Starting phenix.real_space_refine on Sun Apr 14 01:37:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbf_27282/04_2024/8dbf_27282_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbf_27282/04_2024/8dbf_27282.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbf_27282/04_2024/8dbf_27282_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbf_27282/04_2024/8dbf_27282_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbf_27282/04_2024/8dbf_27282_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbf_27282/04_2024/8dbf_27282.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbf_27282/04_2024/8dbf_27282.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbf_27282/04_2024/8dbf_27282_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbf_27282/04_2024/8dbf_27282_updated.pdb" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.390 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 60 5.49 5 Mg 24 5.21 5 S 204 5.16 5 C 18504 2.51 5 N 5256 2.21 5 O 5916 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 26": "OE1" <-> "OE2" Residue "A ARG 49": "NH1" <-> "NH2" Residue "A GLU 51": "OE1" <-> "OE2" Residue "A GLU 62": "OE1" <-> "OE2" Residue "A GLU 148": "OE1" <-> "OE2" Residue "A ARG 196": "NH1" <-> "NH2" Residue "A GLU 201": "OE1" <-> "OE2" Residue "A TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 26": "OE1" <-> "OE2" Residue "B ARG 49": "NH1" <-> "NH2" Residue "B GLU 51": "OE1" <-> "OE2" Residue "B GLU 62": "OE1" <-> "OE2" Residue "B GLU 148": "OE1" <-> "OE2" Residue "B ARG 196": "NH1" <-> "NH2" Residue "B GLU 201": "OE1" <-> "OE2" Residue "B TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 26": "OE1" <-> "OE2" Residue "C ARG 49": "NH1" <-> "NH2" Residue "C GLU 51": "OE1" <-> "OE2" Residue "C GLU 62": "OE1" <-> "OE2" Residue "C GLU 148": "OE1" <-> "OE2" Residue "C ARG 196": "NH1" <-> "NH2" Residue "C GLU 201": "OE1" <-> "OE2" Residue "C TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 26": "OE1" <-> "OE2" Residue "D ARG 49": "NH1" <-> "NH2" Residue "D GLU 51": "OE1" <-> "OE2" Residue "D GLU 62": "OE1" <-> "OE2" Residue "D GLU 148": "OE1" <-> "OE2" Residue "D ARG 196": "NH1" <-> "NH2" Residue "D GLU 201": "OE1" <-> "OE2" Residue "D TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 26": "OE1" <-> "OE2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E GLU 51": "OE1" <-> "OE2" Residue "E GLU 62": "OE1" <-> "OE2" Residue "E GLU 148": "OE1" <-> "OE2" Residue "E ARG 196": "NH1" <-> "NH2" Residue "E GLU 201": "OE1" <-> "OE2" Residue "F GLU 26": "OE1" <-> "OE2" Residue "F ARG 49": "NH1" <-> "NH2" Residue "F GLU 51": "OE1" <-> "OE2" Residue "F GLU 62": "OE1" <-> "OE2" Residue "F GLU 148": "OE1" <-> "OE2" Residue "F ARG 196": "NH1" <-> "NH2" Residue "F GLU 201": "OE1" <-> "OE2" Residue "F TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 26": "OE1" <-> "OE2" Residue "G ARG 49": "NH1" <-> "NH2" Residue "G GLU 51": "OE1" <-> "OE2" Residue "G GLU 62": "OE1" <-> "OE2" Residue "G GLU 148": "OE1" <-> "OE2" Residue "G ARG 196": "NH1" <-> "NH2" Residue "G GLU 201": "OE1" <-> "OE2" Residue "G TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 26": "OE1" <-> "OE2" Residue "H ARG 49": "NH1" <-> "NH2" Residue "H GLU 51": "OE1" <-> "OE2" Residue "H GLU 62": "OE1" <-> "OE2" Residue "H GLU 148": "OE1" <-> "OE2" Residue "H ARG 196": "NH1" <-> "NH2" Residue "H GLU 201": "OE1" <-> "OE2" Residue "H TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 26": "OE1" <-> "OE2" Residue "I ARG 49": "NH1" <-> "NH2" Residue "I GLU 51": "OE1" <-> "OE2" Residue "I GLU 62": "OE1" <-> "OE2" Residue "I GLU 148": "OE1" <-> "OE2" Residue "I ARG 196": "NH1" <-> "NH2" Residue "I GLU 201": "OE1" <-> "OE2" Residue "I TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 26": "OE1" <-> "OE2" Residue "J ARG 49": "NH1" <-> "NH2" Residue "J GLU 51": "OE1" <-> "OE2" Residue "J GLU 62": "OE1" <-> "OE2" Residue "J GLU 148": "OE1" <-> "OE2" Residue "J ARG 196": "NH1" <-> "NH2" Residue "J GLU 201": "OE1" <-> "OE2" Residue "K GLU 26": "OE1" <-> "OE2" Residue "K ARG 49": "NH1" <-> "NH2" Residue "K GLU 51": "OE1" <-> "OE2" Residue "K GLU 62": "OE1" <-> "OE2" Residue "K GLU 148": "OE1" <-> "OE2" Residue "K ARG 196": "NH1" <-> "NH2" Residue "K GLU 201": "OE1" <-> "OE2" Residue "K TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 26": "OE1" <-> "OE2" Residue "L ARG 49": "NH1" <-> "NH2" Residue "L GLU 51": "OE1" <-> "OE2" Residue "L GLU 62": "OE1" <-> "OE2" Residue "L GLU 148": "OE1" <-> "OE2" Residue "L ARG 196": "NH1" <-> "NH2" Residue "L GLU 201": "OE1" <-> "OE2" Residue "L TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 29964 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2420 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain: "B" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2420 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain: "C" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2420 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain: "D" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2420 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain: "E" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2420 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain: "F" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2420 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain: "G" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2420 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain: "H" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2420 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain: "I" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2420 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain: "J" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2420 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain: "K" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2420 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain: "L" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2420 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain: "A" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 97 Unusual residues: {' MG': 2, 'ADP': 3, 'HSX': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' MG': 2, 'ADP': 1, 'HSX': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {' MG': 2, 'ADP': 2, 'HSX': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {' MG': 2, 'ADP': 2, 'HSX': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "E" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 97 Unusual residues: {' MG': 2, 'ADP': 3, 'HSX': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "F" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' MG': 2, 'ADP': 1, 'HSX': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 97 Unusual residues: {' MG': 2, 'ADP': 3, 'HSX': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "H" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' MG': 2, 'ADP': 1, 'HSX': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "I" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {' MG': 2, 'ADP': 2, 'HSX': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "J" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {' MG': 2, 'ADP': 2, 'HSX': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "K" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 97 Unusual residues: {' MG': 2, 'ADP': 3, 'HSX': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "L" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' MG': 2, 'ADP': 1, 'HSX': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "D" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "E" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "F" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "G" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "H" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "I" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "J" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "K" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "L" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Time building chain proxies: 15.24, per 1000 atoms: 0.51 Number of scatterers: 29964 At special positions: 0 Unit cell: (124.844, 134.366, 138.598, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 204 16.00 P 60 15.00 Mg 24 11.99 O 5916 8.00 N 5256 7.00 C 18504 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: 12.75 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: 7176 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 144 helices and 36 sheets defined 36.7% alpha, 18.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.09 Creating SS restraints... Processing helix chain 'A' and resid 13 through 22 Processing helix chain 'A' and resid 63 through 79 Processing helix chain 'A' and resid 108 through 119 Processing helix chain 'A' and resid 132 through 137 Processing helix chain 'A' and resid 148 through 158 Processing helix chain 'A' and resid 162 through 164 No H-bonds generated for 'chain 'A' and resid 162 through 164' Processing helix chain 'A' and resid 172 through 185 removed outlier: 4.562A pdb=" N LYS A 176 " --> pdb=" O GLY A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 238 Processing helix chain 'A' and resid 255 through 262 removed outlier: 4.553A pdb=" N ILE A 258 " --> pdb=" O GLY A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 283 removed outlier: 3.707A pdb=" N HIS A 283 " --> pdb=" O ASP A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 305 Processing helix chain 'A' and resid 310 through 313 Processing helix chain 'B' and resid 13 through 22 Processing helix chain 'B' and resid 63 through 79 Processing helix chain 'B' and resid 108 through 119 Processing helix chain 'B' and resid 132 through 137 Processing helix chain 'B' and resid 148 through 158 Processing helix chain 'B' and resid 162 through 164 No H-bonds generated for 'chain 'B' and resid 162 through 164' Processing helix chain 'B' and resid 172 through 185 removed outlier: 4.562A pdb=" N LYS B 176 " --> pdb=" O GLY B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 238 Processing helix chain 'B' and resid 255 through 262 removed outlier: 4.553A pdb=" N ILE B 258 " --> pdb=" O GLY B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 283 removed outlier: 3.708A pdb=" N HIS B 283 " --> pdb=" O ASP B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 305 Processing helix chain 'B' and resid 310 through 313 Processing helix chain 'C' and resid 13 through 22 Processing helix chain 'C' and resid 63 through 79 Processing helix chain 'C' and resid 108 through 119 Processing helix chain 'C' and resid 132 through 137 Processing helix chain 'C' and resid 148 through 158 Processing helix chain 'C' and resid 162 through 164 No H-bonds generated for 'chain 'C' and resid 162 through 164' Processing