 GLU cc_start: 0.6948 (mt-10) cc_final: 0.6592 (mt-10) REVERT: D 90 ARG cc_start: 0.7036 (mmt90) cc_final: 0.6655 (mmp-170) REVERT: D 94 GLN cc_start: 0.7164 (tt0) cc_final: 0.6924 (mt0) REVERT: D 310 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7291 (mm-30) REVERT: E 123 ARG cc_start: 0.7137 (ptt-90) cc_final: 0.6907 (ptt-90) REVERT: E 227 THR cc_start: 0.8393 (OUTLIER) cc_final: 0.8105 (p) REVERT: F 6 LYS cc_start: 0.7655 (mttp) cc_final: 0.7307 (mtpt) REVERT: G 206 ASN cc_start: 0.8511 (m-40) cc_final: 0.8150 (m-40) REVERT: H 123 ARG cc_start: 0.7403 (ptt180) cc_final: 0.7065 (ptp90) REVERT: K 6 LYS cc_start: 0.8059 (mttp) cc_final: 0.7740 (mttm) REVERT: K 90 ARG cc_start: 0.7231 (mmt90) cc_final: 0.6676 (mmp-170) REVERT: K 94 GLN cc_start: 0.7201 (tt0) cc_final: 0.6761 (mt0) REVERT: K 254 MET cc_start: 0.8357 (mmt) cc_final: 0.8077 (mmp) REVERT: K 310 GLU cc_start: 0.7594 (mm-30) cc_final: 0.7267 (mm-30) REVERT: L 169 GLN cc_start: 0.8036 (mm-40) cc_final: 0.7639 (mm-40) REVERT: L 218 GLN cc_start: 0.7981 (mp10) cc_final: 0.7632 (mp10) REVERT: L 304 ARG cc_start: 0.8179 (mtt180) cc_final: 0.7092 (ttt180) REVERT: L 309 ARG cc_start: 0.6544 (mtm180) cc_final: 0.5875 (mtm180) outliers start: 77 outliers final: 72 residues processed: 509 average time/residue: 0.4422 time to fit residues: 350.0229 Evaluate side-chains 531 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 455 time to evaluate : 3.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 248 GLU Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 123 ARG Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 297 TYR Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain G residue 238 ASP Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain G residue 306 LEU Chi-restraints excluded: chain G residue 313 THR Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 153 ASP Chi-restraints excluded: chain H residue 232 MET Chi-restraints excluded: chain H residue 254 MET Chi-restraints excluded: chain H residue 279 ILE Chi-restraints excluded: chain H residue 297 TYR Chi-restraints excluded: chain H residue 306 LEU Chi-restraints excluded: chain H residue 312 MET Chi-restraints excluded: chain H residue 313 THR Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 267 LEU Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain J residue 153 ASP Chi-restraints excluded: chain J residue 190 SER Chi-restraints excluded: chain J residue 267 LEU Chi-restraints excluded: chain J residue 307 VAL Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 190 SER Chi-restraints excluded: chain K residue 227 THR Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 134 THR Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain L residue 263 LEU Chi-restraints excluded: chain L residue 272 GLU Chi-restraints excluded: chain L residue 313 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 219 optimal weight: 9.9990 chunk 353 optimal weight: 7.9990 chunk 215 optimal weight: 1.9990 chunk 167 optimal weight: 0.9990 chunk 245 optimal weight: 5.9990 chunk 370 optimal weight: 20.0000 chunk 341 optimal weight: 30.0000 chunk 295 optimal weight: 0.6980 chunk 30 optimal weight: 20.0000 chunk 227 optimal weight: 10.0000 chunk 180 optimal weight: 10.0000 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN C 71 GLN F 73 ASN I 73 ASN K 76 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 29544 Z= 0.218 Angle : 0.555 10.007 40236 Z= 0.285 Chirality : 0.043 0.155 4428 Planarity : 0.004 0.041 5268 Dihedral : 4.873 20.032 4128 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.55 % Favored : 97.24 % Rotamer: Outliers : 2.66 % Allowed : 14.52 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.54 (0.14), residues: 3768 helix: 0.07 (0.15), residues: 1224 sheet: -1.15 (0.18), residues: 816 loop : -0.04 (0.15), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 56 HIS 0.004 0.001 HIS F 152 PHE 0.016 0.001 PHE A 69 TYR 0.015 0.001 TYR A 256 ARG 0.003 0.000 ARG G 314 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 463 time to evaluate : 3.141 Fit side-chains REVERT: A 113 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7996 (tt) REVERT: A 148 ASP cc_start: 0.7401 (m-30) cc_final: 0.7186 (m-30) REVERT: A 169 GLN cc_start: 0.6714 (mp10) cc_final: 0.5885 (mp10) REVERT: B 50 TRP cc_start: 0.7924 (t60) cc_final: 