helix chain 'C' and resid 172 through 185 removed outlier: 4.563A pdb=" N LYS C 176 " --> pdb=" O GLY C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 238 Processing helix chain 'C' and resid 255 through 262 removed outlier: 4.554A pdb=" N ILE C 258 " --> pdb=" O GLY C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 283 removed outlier: 3.707A pdb=" N HIS C 283 " --> pdb=" O ASP C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 305 Processing helix chain 'C' and resid 310 through 313 Processing helix chain 'D' and resid 13 through 22 Processing helix chain 'D' and resid 63 through 79 Processing helix chain 'D' and resid 108 through 119 Processing helix chain 'D' and resid 132 through 137 Processing helix chain 'D' and resid 148 through 158 Processing helix chain 'D' and resid 162 through 164 No H-bonds generated for 'chain 'D' and resid 162 through 164' Processing helix chain 'D' and resid 172 through 185 removed outlier: 4.563A pdb=" N LYS D 176 " --> pdb=" O GLY D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 238 Processing helix chain 'D' and resid 255 through 262 removed outlier: 4.554A pdb=" N ILE D 258 " --> pdb=" O GLY D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 283 removed outlier: 3.707A pdb=" N HIS D 283 " --> pdb=" O ASP D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 305 Processing helix chain 'D' and resid 310 through 313 Processing helix chain 'E' and resid 13 through 22 Processing helix chain 'E' and resid 63 through 79 Processing helix chain 'E' and resid 108 through 119 Processing helix chain 'E' and resid 132 through 137 Processing helix chain 'E' and resid 148 through 158 Processing helix chain 'E' and resid 162 through 164 No H-bonds generated for 'chain 'E' and resid 162 through 164' Processing helix chain 'E' and resid 172 through 185 removed outlier: 4.563A pdb=" N LYS E 176 " --> pdb=" O GLY E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 238 Processing helix chain 'E' and resid 255 through 262 removed outlier: 4.554A pdb=" N ILE E 258 " --> pdb=" O GLY E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 283 removed outlier: 3.707A pdb=" N HIS E 283 " --> pdb=" O ASP E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 305 Processing helix chain 'E' and resid 310 through 313 Processing helix chain 'F' and resid 13 through 22 Processing helix chain 'F' and resid 63 through 79 Processing helix chain 'F' and resid 108 through 119 Processing helix chain 'F' and resid 132 through 137 Processing helix chain 'F' and resid 148 through 158 Processing helix chain 'F' and resid 162 through 164 No H-bonds generated for 'chain 'F' and resid 162 through 164' Processing helix chain 'F' and resid 172 through 185 removed outlier: 4.562A pdb=" N LYS F 176 " --> pdb=" O GLY F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 238 Processing helix chain 'F' and resid 255 through 262 removed outlier: 4.553A pdb=" N ILE F 258 " --> pdb=" O GLY F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 283 removed outlier: 3.708A pdb=" N HIS F 283 " --> pdb=" O ASP F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 305 Processing helix chain 'F' and resid 310 through 313 Processing helix chain 'G' and resid 13 through 22 Processing helix chain 'G' and resid 63 through 79 Processing helix chain 'G' and resid 108 through 119 Processing helix chain 'G' and resid 132 through 137 Processing helix chain 'G' and resid 148 through 158 Processing helix chain 'G' and resid 162 through 164 No H-bonds generated for 'chain 'G' and resid 162 through 164' Processing helix chain 'G' and resid 172 through 185 removed outlier: 4.562A pdb=" N LYS G 176 " --> pdb=" O GLY G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 238 Processing helix chain 'G' and resid 255 through 262 removed outlier: 4.553A pdb=" N ILE G 258 " --> pdb=" O GLY G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 278 through 283 removed outlier: 3.707A pdb=" N HIS G 283 " --> pdb=" O ASP G 279 " (cutoff:3.500A) Processing helix chain 'G' and resid 293 through 305 Processing helix chain 'G' and resid 310 through 313 Processing helix chain 'H' and resid 13 through 22 Processing helix chain 'H' and resid 63 through 79 Processing helix chain 'H' and resid 108 through 119 Processing helix chain 'H' and resid 132 through 137 Processing helix chain 'H' and resid 148 through 158 Processing helix chain 'H' and resid 162 through 164 No H-bonds generated for 'chain 'H' and resid 162 through 164' Processing helix chain 'H' and resid 172 through 185 removed outlier: 4.562A pdb=" N LYS H 176 " --> pdb=" O GLY H 173 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 238 Processing helix chain 'H' and resid 255 through 262 removed outlier: 4.553A pdb=" N ILE H 258 " --> pdb=" O GLY H 255 " (cutoff:3.500A) Processing helix chain 'H' and resid 278 through 283 removed outlier: 3.707A pdb=" N HIS H 283 " --> pdb=" O ASP H 279 " (cutoff:3.500A) Processing helix chain 'H' and resid 293 through 305 Processing helix chain 'H' and resid 310 through 313 Processing helix chain 'I' and resid 13 through 22 Processing helix chain 'I' and resid 63 through 79 Processing helix chain 'I' and resid 108 through 119 Processing helix chain 'I' and resid 132 through 137 Processing helix chain 'I' and resid 148 through 158 Processing helix chain 'I' and resid 162 through 164 No H-bonds generated for 'chain 'I' and resid 162 through 164' Processing helix chain 'I' and resid 172 through 185 removed outlier: 4.563A pdb=" N LYS I 176 " --> pdb=" O GLY I 173 " (cutoff:3.500A) Processing helix chain 'I' and resid 227 through 238 Processing helix chain 'I' and resid 255 through 262 removed outlier: 4.553A pdb=" N ILE I 258 " --> pdb=" O GLY I 255 " (cutoff:3.500A) Processing helix chain 'I' and resid 278 through 283 removed outlier: 3.707A pdb=" N HIS I 283 " --> pdb=" O ASP I 279 " (cutoff:3.500A) Processing helix chain 'I' and resid 293 through 305 Processing helix chain 'I' and resid 310 through 313 Processing helix chain 'J' and resid 13 through 22 Processing helix chain 'J' and resid 63 through 79 Processing helix chain 'J' and resid 108 through 119 Processing helix chain 'J' and resid 132 through 137 Processing helix chain 'J' and resid 148 through 158 Processing helix chain 'J' and resid 162 through 164 No H-bonds generated for 'chain 'J' and resid 162 through 164' Processing helix chain 'J' and resid 172 through 185 removed outlier: 4.563A pdb=" N LYS J 176 " --> pdb=" O GLY J 173 " (cutoff:3.500A) Processing helix chain 'J' and resid 227 through 238 Processing helix chain 'J' and resid 255 through 262 removed outlier: 4.554A pdb=" N ILE J 258 " --> pdb=" O GLY J 255 " (cutoff:3.500A) Processing helix chain 'J' and resid 278 through 283 removed outlier: 3.708A pdb=" N HIS J 283 " --> pdb=" O ASP J 279 " (cutoff:3.500A) Processing helix chain 'J' and resid 293 through 305 Processing helix chain 'J' and resid 310 through 313 Processing helix chain 'K' and resid 13 through 22 Processing helix chain 'K' and resid 63 through 79 Processing helix chain 'K' and resid 108 through 119 Processing helix chain 'K' and resid 132 through 137 Processing helix chain 'K' and resid 148 through 158 Processing helix chain 'K' and resid 162 through 164 No H-bonds generated for 'chain 'K' and resid 162 through 164' Processing helix chain 'K' and resid 172 through 185 removed outlier: 4.562A pdb=" N LYS K 176 " --> pdb=" O GLY K 173 " (cutoff:3.500A) Processing helix chain 'K' and resid 227 through 238 Processing helix chain 'K' and resid 255 through 262 removed outlier: 4.553A pdb=" N ILE K 258 " --> pdb=" O GLY K 255 " (cutoff:3.500A) Processing helix chain 'K' and resid 278 through 283 removed outlier: 3.707A pdb=" N HIS K 283 " --> pdb=" O ASP K 279 " (cutoff:3.500A) Processing helix chain 'K' and resid 293 through 305 Processing helix chain 'K' and resid 310 through 313 Processing helix chain 'L' and resid 13 through 22 Processing helix chain 'L' and resid 63 through 79 Processing helix chain 'L' and resid 108 through 119 Processing helix chain 'L' and resid 132 through 137 Processing helix chain 'L' and resid 148 through 158 Processing helix chain 'L' and resid 162 through 164 No H-bonds generated for 'chain 'L' and resid 162 through 164' Processing helix chain 'L' and resid 172 through 185 removed outlier: 4.563A pdb=" N LYS L 176 " --> pdb=" O GLY L 173 " (cutoff:3.500A) Processing helix chain 'L' and resid 227 through 238 Processing helix chain 'L' and resid 255 through 262 removed outlier: 4.553A pdb=" N ILE L 258 " --> pdb=" O GLY L 255 " (cutoff:3.500A) Processing helix chain 'L' and resid 278 through 283 removed outlier: 3.707A pdb=" N HIS L 283 " --> pdb=" O ASP L 279 " (cutoff:3.500A) Processing helix chain 'L' and resid 293 through 305 Processing helix chain 'L' and resid 310 through 313 Processing sheet with id= A, first strand: chain 'A' and resid 4 through 8 removed outlier: 6.277A pdb=" N ASP A 52 " --> pdb=" O LYS A 5 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N PHE A 7 " --> pdb=" O ASP A 52 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N TYR A 54 " --> pdb=" O PHE A 7 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ARG A 84 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ILE A 55 " --> pdb=" O ARG A 84 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N THR A 86 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N HIS A 123 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ILE A 89 " --> pdb=" O HIS A 123 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ILE A 125 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N THR A 126 " --> pdb=" O PRO A 141 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ASP A 143 " --> pdb=" O THR A 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 30 through 34 Processing sheet with id= C, first strand: chain 'A' and resid 287 through 290 removed outlier: 7.884A pdb=" N GLN A 288 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL A 269 " --> pdb=" O GLN A 288 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ILE A 290 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL A 271 " --> pdb=" O ILE A 290 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N VAL A 244 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL A 269 " --> pdb=" O VAL A 244 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA A 246 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N VAL A 271 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU A 248 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA A 216 " --> pdb=" O TYR A 245 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ILE A 247 " --> pdb=" O ALA A 216 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU A 218 " --> pdb=" O ILE A 247 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N THR A 166 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N VAL A 219 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N VAL A 168 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ASP A 188 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N SER A 169 " --> pdb=" O ASP A 188 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ALA A 190 " --> pdb=" O SER A 169 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 4 through 8 removed outlier: 6.278A pdb=" N ASP B 52 " --> pdb=" O LYS B 5 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N PHE B 7 " --> pdb=" O ASP B 52 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N TYR B 54 " --> pdb=" O PHE B 7 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ARG B 84 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ILE B 55 " --> pdb=" O ARG B 84 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR B 86 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N HIS B 123 " --> pdb=" O ALA B 87 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ILE B 89 " --> pdb=" O HIS B 123 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ILE B 125 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N THR B 126 " --> pdb=" O PRO B 141 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ASP B 143 " --> pdb=" O THR B 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 30 through 34 Processing sheet with id= F, first strand: chain 'B' and resid 287 through 290 removed outlier: 7.884A pdb=" N GLN B 288 " --> pdb=" O GLU B 267 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL B 269 " --> pdb=" O GLN B 288 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ILE B 290 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL B 271 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N VAL B 244 " --> pdb=" O GLU B 267 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL B 269 " --> pdb=" O VAL B 244 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA B 246 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N VAL B 271 " --> pdb=" O ALA B 246 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU B 248 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ALA B 216 " --> pdb=" O TYR B 245 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ILE B 247 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU B 218 " --> pdb=" O ILE B 247 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N THR B 166 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL B 219 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N VAL B 168 " --> pdb=" O VAL B 219 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASP B 188 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N SER B 169 " --> pdb=" O ASP B 188 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ALA B 190 " --> pdb=" O SER B 169 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 4 through 8 removed outlier: 6.278A pdb=" N ASP C 52 " --> pdb=" O LYS C 5 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N PHE C 7 " --> pdb=" O ASP C 52 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N TYR C 54 " --> pdb=" O PHE C 7 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ARG C 84 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ILE C 55 " --> pdb=" O ARG C 84 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N THR C 86 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N HIS C 123 " --> pdb=" O ALA C 87 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ILE C 89 " --> pdb=" O HIS C 123 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ILE C 125 " --> pdb=" O ILE C 89 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N THR C 126 " --> pdb=" O PRO C 141 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ASP C 143 " --> pdb=" O THR C 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'C' and resid 30 through 34 Processing sheet with id= I, first strand: chain 'C' and resid 287 through 290 removed outlier: 7.885A pdb=" N GLN C 288 " --> pdb=" O GLU C 267 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N VAL C 269 " --> pdb=" O GLN C 288 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ILE C 290 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL C 271 " --> pdb=" O ILE C 290 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N VAL C 244 " --> pdb=" O GLU C 267 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL C 269 " --> pdb=" O VAL C 244 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ALA C 246 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N VAL C 271 " --> pdb=" O ALA C 246 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU C 248 " --> pdb=" O VAL C 271 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ALA C 216 " --> pdb=" O TYR C 245 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ILE C 247 " --> pdb=" O ALA C 216 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU C 218 " --> pdb=" O ILE C 247 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N THR C 166 " --> pdb=" O ILE C 217 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N VAL C 219 " --> pdb=" O THR C 166 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N VAL C 168 " --> pdb=" O VAL C 219 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASP C 188 " --> pdb=" O ILE C 167 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N SER C 169 " --> pdb=" O ASP C 188 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ALA C 190 " --> pdb=" O SER C 169 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 4 through 8 removed outlier: 6.278A pdb=" N ASP D 52 " --> pdb=" O LYS D 5 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N PHE D 7 " --> pdb=" O ASP D 52 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N TYR D 54 " --> pdb=" O PHE D 7 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ARG D 84 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ILE D 55 " --> pdb=" O ARG D 84 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N THR D 86 " --> pdb=" O ILE D 55 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N HIS D 123 " --> pdb=" O ALA D 87 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ILE D 89 " --> pdb=" O HIS D 123 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ILE D 125 " --> pdb=" O ILE D 89 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N THR D 126 " --> pdb=" O PRO D 141 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ASP D 143 " --> pdb=" O THR D 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'D' and resid 30 through 34 Processing sheet with id= L, first strand: chain 'D' and resid 287 through 290 removed outlier: 7.885A pdb=" N GLN D 288 " --> pdb=" O GLU D 267 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N VAL D 269 " --> pdb=" O GLN D 288 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ILE D 290 " --> pdb=" O VAL D 269 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL D 271 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N VAL D 244 " --> pdb=" O GLU D 267 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL D 269 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ALA D 246 " --> pdb=" O VAL D 269 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N VAL D 271 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU D 248 " --> pdb=" O VAL D 271 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA D 216 " --> pdb=" O TYR D 245 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ILE D 247 " --> pdb=" O ALA D 216 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU D 218 " --> pdb=" O ILE D 247 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N THR D 166 " --> pdb=" O ILE D 217 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N VAL D 219 " --> pdb=" O THR D 166 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N VAL D 168 " --> pdb=" O VAL D 219 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASP D 188 " --> pdb=" O ILE D 167 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N SER D 169 " --> pdb=" O ASP D 188 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ALA D 190 " --> pdb=" O SER D 169 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 4 through 8 removed outlier: 6.278A pdb=" N ASP E 52 " --> pdb=" O LYS E 5 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N PHE E 7 " --> pdb=" O ASP E 52 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N TYR E 54 " --> pdb=" O PHE E 7 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ARG E 84 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ILE E 55 " --> pdb=" O ARG E 84 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N THR E 86 " --> pdb=" O ILE E 55 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N HIS E 123 " --> pdb=" O ALA E 87 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ILE E 89 " --> pdb=" O HIS E 123 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ILE E 125 " --> pdb=" O ILE E 89 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N THR E 126 " --> pdb=" O PRO E 141 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ASP E 143 " --> pdb=" O THR E 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'E' and resid 30 through 34 Processing sheet with id= O, first strand: chain 'E' and resid 287 through 290 removed outlier: 7.885A pdb=" N GLN E 288 " --> pdb=" O GLU E 267 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N VAL E 269 " --> pdb=" O GLN E 288 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ILE E 290 " --> pdb=" O VAL E 269 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL E 271 " --> pdb=" O ILE E 290 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N VAL E 244 " --> pdb=" O GLU E 267 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL E 269 " --> pdb=" O VAL E 244 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ALA E 246 " --> pdb=" O VAL E 269 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N VAL E 271 " --> pdb=" O ALA E 246 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU E 248 " --> pdb=" O VAL E 271 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ALA E 216 " --> pdb=" O TYR E 245 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ILE E 247 " --> pdb=" O ALA E 216 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU E 218 " --> pdb=" O ILE E 247 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N THR E 166 " --> pdb=" O ILE E 217 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N VAL E 219 " --> pdb=" O THR E 166 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N VAL E 168 " --> pdb=" O VAL E 219 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASP E 188 " --> pdb=" O ILE E 167 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N SER E 169 " --> pdb=" O ASP E 188 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ALA E 190 " --> pdb=" O SER E 169 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 4 through 8 removed outlier: 