0.7678 (t60) REVERT: B 134 THR cc_start: 0.7872 (OUTLIER) cc_final: 0.7513 (m) REVERT: C 123 ARG cc_start: 0.6401 (ptp-170) cc_final: 0.6177 (ptp90) REVERT: D 50 TRP cc_start: 0.8268 (t60) cc_final: 0.7925 (t60) REVERT: D 76 ASN cc_start: 0.8387 (m-40) cc_final: 0.7838 (m110) REVERT: D 79 GLU cc_start: 0.6922 (mt-10) cc_final: 0.6516 (mt-10) REVERT: D 90 ARG cc_start: 0.7067 (mmt90) cc_final: 0.6569 (mmp-170) REVERT: D 94 GLN cc_start: 0.7140 (tt0) cc_final: 0.6884 (mt0) REVERT: D 254 MET cc_start: 0.8404 (mmt) cc_final: 0.8147 (mmp) REVERT: D 310 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7277 (mm-30) REVERT: E 123 ARG cc_start: 0.7136 (ptt-90) cc_final: 0.6933 (ptt-90) REVERT: E 227 THR cc_start: 0.8333 (OUTLIER) cc_final: 0.8063 (p) REVERT: F 6 LYS cc_start: 0.7619 (mttp) cc_final: 0.7288 (mtpt) REVERT: F 265 THR cc_start: 0.8055 (OUTLIER) cc_final: 0.7820 (t) REVERT: G 206 ASN cc_start: 0.8396 (m-40) cc_final: 0.8026 (m-40) REVERT: H 123 ARG cc_start: 0.7358 (ptt180) cc_final: 0.7034 (ptp90) REVERT: K 6 LYS cc_start: 0.8072 (mttp) cc_final: 0.7754 (mttm) REVERT: K 90 ARG cc_start: 0.7241 (mmt90) cc_final: 0.6676 (mmp-170) REVERT: K 94 GLN cc_start: 0.7203 (tt0) cc_final: 0.6703 (mt0) REVERT: K 123 ARG cc_start: 0.6950 (ptp90) cc_final: 0.6705 (mtm-85) REVERT: K 141 TYR cc_start: 0.8867 (m-80) cc_final: 0.8335 (m-80) REVERT: K 254 MET cc_start: 0.8324 (mmt) cc_final: 0.8039 (mmp) REVERT: K 310 GLU cc_start: 0.7587 (mm-30) cc_final: 0.7265 (mm-30) REVERT: L 169 GLN cc_start: 0.8043 (mm-40) cc_final: 0.7642 (mm-40) REVERT: L 218 GLN cc_start: 0.7950 (mp10) cc_final: 0.7597 (mp10) REVERT: L 304 ARG cc_start: 0.8147 (mtt180) cc_final: 0.7078 (ttt180) outliers start: 77 outliers final: 62 residues processed: 506 average time/residue: 0.4723 time to fit residues: 375.3347 Evaluate side-chains 516 residues out of total 2892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 450 time to evaluate : 3.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 297 TYR Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain G residue 238 ASP Chi-restraints excluded: chain G residue 306 LEU Chi-restraints excluded: chain G residue 313 THR Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 153 ASP Chi-restraints excluded: chain H residue 297 TYR Chi-restraints excluded: chain H residue 306 LEU Chi-restraints excluded: chain H residue 313 THR Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain J residue 153 ASP Chi-restraints excluded: chain J residue 190 SER Chi-restraints excluded: chain J residue 307 VAL Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 190 SER Chi-restraints excluded: chain K residue 227 THR Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 134 THR Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain L residue 272 GLU Chi-restraints excluded: chain L residue 313 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 234 optimal weight: 4.9990 chunk 314 optimal weight: 5.9990 chunk 90 optimal weight: 30.0000 chunk 272 optimal weight: 6.9990 chunk 43 optimal weight: 7.9990 chunk 82 optimal weight: 20.0000 chunk 295 optimal weight: 10.0000 chunk 123 optimal weight: 20.0000 chunk 303 optimal weight: 5.9990 chunk 37 optimal weight: 50.0000 chunk 54 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN I 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.121064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.092205 restraints weight = 36774.051| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 1.51 r_work: 0.2787 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 29544 Z= 0.332 Angle : 0.613 9.742 40236 Z= 0.314 Chirality : 0.045 0.154 4428 Planarity : 0.004 0.046 5268 Dihedral : 5.164 21.443 4128 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.81 % Favored : 96.97 % Rotamer: Outliers : 2.70 % Allowed : 14.70 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.43 (0.14), residues: 3768 helix: 0.24 (0.15), residues: 1152 sheet: -1.12 (0.17), residues: 852 loop : -0.00 (0.15), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 56 HIS 0.005 0.001 HIS H 167 PHE 0.019 0.002 PHE A 69 TYR 0.016 0.002 TYR A 256 ARG 0.006 0.000 ARG G 314 =============================================================================== Job complete usr+sys time: 7019.82 seconds wall clock time: 127 minutes 0.17 seconds (7620.17 seconds total)