6.278A pdb=" N ASP F 52 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N PHE F 7 " --> pdb=" O ASP F 52 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N TYR F 54 " --> pdb=" O PHE F 7 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ARG F 84 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ILE F 55 " --> pdb=" O ARG F 84 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR F 86 " --> pdb=" O ILE F 55 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N HIS F 123 " --> pdb=" O ALA F 87 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ILE F 89 " --> pdb=" O HIS F 123 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ILE F 125 " --> pdb=" O ILE F 89 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N THR F 126 " --> pdb=" O PRO F 141 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ASP F 143 " --> pdb=" O THR F 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'F' and resid 30 through 34 Processing sheet with id= R, first strand: chain 'F' and resid 287 through 290 removed outlier: 7.884A pdb=" N GLN F 288 " --> pdb=" O GLU F 267 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL F 269 " --> pdb=" O GLN F 288 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ILE F 290 " --> pdb=" O VAL F 269 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL F 271 " --> pdb=" O ILE F 290 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N VAL F 244 " --> pdb=" O GLU F 267 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL F 269 " --> pdb=" O VAL F 244 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA F 246 " --> pdb=" O VAL F 269 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N VAL F 271 " --> pdb=" O ALA F 246 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU F 248 " --> pdb=" O VAL F 271 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ALA F 216 " --> pdb=" O TYR F 245 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ILE F 247 " --> pdb=" O ALA F 216 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU F 218 " --> pdb=" O ILE F 247 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N THR F 166 " --> pdb=" O ILE F 217 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N VAL F 219 " --> pdb=" O THR F 166 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N VAL F 168 " --> pdb=" O VAL F 219 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASP F 188 " --> pdb=" O ILE F 167 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N SER F 169 " --> pdb=" O ASP F 188 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ALA F 190 " --> pdb=" O SER F 169 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'G' and resid 4 through 8 removed outlier: 6.279A pdb=" N ASP G 52 " --> pdb=" O LYS G 5 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N PHE G 7 " --> pdb=" O ASP G 52 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N TYR G 54 " --> pdb=" O PHE G 7 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ARG G 84 " --> pdb=" O VAL G 53 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ILE G 55 " --> pdb=" O ARG G 84 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N THR G 86 " --> pdb=" O ILE G 55 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N HIS G 123 " --> pdb=" O ALA G 87 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ILE G 89 " --> pdb=" O HIS G 123 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ILE G 125 " --> pdb=" O ILE G 89 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N THR G 126 " --> pdb=" O PRO G 141 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ASP G 143 " --> pdb=" O THR G 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'G' and resid 30 through 34 Processing sheet with id= U, first strand: chain 'G' and resid 287 through 290 removed outlier: 7.885A pdb=" N GLN G 288 " --> pdb=" O GLU G 267 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N VAL G 269 " --> pdb=" O GLN G 288 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ILE G 290 " --> pdb=" O VAL G 269 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL G 271 " --> pdb=" O ILE G 290 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N VAL G 244 " --> pdb=" O GLU G 267 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL G 269 " --> pdb=" O VAL G 244 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA G 246 " --> pdb=" O VAL G 269 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N VAL G 271 " --> pdb=" O ALA G 246 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU G 248 " --> pdb=" O VAL G 271 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA G 216 " --> pdb=" O TYR G 245 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ILE G 247 " --> pdb=" O ALA G 216 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU G 218 " --> pdb=" O ILE G 247 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N THR G 166 " --> pdb=" O ILE G 217 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N VAL G 219 " --> pdb=" O THR G 166 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N VAL G 168 " --> pdb=" O VAL G 219 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASP G 188 " --> pdb=" O ILE G 167 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N SER G 169 " --> pdb=" O ASP G 188 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ALA G 190 " --> pdb=" O SER G 169 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'H' and resid 4 through 8 removed outlier: 6.278A pdb=" N ASP H 52 " --> pdb=" O LYS H 5 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N PHE H 7 " --> pdb=" O ASP H 52 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N TYR H 54 " --> pdb=" O PHE H 7 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ARG H 84 " --> pdb=" O VAL H 53 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ILE H 55 " --> pdb=" O ARG H 84 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR H 86 " --> pdb=" O ILE H 55 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N HIS H 123 " --> pdb=" O ALA H 87 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N ILE H 89 " --> pdb=" O HIS H 123 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ILE H 125 " --> pdb=" O ILE H 89 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N THR H 126 " --> pdb=" O PRO H 141 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ASP H 143 " --> pdb=" O THR H 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'H' and resid 30 through 34 Processing sheet with id= X, first strand: chain 'H' and resid 287 through 290 removed outlier: 7.885A pdb=" N GLN H 288 " --> pdb=" O GLU H 267 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL H 269 " --> pdb=" O GLN H 288 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ILE H 290 " --> pdb=" O VAL H 269 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL H 271 " --> pdb=" O ILE H 290 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N VAL H 244 " --> pdb=" O GLU H 267 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL H 269 " --> pdb=" O VAL H 244 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA H 246 " --> pdb=" O VAL H 269 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N VAL H 271 " --> pdb=" O ALA H 246 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU H 248 " --> pdb=" O VAL H 271 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ALA H 216 " --> pdb=" O TYR H 245 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ILE H 247 " --> pdb=" O ALA H 216 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU H 218 " --> pdb=" O ILE H 247 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N THR H 166 " --> pdb=" O ILE H 217 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N VAL H 219 " --> pdb=" O THR H 166 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N VAL H 168 " --> pdb=" O VAL H 219 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ASP H 188 " --> pdb=" O ILE H 167 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N SER H 169 " --> pdb=" O ASP H 188 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ALA H 190 " --> pdb=" O SER H 169 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'I' and resid 4 through 8 removed outlier: 6.278A pdb=" N ASP I 52 " --> pdb=" O LYS I 5 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N PHE I 7 " --> pdb=" O ASP I 52 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N TYR I 54 " --> pdb=" O PHE I 7 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ARG I 84 " --> pdb=" O VAL I 53 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ILE I 55 " --> pdb=" O ARG I 84 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N THR I 86 " --> pdb=" O ILE I 55 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N HIS I 123 " --> pdb=" O ALA I 87 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N ILE I 89 " --> pdb=" O HIS I 123 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ILE I 125 " --> pdb=" O ILE I 89 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N THR I 126 " --> pdb=" O PRO I 141 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ASP I 143 " --> pdb=" O THR I 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'I' and resid 30 through 34 Processing sheet with id= AA, first strand: chain 'I' and resid 287 through 290 removed outlier: 7.885A pdb=" N GLN I 288 " --> pdb=" O GLU I 267 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N VAL I 269 " --> pdb=" O GLN I 288 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ILE I 290 " --> pdb=" O VAL I 269 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL I 271 " --> pdb=" O ILE I 290 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N VAL I 244 " --> pdb=" O GLU I 267 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL I 269 " --> pdb=" O VAL I 244 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ALA I 246 " --> pdb=" O VAL I 269 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N VAL I 271 " --> pdb=" O ALA I 246 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU I 248 " --> pdb=" O VAL I 271 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA I 216 " --> pdb=" O TYR I 245 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ILE I 247 " --> pdb=" O ALA I 216 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU I 218 " --> pdb=" O ILE I 247 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N THR I 166 " --> pdb=" O ILE I 217 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N VAL I 219 " --> pdb=" O THR I 166 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N VAL I 168 " --> pdb=" O VAL I 219 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASP I 188 " --> pdb=" O ILE I 167 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N SER I 169 " --> pdb=" O ASP I 188 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ALA I 190 " --> pdb=" O SER I 169 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'J' and resid 4 through 8 removed outlier: 6.277A pdb=" N ASP J 52 " --> pdb=" O LYS J 5 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N PHE J 7 " --> pdb=" O ASP J 52 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N TYR J 54 " --> pdb=" O PHE J 7 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ARG J 84 " --> pdb=" O VAL J 53 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ILE J 55 " --> pdb=" O ARG J 84 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N THR J 86 " --> pdb=" O ILE J 55 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N HIS J 123 " --> pdb=" O ALA J 87 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ILE J 89 " --> pdb=" O HIS J 123 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ILE J 125 " --> pdb=" O ILE J 89 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N THR J 126 " --> pdb=" O PRO J 141 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ASP J 143 " --> pdb=" O THR J 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'J' and resid 30 through 34 Processing sheet with id= AD, first strand: chain 'J' and resid 287 through 290 removed outlier: 7.884A pdb=" N GLN J 288 " --> pdb=" O GLU J 267 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL J 269 " --> pdb=" O GLN J 288 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ILE J 290 " --> pdb=" O VAL J 269 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL J 271 " --> pdb=" O ILE J 290 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N VAL J 244 " --> pdb=" O GLU J 267 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL J 269 " --> pdb=" O VAL J 244 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA J 246 " --> pdb=" O VAL J 269 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N VAL J 271 " --> pdb=" O ALA J 246 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU J 248 " --> pdb=" O VAL J 271 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA J 216 " --> pdb=" O TYR J 245 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ILE J 247 " --> pdb=" O ALA J 216 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU J 218 " --> pdb=" O ILE J 247 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N THR J 166 " --> pdb=" O ILE J 217 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N VAL J 219 " --> pdb=" O THR J 166 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N VAL J 168 " --> pdb=" O VAL J 219 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASP J 188 " --> pdb=" O ILE J 167 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N SER J 169 " --> pdb=" O ASP J 188 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ALA J 190 " --> pdb=" O SER J 169 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'K' and resid 4 through 8 removed outlier: 6.277A pdb=" N ASP K 52 " --> pdb=" O LYS K 5 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N PHE K 7 " --> pdb=" O ASP K 52 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N TYR K 54 " --> pdb=" O PHE K 7 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ARG K 84 " --> pdb=" O VAL K 53 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ILE K 55 " --> pdb=" O ARG K 84 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR K 86 " --> pdb=" O ILE K 55 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N HIS K 123 " --> pdb=" O ALA K 87 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ILE K 89 " --> pdb=" O HIS K 123 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ILE K 125 " --> pdb=" O ILE K 89 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N THR K 126 " --> pdb=" O PRO K 141 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ASP K 143 " --> pdb=" O THR K 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain 'K' and resid 30 through 34 Processing sheet with id= AG, first strand: chain 'K' and resid 287 through 290 removed outlier: 7.885A pdb=" N GLN K 288 " --> pdb=" O GLU K 267 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N VAL K 269 " --> pdb=" O GLN K 288 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ILE K 290 " --> pdb=" O VAL K 269 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL K 271 " --> pdb=" O ILE K 290 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N VAL K 244 " --> pdb=" O GLU K 267 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL K 269 " --> pdb=" O VAL K 244 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA K 246 " --> pdb=" O VAL K 269 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N VAL K 271 " --> pdb=" O ALA K 246 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU K 248 " --> pdb=" O VAL K 271 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ALA K 216 " --> pdb=" O TYR K 245 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ILE K 247 " --> pdb=" O ALA K 216 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU K 218 " --> pdb=" O ILE K 247 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N THR K 166 " --> pdb=" O ILE K 217 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL K 219 " --> pdb=" O THR K 166 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N VAL K 168 " --> pdb=" O VAL K 219 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ASP K 188 " --> pdb=" O ILE K 167 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N SER K 169 " --> pdb=" O ASP K 188 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ALA K 190 " --> pdb=" O SER K 169 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'L' and resid 4 through 8 removed outlier: 6.277A pdb=" N ASP L 52 " --> pdb=" O LYS L 5 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N PHE L 7 " --> pdb=" O ASP L 52 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N TYR L 54 " --> pdb=" O PHE L 7 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ARG L 84 " --> pdb=" O VAL L 53 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N ILE L 55 " --> pdb=" O ARG L 84 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N THR L 86 " --> pdb=" O ILE L 55 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N HIS L 123 " --> pdb=" O ALA L 87 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ILE L 89 " --> pdb=" O HIS L 123 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ILE L 125 " --> pdb=" O ILE L 89 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N THR L 126 " --> pdb=" O PRO L 141 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ASP L 143 " --> pdb=" O THR L 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= AH Processing sheet with id= AI, first strand: chain 'L' and resid 30 through 34 Processing sheet with id= AJ, first strand: chain 'L' and resid 287 through 290 removed outlier: 7.885A pdb=" N GLN L 288 " --> pdb=" O GLU L 267 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL L 269 " --> pdb=" O GLN L 288 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ILE L 290 " --> pdb=" O VAL L 269 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL L 271 " --> pdb=" O ILE L 290 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N VAL L 244 " --> pdb=" O GLU L 267 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL L 269 " --> pdb=" O VAL L 244 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA L 246 " --> pdb=" O VAL L 269 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N VAL L 271 " --> pdb=" O ALA L 246 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU L 248 " --> pdb=" O VAL L 271 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA L 216 " --> pdb=" O TYR L 245 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ILE L 247 " --> pdb=" O ALA L 216 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU L 218 " --> pdb=" O ILE L 247 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N THR L 166 " --> pdb=" O ILE L 217 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N VAL L 219 " --> pdb=" O THR L 166 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N VAL L 168 " --> pdb=" O VAL L 219 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASP L 188 " --> pdb=" O ILE L 167 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N SER L 169 " --> pdb=" O ASP L 188 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ALA L 190 " --> pdb=" O SER L 169 " (cutoff:3.500A) 936 hydrogen bonds defined for protein. 2160 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: 10.77 Time building geometry restraints manager: 13.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9944 1.34 - 1.46: 4283 1.46 - 1.57: 15725 1.57 - 1.69: 84 1.69 - 1.81: 300 Bond restraints: 30336 Sorted by residual: bond pdb=" C1' ADP C 402 " pdb=" C2' ADP C 402 " ideal model delta sigma weight residual 1.306 1.535 -0.229 2.00e-02 2.50e+03 1.31e+02 bond pdb=" C1' ADP H 402 " pdb=" C2' ADP H 402 " ideal model delta sigma weight residual 1.306 1.534 -0.228 2.00e-02 2.50e+03 1.30e+02 bond pdb=" C1' ADP L 402 " pdb=" C2' ADP L 402 " ideal model delta sigma weight residual 1.306 1.534 -0.228 2.00e-02 2.50e+03 1.30e+02 bond pdb=" C1' ADP F 402 " pdb=" C2' ADP F 402 " ideal model delta sigma weight residual 1.306 1.534 -0.228 2.00e-02 2.50e+03 1.30e+02 bond pdb=" C1' ADP A 402 " pdb=" C2' ADP A 402 " ideal model delta sigma weight residual 1.306 1.534 -0.228 2.00e-02 2.50e+03 1.30e+02 ... (remaining 30331 not shown) Histogram of bond angle deviations from ideal: 98.64 - 105.99: 732 105.99 - 113.34: 17805 113.34 - 120.68: 12500 120.68 - 128.03: 9871 128.03 - 135.37: 276 Bond angle restraints: 41184 Sorted by residual: angle pdb=" PA ADP H 402 " pdb=" O3A ADP H 402 " pdb=" PB ADP H 402 " ideal model delta sigma weight residual 123.64 135.37 -11.73 3.00e+00 1.11e-01 1.53e+01 angle pdb=" PA ADP L 402 " pdb=" O3A ADP L 402 " pdb=" PB ADP L 402 " ideal model delta sigma weight residual 123.64 135.37 -11.73 3.00e+00 1.11e-01 1.53e+01 angle pdb=" PA ADP B 402 " pdb=" O3A ADP B 402 " pdb=" PB ADP B 402 " ideal model delta sigma weight residual 123.64 135.36 -11.72 3.00e+00 1.11e-01 1.53e+01 angle pdb=" PA ADP F 402 " pdb=" O3A ADP F 402 " pdb=" PB ADP F 402 " ideal model delta sigma weight residual 123.64 135.35 -11.71 3.00e+00 1.11e-01 1.52e+01 angle pdb=" PA ADP C 402 " pdb=" O3A ADP C 402 " pdb=" PB ADP C 402 " ideal model delta sigma weight residual 123.64 135.35 -11.71 3.00e+00 1.11e-01 1.52e+01 ... (remaining 41179 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 16447 17.98 - 35.95: 1421 35.95 - 53.93: 414 53.93 - 71.91: 192 71.91 - 89.88: 114 Dihedral angle restraints: 18588 sinusoidal: 7572 harmonic: 11016 Sorted by residual: dihedral pdb=" CA SER D 8 " pdb=" C SER D 8 " pdb=" N GLY D 9 " pdb=" CA GLY D 9 " ideal model delta harmonic sigma weight residual 180.00 163.02 16.98 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA SER C 8 " pdb=" C SER C 8 " pdb=" N GLY C 9 " pdb=" CA GLY C 9 " ideal model delta harmonic sigma weight residual 180.00 163.03 16.97 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA SER J 8 " pdb=" C SER J 8 " pdb=" N GLY J 9 " pdb=" CA GLY J 9 " ideal model delta harmonic sigma weight residual 180.00 163.03 16.97 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 18585 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 2424 0.033 - 0.066: 1412 0.066 - 0.099: 552 0.099 - 0.132: 301 0.132 - 0.165: 27 Chirality restraints: 4716 Sorted by residual: chirality pdb=" CA ILE C 275 " pdb=" N ILE C 275 " pdb=" C ILE C 275 " pdb=" CB ILE C 275 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.79e-01 chirality pdb=" CA ILE I 275 " pdb=" N ILE I 275 " pdb=" C ILE I 275 " pdb=" CB ILE I 275 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.68e-01 chirality pdb=" CA ILE D 275 " pdb=" N ILE D 275 " pdb=" C ILE D 275 " pdb=" CB ILE D 275 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.38e-01 ... (remaining 4713 not shown) Planarity restraints: 5184 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 HSX E 401 " -0.249 2.00e-02 2.50e+03 6.60e-01 9.81e+03 pdb=" C2 HSX E 401 " -0.886 2.00e-02 2.50e+03 pdb=" C3 HSX E 401 " -0.025 2.00e-02 2.50e+03 pdb=" C4 HSX E 401 " 0.319 2.00e-02 2.50e+03 pdb=" C5 HSX E 401 " -0.478 2.00e-02 2.50e+03 pdb=" O1 HSX E 401 " 0.877 2.00e-02 2.50e+03 pdb=" O2 HSX E 401 " -0.807 2.00e-02 2.50e+03 pdb=" O3 HSX E 401 " 1.148 2.00e-02 2.50e+03 pdb=" O4 HSX E 401 " 0.100 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 HSX G 401 " 0.249 2.00e-02 2.50e+03 6.60e-01 9.81e+03 pdb=" C2 HSX G 401 " 0.886 2.00e-02 2.50e+03 pdb=" C3 HSX G 401 " 0.025 2.00e-02 2.50e+03 pdb=" C4 HSX G 401 " -0.319 2.00e-02 2.50e+03 pdb=" C5 HSX G 401 " 0.478 2.00e-02 2.50e+03 pdb=" O1 HSX G 401 " -0.878 2.00e-02 2.50e+03 pdb=" O2 HSX G 401 " 0.806 2.00e-02 2.50e+03 pdb=" O3 HSX G 401 " -1.147 2.00e-02 2.50e+03 pdb=" O4 HSX G 401 " -0.101 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 HSX C 401 " -0.249 2.00e-02 2.50e+03 6.60e-01 9.81e+03 pdb=" C2 HSX C 401 " -0.886 2.00e-02 2.50e+03 pdb=" C3 HSX C 401 " -0.025 2.00e-02 2.50e+03 pdb=" C4 HSX C 401 " 0.319 2.00e-02 2.50e+03 pdb=" C5 HSX C 401 " -0.478 2.00e-02 2.50e+03 pdb=" O1 HSX C 401 " 0.878 2.00e-02 2.50e+03 pdb=" O2 HSX C 401 " -0.806 2.00e-02 2.50e+03 pdb=" O3 HSX C 401 " 1.147 2.00e-02 2.50e+03 pdb=" O4 HSX C 401 " 0.100 2.00e-02 2.50e+03 ... (remaining 5181 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.47: 252 2.47 - 3.08: 22026 3.08 - 3.69: 49111 3.69 - 4.29: 76170 4.29 - 4.90: 120149 Nonbonded interactions: 267708 Sorted by model distance: nonbonded pdb="MG MG E 404 " pdb=" O HOH E 509 " model vdw 1.866 2.170 nonbonded pdb="MG MG L 403 " pdb=" O HOH L 505 " model vdw 1.867 2.170 nonbonded pdb="MG MG H 403 " pdb=" O HOH H 505 " model vdw 1.867 2.170 nonbonded pdb="MG MG K 404 " pdb=" O HOH K 509 " model vdw 1.867 2.170 nonbonded pdb="MG MG J 404 " pdb=" O HOH J 507 " model vdw 1.867 2.170 ... (remaining 267703 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 317 or resid 401 through 402 or resid 404)) selection = (chain 'B' and (resid 2 through 317 or resid 401 through 402 or resid 404)) selection = (chain 'C' and (resid 2 through 317 or resid 401 through 402 or resid 404)) selection = (chain 'D' and (resid 2 through 317 or resid 401 through 402 or resid 404)) selection = (chain 'E' and (resid 2 through 317 or resid 401 through 402 or resid 404)) selection = (chain 'F' and (resid 2 through 317 or resid 401 through 402 or resid 404)) selection = (chain 'G' and (resid 2 through 317 or resid 401 through 402 or resid 404)) selection = (chain 'H' and (resid 2 through 317 or resid 401 through 402 or resid 404)) selection = (chain 'I' and (resid 2 through 317 or resid 401 through 402 or resid 404)) selection = (chain 'J' and (resid 2 through 317 or resid 401 through 402 or resid 404)) selection = (chain 'K' and (resid 2 through 317 or resid 401 through 402 or resid 404)) selection = (chain 'L' and (resid 2 through 317 or resid 401 through 402 or resid 404)) } 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: 0.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.450 Check model and map are aligned: 0.470 Set scattering table: 0.270 Process input model: 80.020 Find NCS groups from input model: 2.680 Set up NCS constraints: 0.310 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:12.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 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 : 0.014 0.229 30336 Z= 0.940 Angle : 0.988 11.735 41184 Z= 0.428 Chirality : 0.050 0.165 4716 Planarity : 0.050 0.660 5184 Dihedral : 17.663 89.882 11412 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.08 % Allowed : 14.46 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.14), residues: 3768 helix: 1.88 (0.14), residues: 1404 sheet: -0.38 (0.17), residues: 900 loop : 0.24 (0.15), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP C 162 HIS 0.007 0.001 HIS I 12 PHE 0.012 0.002 PHE I 138 TYR 0.011 0.002 TYR F 311 ARG 0.008 0.001 ARG D 214 *********************** 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 936 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 837 time to evaluate : 3.254 Fit side-chains REVERT: B 3 ASN cc_start: 0.8878 (m110) cc_final: 0.8652 (m110) REVERT: B 231 HIS cc_start: 0.8419 (m170) cc_final: 0.8147 (m90) REVERT: B 294 MET cc_start: 0.8458 (pmm) cc_final: 0.7837 (pmm) REVERT: B 298 GLU cc_start: 0.8697 (tp30) cc_final: 0.8494 (mm-30) REVERT: B 307 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7980 (mt-10) REVERT: D 102 LYS cc_start: 0.7711 (mttm) cc_final: 0.7507 (mtpp) REVERT: D 280 LYS cc_start: 0.8765 (mmtm) cc_final: 0.8457 (mmtt) REVERT: E 128 ASP cc_start: 0.8777 (m-30) cc_final: 0.8445 (m-30) REVERT: E 261 ILE cc_start: 0.9070 (mt) cc_final: 0.8828 (mm) REVERT: F 3 ASN cc_start: 0.9017 (m110) cc_final: 0.8739 (m110) REVERT: F 231 HIS cc_start: 0.8267 (m170) cc_final: 0.8009 (m90) REVERT: F 237 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8550 (mt) REVERT: F 294 MET cc_start: 0.8517 (pmm) cc_final: 0.7993 (pmm) REVERT: G 102 LYS cc_start: 0.7705 (mttm) cc_final: 0.7501 (mtpp) REVERT: G 280 LYS cc_start: 0.8763 (mmtm) cc_final: 0.8456 (mmtt) REVERT: H 195 GLU cc_start: 0.7441 (pt0) cc_final: 0.7195 (pt0) REVERT: H 204 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.7515 (ptt180) REVERT: I 3 ASN cc_start: 0.8904 (m110) cc_final: 0.8678 (m110) REVERT: I 231 HIS cc_start: 0.8413 (m170) cc_final: 0.8144 (m90) REVERT: I 294 MET cc_start: 0.8468 (pmm) cc_final: 0.7861 (pmm) REVERT: I 298 GLU cc_start: 0.8726 (tp30) cc_final: 0.8525 (mm-30) REVERT: I 307 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7996 (mt-10) REVERT: K 3 ASN cc_start: 0.9015 (m110) cc_final: 0.8724 (m110) REVERT: K 231 HIS cc_start: 0.8244 (m170) cc_final: 0.7992 (m90) REVERT: K 237 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8525 (mt) REVERT: K 294 MET cc_start: 0.8525 (pmm) cc_final: 0.7998 (pmm) REVERT: L 128 ASP cc_start: 0.8771 (m-30) cc_final: 0.8439 (m-30) REVERT: L 261 ILE cc_start: 0.9071 (mt) cc_final: 0.8841 (mm) outliers start: 99 outliers final: 18 residues processed: 853 average time/residue: 1.6066 time to fit residues: 1580.9990 Evaluate side-chains 687 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 666 time to evaluate : 3.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 204 ARG Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 204 ARG Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 204 ARG Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain G residue 204 ARG Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain H residue 204 ARG Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain I residue 204 ARG Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain K residue 204 ARG Chi-restraints excluded: chain K residue 237 LEU Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain L residue 249 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 314 optimal weight: 0.9990 chunk 281 optimal weight: 0.5980 chunk 156 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 190 optimal weight: 0.9990 chunk 150 optimal weight: 0.3980 chunk 291 optimal weight: 0.7980 chunk 112 optimal weight: 0.0020 chunk 177 optimal weight: 6.9990 chunk 217 optimal weight: 2.9990 chunk 337 optimal weight: 3.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 ASN A 262 ASN A 263 ASN B 262 ASN C 3 ASN D 262 ASN D 288 GLN E 3 ASN E 17 GLN E 262 ASN F 262 ASN G 262 ASN G 288 GLN H 3 ASN I 262 ASN J 3 ASN J 262 ASN J 263 ASN K 262 ASN L 3 ASN L 17 GLN L 262 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 30336 Z= 0.184 Angle : 1.573 47.483 41184 Z= 0.558 Chirality : 0.045 0.164 4716 Planarity : 0.004 0.034 5184 Dihedral : 13.938 110.353 4532 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.15 % Allowed : 14.43 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.14), residues: 3768 helix: 1.68 (0.15), residues: 1416 sheet: -0.62 (0.16), residues: 996 loop : 0.03 (0.15), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 162 HIS 0.005 0.001 HIS E 12 PHE 0.011 0.001 PHE F 138 TYR 0.008 0.001 TYR J 311 ARG 0.005 0.001 ARG K 184 *********************** 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 747 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 678 time to evaluate : 3.510 Fit side-chains REVERT: A 298 GLU cc_start: 0.8709 (tp30) cc_final: 0.8339 (mm-30) REVERT: B 3 ASN cc_start: 0.8953 (m110) cc_final: 0.8729 (m110) REVERT: B 231 HIS cc_start: 0.8534 (m170) cc_final: 0.8169 (m90) REVERT: B 281 MET cc_start: 0.8526 (mtp) cc_final: 0.8295 (mtm) REVERT: B 294 MET cc_start: 0.8476 (pmm) cc_final: 0.7898 (pmm) REVERT: B 298 GLU cc_start: 0.8738 (tp30) cc_final: 0.8485 (mm-30) REVERT: B 307 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7901 (mt-10) REVERT: D 13 GLN cc_start: 0.8120 (tp40) cc_final: 0.7712 (tp-100) REVERT: E 127 MET cc_start: 0.8443 (ttm) cc_final: 0.8122 (ttm) REVERT: F 166 THR cc_start: 0.9140 (OUTLIER) cc_final: 0.8939 (t) REVERT: F 237 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8664 (mt) REVERT: F 294 MET cc_start: 0.8503 (pmm) cc_final: 0.8106 (pmm) REVERT: G 13 GLN cc_start: 0.8086 (tp40) cc_final: 0.7681 (tp-100) REVERT: I 3 ASN cc_start: 0.8960 (m110) cc_final: 0.8733 (m110) REVERT: I 231 HIS cc_start: 0.8528 (m170) cc_final: 0.8159 (m90) REVERT: I 281 MET cc_start: 0.8538 (mtp) cc_final: 0.8282 (mtm) REVERT: I 294 MET cc_start: 0.8487 (pmm) cc_final: 0.8071 (pmm) REVERT: I 298 GLU cc_start: 0.8741 (tp30) cc_final: 0.8492 (mm-30) REVERT: I 307 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7899 (mt-10) REVERT: J 298 GLU cc_start: 0.8728 (tp30) cc_final: 0.8347 (mm-30) REVERT: K 237 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8675 (mt) REVERT: K 294 MET cc_start: 0.8520 (pmm) cc_final: 0.8128 (pmm) outliers start: 69 outliers final: 27 residues processed: 731 average time/residue: 1.5752 time to fit residues: 1336.2119 Evaluate side-chains 660 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 630 time to evaluate : 3.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain G residue 166 THR Chi-restraints excluded: chain G residue 237 LEU Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain J residue 238 SER Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain K residue 237 LEU Chi-restraints excluded: chain K residue 248 LEU Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain L residue 249 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 187 optimal weight: 5.9990 chunk 104 optimal weight: 8.9990 chunk 281 optimal weight: 0.0010 chunk 230 optimal weight: 0.6980 chunk 93 optimal weight: 7.9990 chunk 338 optimal weight: 7.9990 chunk 365 optimal weight: 4.9990 chunk 301 optimal weight: 0.9990 chunk 335 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 271 optimal weight: 6.9990 overall best weight: 1.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 GLN A 263 ASN B 262 ASN B 263 ASN D 262 ASN D 288 GLN F 38 GLN G 262 ASN G 288 GLN I 262 ASN I 263 ASN J 17 GLN J 263 ASN K 38 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 30336 Z= 0.250 Angle : 1.580 46.721 41184 Z= 0.569 Chirality : 0.047 0.174 4716 Planarity : 0.004 0.027 5184 Dihedral : 14.352 102.180 4504 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.52 % Allowed : 13.31 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.14), residues: 3768 helix: 1.46 (0.15), residues: 1428 sheet: -0.69 (0.16), residues: 996 loop : -0.18 (0.15), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP I 162 HIS 0.005 0.001 HIS H 123 PHE 0.012 0.002 PHE J 313 TYR 0.010 0.002 TYR A 311 ARG 0.008 0.001 ARG D 184 *********************** 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 706 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 625 time to evaluate : 3.572 Fit side-chains REVERT: A 307 GLU cc_start: 0.8474 (mt-10) cc_final: 0.8236 (mt-10) REVERT: B 13 GLN cc_start: 0.8409 (tp40) cc_final: 0.7997 (tp-100) REVERT: B 231 HIS cc_start: 0.8630 (m170) cc_final: 0.8116 (m90) REVERT: B 294 MET cc_start: 0.8532 (pmm) cc_final: 0.8004 (pmm) REVERT: B 307 GLU cc_start: 0.8249 (mt-10) cc_final: 0.8029 (mt-10) REVERT: D 13 GLN cc_start: 0.8390 (tp40) cc_final: 0.7942 (tp-100) REVERT: D 68 MET cc_start: 0.8881 (tpt) cc_final: 0.8662 (mmm) REVERT: D 222 MET cc_start: 0.8728 (ptp) cc_final: 0.8524 (ptp) REVERT: E 127 MET cc_start: 0.8596 (ttm) cc_final: 0.8152 (ttm) REVERT: E 184 ARG cc_start: 0.8593 (mmt90) cc_final: 0.8309 (mmt-90) REVERT: F 13 GLN cc_start: 0.8471 (tp40) cc_final: 0.8103 (mm-40) REVERT: F 237 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8811 (mt) REVERT: F 294 MET cc_start: 0.8581 (pmm) cc_final: 0.8037 (pmm) REVERT: G 13 GLN cc_start: 0.8375 (tp40) cc_final: 0.7922 (tp-100) REVERT: G 139 ASP cc_start: 0.8569 (m-30) cc_final: 0.8278 (m-30) REVERT: G 222 MET cc_start: 0.8724 (ptp) cc_final: 0.8495 (ptp) REVERT: I 13 GLN cc_start: 0.8409 (tp40) cc_final: 0.8004 (tp-100) REVERT: I 231 HIS cc_start: 0.8632 (m170) cc_final: 0.8115 (m90) REVERT: I 294 MET cc_start: 0.8529 (pmm) cc_final: 0.8003 (pmm) REVERT: I 307 GLU cc_start: 0.8262 (mt-10) cc_final: 0.8039 (mt-10) REVERT: J 286 LYS cc_start: 0.9130 (OUTLIER) cc_final: 0.8865 (mtmt) REVERT: K 13 GLN cc_start: 0.8469 (tp40) cc_final: 0.8103 (mm-40) REVERT: K 237 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8814 (mt) REVERT: K 294 MET cc_start: 0.8580 (pmm) cc_final: 0.8036 (pmm) REVERT: L 127 MET cc_start: 0.8594 (ttm) cc_final: 0.8150 (ttm) REVERT: L 184 ARG cc_start: 0.8583 (mmt90) cc_final: 0.8306 (mmt-90) outliers start: 81 outliers final: 50 residues processed: 669 average time/residue: 1.5787 time to fit residues: 1225.3653 Evaluate side-chains 648 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 595 time to evaluate : 4.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 282 LYS Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 237 LEU Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain G residue 282 LYS Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain H residue 259 SER Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain J residue 12 HIS Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain J residue 282 LYS Chi-restraints excluded: chain J residue 286 LYS Chi-restraints excluded: chain J residue 314 SER Chi-restraints excluded: chain K residue 12 HIS Chi-restraints excluded: chain K residue 237 LEU Chi-restraints excluded: chain K residue 248 LEU Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain K residue 259 SER Chi-restraints excluded: chain L residue 12 HIS Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain L residue 178 VAL Chi-restraints excluded: chain L residue 249 THR Chi-restraints excluded: chain L residue 259 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 334 optimal weight: 4.9990 chunk 254 optimal weight: 1.9990 chunk 175 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 161 optimal weight: 1.9990 chunk 227 optimal weight: 0.8980 chunk 339 optimal weight: 1.9990 chunk 359 optimal weight: 8.9990 chunk 177 optimal weight: 0.8980 chunk 321 optimal weight: 8.9990 chunk 96 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 ASN A 288 GLN B 186 ASN B 262 ASN B 263 ASN D 262 ASN D 288 GLN G 262 ASN G 288 GLN I 186 ASN I 262 ASN I 263 ASN J 263 ASN J 288 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30336 Z= 0.213 Angle : 1.555 46.928 41184 Z= 0.557 Chirality : 0.046 0.168 4716 Planarity : 0.004 0.027 5184 Dihedral : 14.168 110.900 4504 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.27 % Allowed : 13.65 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.13), residues: 3768 helix: 1.45 (0.15), residues: 1428 sheet: -0.63 (0.16), residues: 984 loop : -0.27 (0.15), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP I 162 HIS 0.004 0.001 HIS H 123 PHE 0.011 0.001 PHE K 138 TYR 0.009 0.001 TYR J 311 ARG 0.006 0.000 ARG G 184 *********************** 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 667 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 594 time to evaluate : 3.655 Fit side-chains REVERT: A 237 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8525 (mt) REVERT: A 294 MET cc_start: 0.8467 (pmm) cc_final: 0.8185 (pmm) REVERT: B 13 GLN cc_start: 0.8383 (tp40) cc_final: 0.8014 (tp-100) REVERT: B 294 MET cc_start: 0.8536 (pmm) cc_final: 0.8001 (pmm) REVERT: B 307 GLU cc_start: 0.8267 (mt-10) cc_final: 0.8028 (mt-10) REVERT: D 13 GLN cc_start: 0.8395 (tp40) cc_final: 0.7945 (tp-100) REVERT: D 204 ARG cc_start: 0.8039 (ptm-80) cc_final: 0.7769 (ptt90) REVERT: E 127 MET cc_start: 0.8622 (ttm) cc_final: 0.8181 (ttm) REVERT: F 13 GLN cc_start: 0.8466 (tp40) cc_final: 0.8178 (mm-40) REVERT: F 237 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8814 (mt) REVERT: F 294 MET cc_start: 0.8575 (pmm) cc_final: 0.8097 (pmm) REVERT: G 13 GLN cc_start: 0.8387 (tp40) cc_final: 0.7919 (tp-100) REVERT: G 204 ARG cc_start: 0.8036 (ptm-80) cc_final: 0.7762 (ptt90) REVERT: I 13 GLN cc_start: 0.8378 (tp40) cc_final: 0.8009 (tp-100) REVERT: I 294 MET cc_start: 0.8535 (pmm) cc_final: 0.7999 (pmm) REVERT: I 307 GLU cc_start: 0.8256 (mt-10) cc_final: 0.8011 (mt-10) REVERT: J 294 MET cc_start: 0.8469 (pmm) cc_final: 0.8189 (pmm) REVERT: K 13 GLN cc_start: 0.8462 (tp40) cc_final: 0.8172 (mm-40) REVERT: K 237 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8821 (mt) REVERT: K 294 MET cc_start: 0.8576 (pmm) cc_final: 0.8100 (pmm) REVERT: L 127 MET cc_start: 0.8620 (ttm) cc_final: 0.8186 (ttm) outliers start: 73 outliers final: 52 residues processed: 638 average time/residue: 1.5769 time to fit residues: 1167.3499 Evaluate side-chains 645 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 590 time to evaluate : 3.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 238 SER Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 12 HIS Chi-restraints excluded: chain F residue 212 LYS Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain G residue 237 LEU Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain G residue 314 SER Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain I residue 248 LEU Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain J residue 12 HIS Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain J residue 282 LYS Chi-restraints excluded: chain J residue 314 SER Chi-restraints excluded: chain K residue 12 HIS Chi-restraints excluded: chain K residue 160 SER Chi-restraints excluded: chain K residue 212 LYS Chi-restraints excluded: chain K residue 237 LEU Chi-restraints excluded: chain K residue 248 LEU Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain K residue 259 SER Chi-restraints excluded: chain L residue 12 HIS Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain L residue 178 VAL Chi-restraints excluded: chain L residue 238 SER Chi-restraints excluded: chain L residue 249 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 299 optimal weight: 0.0770 chunk 204 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 267 optimal weight: 1.9990 chunk 148 optimal weight: 8.9990 chunk 306 optimal weight: 1.9990 chunk 248 optimal weight: 8.9990 chunk 0 optimal weight: 0.6980 chunk 183 optimal weight: 0.9990 chunk 322 optimal weight: 10.0000 chunk 90 optimal weight: 8.9990 overall best weight: 0.6942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN B 262 ASN B 263 ASN C 17 GLN D 262 ASN D 288 GLN G 262 ASN G 288 GLN H 17 GLN I 262 ASN I 263 ASN J 288 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 30336 Z= 0.149 Angle : 1.528 47.187 41184 Z= 0.540 Chirality : 0.045 0.161 4716 Planarity : 0.003 0.026 5184 Dihedral : 13.351 103.586 4504 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.83 % Allowed : 14.74 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.14), residues: 3768 helix: 1.54 (0.15), residues: 1428 sheet: -0.49 (0.16), residues: 972 loop : -0.18 (0.15), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 162 HIS 0.003 0.001 HIS L 12 PHE 0.011 0.001 PHE K 138 TYR 0.008 0.001 TYR J 311 ARG 0.006 0.000 ARG G 184 *********************** 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 643 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 584 time to evaluate : 3.361 Fit side-chains REVERT: A 298 GLU cc_start: 0.8738 (tp30) cc_final: 0.8433 (mm-30) REVERT: B 13 GLN cc_start: 0.8355 (tp40) cc_final: 0.7975 (tp-100) REVERT: B 294 MET cc_start: 0.8527 (pmm) cc_final: 0.7970 (pmm) REVERT: D 13 GLN cc_start: 0.8382 (tp40) cc_final: 0.8004 (tp-100) REVERT: E 78 LYS cc_start: 0.8570 (tptp) cc_final: 0.8364 (tppp) REVERT: E 127 MET cc_start: 0.8603 (ttm) cc_final: 0.8179 (ttm) REVERT: F 13 GLN cc_start: 0.8385 (tp40) cc_final: 0.8139 (mm-40) REVERT: F 237 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8825 (mt) REVERT: F 294 MET cc_start: 0.8553 (pmm) cc_final: 0.7979 (pmm) REVERT: G 13 GLN cc_start: 0.8408 (tp40) cc_final: 0.8031 (tp-100) REVERT: G 68 MET cc_start: 0.8906 (tpt) cc_final: 0.8692 (mmm) REVERT: I 13 GLN cc_start: 0.8354 (tp40) cc_final: 0.7975 (tp-100) REVERT: I 294 MET cc_start: 0.8525 (pmm) cc_final: 0.7966 (pmm) REVERT: J 298 GLU cc_start: 0.8741 (tp30) cc_final: 0.8433 (mm-30) REVERT: K 13 GLN cc_start: 0.8382 (tp40) cc_final: 0.8135 (mm-40) REVERT: K 237 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8827 (mt) REVERT: K 294 MET cc_start: 0.8556 (pmm) cc_final: 0.7980 (pmm) REVERT: L 78 LYS cc_start: 0.8574 (tptp) cc_final: 0.8372 (tppp) REVERT: L 127 MET cc_start: 0.8606 (ttm) cc_final: 0.8184 (ttm) outliers start: 59 outliers final: 40 residues processed: 620 average time/residue: 1.5605 time to fit residues: 1122.4768 Evaluate side-chains 606 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 564 time to evaluate : 3.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 238 SER Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 12 HIS Chi-restraints excluded: chain F residue 160 SER Chi-restraints excluded: chain F residue 212 LYS Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain G residue 12 HIS Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain I residue 12 HIS Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain J residue 12 HIS Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain J residue 282 LYS Chi-restraints excluded: chain K residue 12 HIS Chi-restraints excluded: chain K residue 160 SER Chi-restraints excluded: chain K residue 237 LEU Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain K residue 259 SER Chi-restraints excluded: chain L residue 73 MET Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain L residue 238 SER Chi-restraints excluded: chain L residue 249 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 120 optimal weight: 0.9990 chunk 323 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 211 optimal weight: 6.9990 chunk 88 optimal weight: 7.9990 chunk 359 optimal weight: 4.9990 chunk 298 optimal weight: 6.9990 chunk 166 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 188 optimal weight: 7.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN B 263 ASN C 38 GLN D 262 ASN D 288 GLN G 262 ASN G 288 GLN I 262 ASN I 263 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 30336 Z= 0.267 Angle : 1.579 46.897 41184 Z= 0.569 Chirality : 0.047 0.175 4716 Planarity : 0.004 0.036 5184 Dihedral : 14.039 113.496 4504 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.67 % Allowed : 13.93 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.13), residues: 3768 helix: 1.45 (0.15), residues: 1428 sheet: -0.65 (0.16), residues: 984 loop : -0.27 (0.15), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 162 HIS 0.005 0.001 HIS E 123 PHE 0.012 0.002 PHE C 138 TYR 0.010 0.002 TYR J 311 ARG 0.006 0.001 ARG I 196 *********************** 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 675 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 589 time to evaluate : 3.305 Fit side-chains REVERT: B 13 GLN cc_start: 0.8420 (tp40) cc_final: 0.8055 (tp-100) REVERT: B 231 HIS cc_start: 0.8618 (m170) cc_final: 0.8107 (m90) REVERT: B 294 MET cc_start: 0.8532 (pmm) cc_final: 0.7985 (pmm) REVERT: B 307 GLU cc_start: 0.8293 (mt-10) cc_final: 0.8063 (mt-10) REVERT: D 13 GLN cc_start: 0.8408 (tp40) cc_final: 0.7970 (tp-100) REVERT: D 204 ARG cc_start: 0.8109 (ptm-80) cc_final: 0.7801 (ptt90) REVERT: E 127 MET cc_start: 0.8622 (ttm) cc_final: 0.8166 (ttm) REVERT: F 13 GLN cc_start: 0.8487 (tp40) cc_final: 0.8188 (mm-40) REVERT: F 237 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8833 (mt) REVERT: F 294 MET cc_start: 0.8574 (pmm) cc_final: 0.8099 (pmm) REVERT: G 13 GLN cc_start: 0.8421 (tp40) cc_final: 0.7972 (tp-100) REVERT: G 204 ARG cc_start: 0.8104 (ptm-80) cc_final: 0.7789 (ptt90) REVERT: H 69 GLU cc_start: 0.8679 (tt0) cc_final: 0.8449 (tt0) REVERT: I 13 GLN cc_start: 0.8420 (tp40) cc_final: 0.8054 (tp-100) REVERT: I 231 HIS cc_start: 0.8583 (m170) cc_final: 0.8094 (m90) REVERT: I 294 MET cc_start: 0.8529 (pmm) cc_final: 0.7983 (pmm) REVERT: J 286 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8845 (mtmt) REVERT: K 13 GLN cc_start: 0.8484 (tp40) cc_final: 0.8185 (mm-40) REVERT: K 237 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8835 (mt) REVERT: K 294 MET cc_start: 0.8575 (pmm) cc_final: 0.8099 (pmm) REVERT: L 127 MET cc_start: 0.8614 (ttm) cc_final: 0.8148 (ttm) outliers start: 86 outliers final: 62 residues processed: 647 average time/residue: 1.5813 time to fit residues: 1186.0388 Evaluate side-chains 649 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 584 time to evaluate : 3.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 282 LYS Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 12 HIS Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 160 SER Chi-restraints excluded: chain F residue 212 LYS Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain G residue 282 LYS Chi-restraints excluded: chain G residue 314 SER Chi-restraints excluded: chain H residue 12 HIS Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain J residue 12 HIS Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain J residue 282 LYS Chi-restraints excluded: chain J residue 286 LYS Chi-restraints excluded: chain J residue 314 SER Chi-restraints excluded: chain K residue 12 HIS Chi-restraints excluded: chain K residue 78 LYS Chi-restraints excluded: chain K residue 160 SER Chi-restraints excluded: chain K residue 212 LYS Chi-restraints excluded: chain K residue 237 LEU Chi-restraints excluded: chain K residue 248 LEU Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain K residue 259 SER Chi-restraints excluded: chain L residue 12 HIS Chi-restraints excluded: chain L residue 73 MET Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain L residue 178 VAL Chi-restraints excluded: chain L residue 238 SER Chi-restraints excluded: chain L residue 249 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 347 optimal weight: 10.0000 chunk 40 optimal weight: 0.7980 chunk 205 optimal weight: 1.9990 chunk 262 optimal weight: 2.9990 chunk 203 optimal weight: 1.9990 chunk 302 optimal weight: 6.9990 chunk 200 optimal weight: 0.7980 chunk 358 optimal weight: 0.9980 chunk 224 optimal weight: 0.9990 chunk 218 optimal weight: 2.9990 chunk 165 optimal weight: 9.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN B 262 ASN B 263 ASN D 262 ASN D 288 GLN F 38 GLN G 262 ASN G 288 GLN I 262 ASN I 263 ASN K 38 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30336 Z= 0.176 Angle : 1.541 47.134 41184 Z= 0.548 Chirality : 0.045 0.164 4716 Planarity : 0.003 0.037 5184 Dihedral : 13.614 113.142 4504 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.18 % Allowed : 14.49 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.13), residues: 3768 helix: 1.49 (0.14), residues: 1428 sheet: -0.63 (0.16), residues: 984 loop : -0.28 (0.15), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP I 162 HIS 0.004 0.001 HIS C 123 PHE 0.011 0.001 PHE F 138 TYR 0.009 0.001 TYR J 311 ARG 0.007 0.000 ARG G 214 *********************** 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 661 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 591 time to evaluate : 3.699 Fit side-chains REVERT: B 13 GLN cc_start: 0.8366 (tp40) cc_final: 0.7983 (tp-100) REVERT: B 294 MET cc_start: 0.8534 (pmm) cc_final: 0.7960 (pmm) REVERT: B 307 GLU cc_start: 0.8269 (mt-10) cc_final: 0.8043 (mt-10) REVERT: C 298 GLU cc_start: 0.8699 (tp30) cc_final: 0.8372 (mm-30) REVERT: D 13 GLN cc_start: 0.8421 (tp40) cc_final: 0.8047 (tp-100) REVERT: D 204 ARG cc_start: 0.8106 (ptm-80) cc_final: 0.7829 (ptt90) REVERT: E 127 MET cc_start: 0.8611 (ttm) cc_final: 0.8157 (ttm) REVERT: E 184 ARG cc_start: 0.8499 (mmt90) cc_final: 0.8235 (mmt-90) REVERT: F 13 GLN cc_start: 0.8465 (tp40) cc_final: 0.8201 (mm-40) REVERT: F 294 MET cc_start: 0.8560 (pmm) cc_final: 0.8000 (pmm) REVERT: G 13 GLN cc_start: 0.8410 (tp40) cc_final: 0.8028 (tp-100) REVERT: G 204 ARG cc_start: 0.8103 (ptm-80) cc_final: 0.7774 (ptt90) REVERT: I 13 GLN cc_start: 0.8363 (tp40) cc_final: 0.7981 (tp-100) REVERT: I 231 HIS cc_start: 0.8521 (m170) cc_final: 0.8035 (m90) REVERT: I 294 MET cc_start: 0.8529 (pmm) cc_final: 0.7956 (pmm) REVERT: K 13 GLN cc_start: 0.8464 (tp40) cc_final: 0.8200 (mm-40) REVERT: K 294 MET cc_start: 0.8562 (pmm) cc_final: 0.8001 (pmm) REVERT: L 127 MET cc_start: 0.8601 (ttm) cc_final: 0.8146 (ttm) REVERT: L 184 ARG cc_start: 0.8501 (mmt90) cc_final: 0.8237 (mmt-90) outliers start: 70 outliers final: 53 residues processed: 631 average time/residue: 1.6223 time to fit residues: 1187.5314 Evaluate side-chains 651 residues out of total 3216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 598 time to evaluate : 3.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 282 LYS Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 238 SER Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 12 HIS Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 160 SER Chi-restraints excluded: chain F residue 212 LYS Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain G residue 282 LYS Chi-restraints excluded: chain H residue 12 HIS Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain I residue 12 HIS Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain J residue 12 HIS Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain J residue 282 LYS Chi-restraints excluded: chain K residue 12 HIS Chi-restraints excluded: chain K residue 78 LYS Chi-restraints excluded: chain K residue 160 SER Chi-restraints excluded: chain K residue 212 LYS Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain K residue 259 SER Chi-restraints excluded: chain L residue 12 HIS Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 73 MET Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain L residue 238 SER Chi-restraints excluded: chain L residue 249 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 221 optimal weight: 7.9990 chunk 143 optimal weight: 7.9990 chunk 214 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 chunk 70 optimal weight: 0.4980 chunk 69 optimal weight: 1.9990 chunk 227 optimal weight: 0.4980 chunk 244 optimal weight: 0.7980 chunk 177 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 281 optimal weight: 7.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN B 262 ASN B 263 ASN C 38 GLN D 262 ASN D 288 GLN E 263 ASN E 288 GLN G 262 ASN G 288 GLN I 262 ASN I 263 ASN J 288 GLN L 288 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2656 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: