Starting phenix.real_space_refine on Mon Mar 25 12:36:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uqo_20851/03_2024/6uqo_20851_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uqo_20851/03_2024/6uqo_20851.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uqo_20851/03_2024/6uqo_20851.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uqo_20851/03_2024/6uqo_20851.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uqo_20851/03_2024/6uqo_20851_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uqo_20851/03_2024/6uqo_20851_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.077 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: 5 Type Number sf(0) Gaussians P 31 5.49 5 S 259 5.16 5 C 30464 2.51 5 N 8548 2.21 5 O 9220 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 665": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 722": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 744": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 277": "OD1" <-> "OD2" Residue "B TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 665": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 722": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 746": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 332": "OE1" <-> "OE2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 665": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 722": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 744": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 746": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 286": "OE1" <-> "OE2" Residue "D TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 665": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 722": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 744": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 611": "OE1" <-> "OE2" Residue "E PHE 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 665": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 722": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 741": "OE1" <-> "OE2" Residue "E PHE 746": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 665": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 722": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 744": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 746": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 183": "OE1" <-> "OE2" Residue "J TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 183": "OE1" <-> "OE2" Residue "L PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 32": "OD1" <-> "OD2" Residue "L TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 183": "OE1" <-> "OE2" Residue "P TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 183": "OE1" <-> "OE2" Residue "S TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 48522 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 4511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4511 Classifications: {'peptide': 578} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 558} Chain: "B" Number of atoms: 4511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4511 Classifications: {'peptide': 578} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 559} Chain: "C" Number of atoms: 4511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4511 Classifications: {'peptide': 578} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 17, 'TRANS': 556} Chain: "D" Number of atoms: 4511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4511 Classifications: {'peptide': 578} Modifications used: {'COO': 1} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 17, 'TRANS': 555} Chain: "E" Number of atoms: 4511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4511 Classifications: {'peptide': 578} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 18, 'TRANS': 557} Chain: "F" Number of atoms: 4511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4511 Classifications: {'peptide': 578} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PTRANS': 18, 'TRANS': 556} Chain: "G" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1501 Classifications: {'peptide': 192} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 183} Chain: "H" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1501 Classifications: {'peptide': 192} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 183} Chain: "I" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1501 Classifications: {'peptide': 192} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "J" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1501 Classifications: {'peptide': 192} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "K" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1501 Classifications: {'peptide': 192} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "L" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1501 Classifications: {'peptide': 192} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 183} Chain: "M" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1501 Classifications: {'peptide': 192} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 7, 'TRANS': 182} Chain: "N" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1501 Classifications: {'peptide': 192} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "O" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1501 Classifications: {'peptide': 192} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "P" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1501 Classifications: {'peptide': 192} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "Q" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1501 Classifications: {'peptide': 192} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "R" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1501 Classifications: {'peptide': 192} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "S" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1501 Classifications: {'peptide': 192} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "T" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1501 Classifications: {'peptide': 192} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "X" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "Y" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 23.69, per 1000 atoms: 0.49 Number of scatterers: 48522 At special positions: 0 Unit cell: (145.01, 142.451, 218.368, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 259 16.00 P 31 15.00 O 9220 8.00 N 8548 7.00 C 30464 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 Atom "HETATM48490 O3A ADP F 801 .*. O " rejected from bonding due to valence issues. Atom "HETATM48219 O3A ADP A 802 .*. O " rejected from bonding due to valence issues. Atom "HETATM48490 O3A ADP F 801 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 18.14 Conformation dependent library (CDL) restraints added in 8.7 seconds 12232 Ramachandran restraints generated. 6116 Oldfield, 0 Emsley, 6116 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11400 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 277 helices and 81 sheets defined 47.5% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.95 Creating SS restraints... Processing helix chain 'A' and resid 176 through 182 Processing helix chain 'A' and resid 192 through 202 Processing helix chain 'A' and resid 220 through 232 removed outlier: 4.289A pdb=" N ALA A 224 " --> pdb=" O LYS A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 240 No H-bonds generated for 'chain 'A' and resid 238 through 240' Processing helix chain 'A' and resid 250 through 254 Processing helix chain 'A' and resid 262 through 275 removed outlier: 3.541A pdb=" N PHE A 267 " --> pdb=" O PHE A 263 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS A 268 " --> pdb=" O GLU A 264 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 274 " --> pdb=" O LEU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 293 removed outlier: 3.585A pdb=" N ILE A 291 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N GLY A 292 " --> pdb=" O HIS A 288 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ALA A 293 " --> pdb=" O THR A 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 287 through 293' Processing helix chain 'A' and resid 303 through 311 Proline residue: A 309 - end of helix Processing helix chain 'A' and resid 324 through 330 Processing helix chain 'A' and resid 335 through 337 No H-bonds generated for 'chain 'A' and resid 335 through 337' Processing helix chain 'A' and resid 351 through 369 Proline residue: A 363 - end of helix Processing helix chain 'A' and resid 375 through 388 Processing helix chain 'A' and resid 394 through 415 removed outlier: 4.695A pdb=" N ILE A 399 " --> pdb=" O PRO A 395 " (cutoff:3.500A) Proline residue: A 413 - end of helix Processing helix chain 'A' and resid 423 through 434 Processing helix chain 'A' and resid 444 through 457 removed outlier: 4.094A pdb=" N LEU A 449 " --> pdb=" O ARG A 446 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N LYS A 450 " --> pdb=" O ASP A 447 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N GLY A 453 " --> pdb=" O LYS A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 478 Processing helix chain 'A' and resid 501 through 512 Processing helix chain 'A' and resid 521 through 523 No H-bonds generated for 'chain 'A' and resid 521 through 523' Processing helix chain 'A' and resid 527 through 534 removed outlier: 3.591A pdb=" N VAL A 530 " --> pdb=" O ARG A 527 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N SER A 531 " --> pdb=" O HIS A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 555 Processing helix chain 'A' and resid 571 through 583 removed outlier: 3.782A pdb=" N ILE A 576 " --> pdb=" O ASP A 572 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLN A 579 " --> pdb=" O ASN A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 611 No H-bonds generated for 'chain 'A' and resid 609 through 611' Processing helix chain 'A' and resid 630 through 635 Processing helix chain 'A' and resid 638 through 643 removed outlier: 3.998A pdb=" N ARG A 643 " --> pdb=" O GLU A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 676 removed outlier: 3.661A pdb=" N LYS A 676 " --> pdb=" O GLN A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 694 removed outlier: 3.779A pdb=" N GLU A 692 " --> pdb=" O ASN A 688 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS A 693 " --> pdb=" O TRP A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 712 removed outlier: 3.570A pdb=" N ILE A 708 " --> pdb=" O ALA A 705 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP A 710 " --> pdb=" O VAL A 707 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU A 712 " --> pdb=" O GLN A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 721 removed outlier: 3.946A pdb=" N ASN A 718 " --> pdb=" O LYS A 714 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N GLU A 719 " --> pdb=" O PRO A 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 182 removed outlier: 3.766A pdb=" N ARG B 181 " --> pdb=" O GLN B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 202 Processing helix chain 'B' and resid 220 through 233 removed outlier: 4.111A pdb=" N ALA B 228 " --> pdb=" O ALA B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 254 No H-bonds generated for 'chain 'B' and resid 251 through 254' Processing helix chain 'B' and resid 262 through 275 Processing helix chain 'B' and resid 287 through 292 removed outlier: 3.973A pdb=" N GLY B 292 " --> pdb=" O THR B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 313 Processing helix chain 'B' and resid 324 through 329 Processing helix chain 'B' and resid 335 through 340 removed outlier: 4.141A pdb=" N ARG B 340 " --> pdb=" O ALA B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 369 Proline residue: B 363 - end of helix Processing helix chain 'B' and resid 375 through 388 Processing helix chain 'B' and resid 394 through 410 removed outlier: 3.553A pdb=" N VAL B 401 " --> pdb=" O LYS B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 434 removed outlier: 3.998A pdb=" N ILE B 433 " --> pdb=" O VAL B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 442 No H-bonds generated for 'chain 'B' and resid 440 through 442' Processing helix chain 'B' and resid 444 through 450 removed outlier: 3.533A pdb=" N LEU B 449 " --> pdb=" O ARG B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 457 Processing helix chain 'B' and resid 464 through 479 Processing helix chain 'B' and resid 501 through 512 removed outlier: 4.200A pdb=" N THR B 505 " --> pdb=" O LYS B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 523 No H-bonds generated for 'chain 'B' and resid 521 through 523' Processing helix chain 'B' and resid 527 through 534 Processing helix chain 'B' and resid 543 through 545 No H-bonds generated for 'chain 'B' and resid 543 through 545' Processing helix chain 'B' and resid 548 through 555 Processing helix chain 'B' and resid 571 through 583 removed outlier: 3.583A pdb=" N LEU B 578 " --> pdb=" O ASN B 575 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET B 581 " --> pdb=" O LEU B 578 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP B 582 " --> pdb=" O GLN B 579 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN B 583 " --> pdb=" O VAL B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 612 No H-bonds generated for 'chain 'B' and resid 610 through 612' Processing helix chain 'B' and resid 627 through 635 removed outlier: 3.503A pdb=" N ILE B 635 " --> pdb=" O GLU B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 643 removed outlier: 4.167A pdb=" N ARG B 643 " --> pdb=" O GLU B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 676 removed outlier: 4.189A pdb=" N LYS B 676 " --> pdb=" O GLN B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 684 through 694 Processing helix chain 'B' and resid 697 through 699 No H-bonds generated for 'chain 'B' and resid 697 through 699' Processing helix chain 'B' and resid 702 through 711 removed outlier: 3.526A pdb=" N ILE B 708 " --> pdb=" O ALA B 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 721 Processing helix chain 'C' and resid 176 through 182 Processing helix chain 'C' and resid 192 through 202 Processing helix chain 'C' and resid 220 through 232 removed outlier: 3.726A pdb=" N ALA C 228 " --> pdb=" O ALA C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 254 Processing helix chain 'C' and resid 262 through 277 Processing helix chain 'C' and resid 287 through 289 No H-bonds generated for 'chain 'C' and resid 287 through 289' Processing helix chain 'C' and resid 307 through 312 removed outlier: 3.770A pdb=" N SER C 312 " --> pdb=" O PRO C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 328 removed outlier: 3.672A pdb=" N SER C 328 " --> pdb=" O TYR C 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 324 through 328' Processing helix chain 'C' and resid 335 through 340 removed outlier: 3.893A pdb=" N ARG C 340 " --> pdb=" O ALA C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 369 Proline residue: C 363 - end of helix Processing helix chain 'C' and resid 375 through 388 Processing helix chain 'C' and resid 396 through 415 removed outlier: 3.543A pdb=" N LEU C 411 " --> pdb=" O ALA C 407 " (cutoff:3.500A) Proline residue: C 413 - end of helix Processing helix chain 'C' and resid 423 through 433 Processing helix chain 'C' and resid 440 through 442 No H-bonds generated for 'chain 'C' and resid 440 through 442' Processing helix chain 'C' and resid 444 through 450 removed outlier: 3.545A pdb=" N LEU C 449 " --> pdb=" O ARG C 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 458 removed outlier: 3.806A pdb=" N LYS C 457 " --> pdb=" O GLY C 453 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N MET C 458 " --> pdb=" O ASP C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 479 Processing helix chain 'C' and resid 503 through 512 Processing helix chain 'C' and resid 521 through 523 No H-bonds generated for 'chain 'C' and resid 521 through 523' Processing helix chain 'C' and resid 527 through 534 removed outlier: 3.677A pdb=" N SER C 531 " --> pdb=" O HIS C 528 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE C 534 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 555 Processing helix chain 'C' and resid 566 through 568 No H-bonds generated for 'chain 'C' and resid 566 through 568' Processing helix chain 'C' and resid 571 through 583 removed outlier: 3.669A pdb=" N GLN C 579 " --> pdb=" O ILE C 576 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET C 581 " --> pdb=" O LEU C 578 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP C 582 " --> pdb=" O GLN C 579 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASN C 583 " --> pdb=" O VAL C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 612 No H-bonds generated for 'chain 'C' and resid 609 through 612' Processing helix chain 'C' and resid 631 through 635 Processing helix chain 'C' and resid 638 through 643 removed outlier: 4.022A pdb=" N ARG C 643 " --> pdb=" O GLU C 639 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 676 removed outlier: 3.731A pdb=" N LYS C 676 " --> pdb=" O GLN C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 684 through 694 Processing helix chain 'C' and resid 697 through 699 No H-bonds generated for 'chain 'C' and resid 697 through 699' Processing helix chain 'C' and resid 702 through 711 removed outlier: 3.657A pdb=" N ILE C 708 " --> pdb=" O ALA C 705 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 721 Processing helix chain 'D' and resid 176 through 182 Processing helix chain 'D' and resid 192 through 202 Processing helix chain 'D' and resid 220 through 233 removed outlier: 3.549A pdb=" N GLU D 225 " --> pdb=" O ALA D 222 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU D 227 " --> pdb=" O ALA D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 240 No H-bonds generated for 'chain 'D' and resid 238 through 240' Processing helix chain 'D' and resid 250 through 253 No H-bonds generated for 'chain 'D' and resid 250 through 253' Processing helix chain 'D' and resid 262 through 277 Processing helix chain 'D' and resid 287 through 289 No H-bonds generated for 'chain 'D' and resid 287 through 289' Processing helix chain 'D' and resid 303 through 312 removed outlier: 3.641A pdb=" N ILE D 307 " --> pdb=" O ALA D 303 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) Proline residue: D 309 - end of helix Processing helix chain 'D' and resid 324 through 329 Processing helix chain 'D' and resid 331 through 333 No H-bonds generated for 'chain 'D' and resid 331 through 333' Processing helix chain 'D' and resid 335 through 340 removed outlier: 4.693A pdb=" N ARG D 340 " --> pdb=" O ALA D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 369 Proline residue: D 363 - end of helix Processing helix chain 'D' and resid 375 through 386 Processing helix chain 'D' and resid 396 through 410 removed outlier: 3.701A pdb=" N VAL D 401 " --> pdb=" O LYS D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 433 Processing helix chain 'D' and resid 444 through 450 removed outlier: 3.847A pdb=" N LEU D 449 " --> pdb=" O ARG D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 458 removed outlier: 3.919A pdb=" N MET D 458 " --> pdb=" O ASP D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 479 Processing helix chain 'D' and resid 502 through 512 Processing helix chain 'D' and resid 521 through 523 No H-bonds generated for 'chain 'D' and resid 521 through 523' Processing helix chain 'D' and resid 527 through 534 removed outlier: 3.502A pdb=" N VAL D 530 " --> pdb=" O ARG D 527 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER D 531 " --> pdb=" O HIS D 528 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE D 534 " --> pdb=" O SER D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 555 Processing helix chain 'D' and resid 566 through 568 No H-bonds generated for 'chain 'D' and resid 566 through 568' Processing helix chain 'D' and resid 571 through 583 Processing helix chain 'D' and resid 609 through 612 No H-bonds generated for 'chain 'D' and resid 609 through 612' Processing helix chain 'D' and resid 625 through 635 removed outlier: 3.750A pdb=" N GLU D 630 " --> pdb=" O THR D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 643 removed outlier: 4.190A pdb=" N ARG D 643 " --> pdb=" O GLU D 639 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 676 removed outlier: 3.899A pdb=" N LYS D 676 " --> pdb=" O GLN D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 684 through 694 Processing helix chain 'D' and resid 702 through 711 removed outlier: 3.641A pdb=" N ILE D 708 " --> pdb=" O ALA D 705 " (cutoff:3.500A) Processing helix chain 'D' and resid 713 through 722 Processing helix chain 'E' and resid 176 through 182 Processing helix chain 'E' and resid 192 through 202 Processing helix chain 'E' and resid 220 through 233 Processing helix chain 'E' and resid 250 through 256 removed outlier: 3.872A pdb=" N GLY E 256 " --> pdb=" O SER E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 262 through 276 Processing helix chain 'E' and resid 287 through 289 No H-bonds generated for 'chain 'E' and resid 287 through 289' Processing helix chain 'E' and resid 299 through 312 Proline residue: E 309 - end of helix Processing helix chain 'E' and resid 324 through 330 Processing helix chain 'E' and resid 335 through 338 No H-bonds generated for 'chain 'E' and resid 335 through 338' Processing helix chain 'E' and resid 351 through 369 Proline residue: E 363 - end of helix removed outlier: 3.613A pdb=" N HIS E 368 " --> pdb=" O LYS E 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 375 through 388 Processing helix chain 'E' and resid 394 through 409 Processing helix chain 'E' and resid 423 through 433 Processing helix chain 'E' and resid 446 through 450 Processing helix chain 'E' and resid 452 through 457 Processing helix chain 'E' and resid 464 through 478 Processing helix chain 'E' and resid 503 through 511 Processing helix chain 'E' and resid 521 through 523 No H-bonds generated for 'chain 'E' and resid 521 through 523' Processing helix chain 'E' and resid 530 through 533 No H-bonds generated for 'chain 'E' and resid 530 through 533' Processing helix chain 'E' and resid 548 through 555 Processing helix chain 'E' and resid 566 through 568 No H-bonds generated for 'chain 'E' and resid 566 through 568' Processing helix chain 'E' and resid 571 through 583 Processing helix chain 'E' and resid 607 through 609 No H-bonds generated for 'chain 'E' and resid 607 through 609' Processing helix chain 'E' and resid 630 through 633 No H-bonds generated for 'chain 'E' and resid 630 through 633' Processing helix chain 'E' and resid 638 through 643 removed outlier: 4.031A pdb=" N ARG E 643 " --> pdb=" O GLU E 639 " (cutoff:3.500A) Processing helix chain 'E' and resid 655 through 676 removed outlier: 3.535A pdb=" N GLN E 675 " --> pdb=" O VAL E 671 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS E 676 " --> pdb=" O GLN E 672 " (cutoff:3.500A) Processing helix chain 'E' and resid 684 through 693 Processing helix chain 'E' and resid 702 through 711 Processing helix chain 'E' and resid 713 through 722 Processing helix chain 'F' and resid 176 through 182 Processing helix chain 'F' and resid 192 through 202 Processing helix chain 'F' and resid 220 through 232 removed outlier: 3.654A pdb=" N ALA F 224 " --> pdb=" O LYS F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 254 Processing helix chain 'F' and resid 260 through 276 Processing helix chain 'F' and resid 287 through 289 No H-bonds generated for 'chain 'F' and resid 287 through 289' Processing helix chain 'F' and resid 303 through 313 Proline residue: F 309 - end of helix Processing helix chain 'F' and resid 324 through 330 removed outlier: 4.231A pdb=" N SER F 328 " --> pdb=" O TYR F 324 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASN F 329 " --> pdb=" O GLN F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 338 No H-bonds generated for 'chain 'F' and resid 335 through 338' Processing helix chain 'F' and resid 351 through 369 Proline residue: F 363 - end of helix Processing helix chain 'F' and resid 375 through 388 removed outlier: 4.536A pdb=" N LYS F 387 " --> pdb=" O GLU F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 411 removed outlier: 3.885A pdb=" N ILE F 399 " --> pdb=" O PRO F 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 423 through 434 removed outlier: 3.710A pdb=" N ILE F 433 " --> pdb=" O VAL F 429 " (cutoff:3.500A) Processing helix chain 'F' and resid 437 through 440 No H-bonds generated for 'chain 'F' and resid 437 through 440' Processing helix chain 'F' and resid 447 through 458 removed outlier: 3.797A pdb=" N GLY F 453 " --> pdb=" O LEU F 449 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ASP F 454 " --> pdb=" O LYS F 450 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET F 458 " --> pdb=" O ASP F 454 " (cutoff:3.500A) Processing helix chain 'F' and resid 464 through 478 Processing helix chain 'F' and resid 501 through 512 Processing helix chain 'F' and resid 521 through 523 No H-bonds generated for 'chain 'F' and resid 521 through 523' Processing helix chain 'F' and resid 527 through 534 removed outlier: 3.500A pdb=" N SER F 531 " --> pdb=" O ARG F 527 " (cutoff:3.500A) Processing helix chain 'F' and resid 548 through 555 Processing helix chain 'F' and resid 566 through 568 No H-bonds generated for 'chain 'F' and resid 566 through 568' Processing helix chain 'F' and resid 571 through 583 Processing helix chain 'F' and resid 611 through 613 No H-bonds generated for 'chain 'F' and resid 611 through 613' Processing helix chain 'F' and resid 628 through 635 Processing helix chain 'F' and resid 638 through 643 removed outlier: 3.613A pdb=" N ARG F 643 " --> pdb=" O GLU F 639 " (cutoff:3.500A) Processing helix chain 'F' and resid 655 through 676 Processing helix chain 'F' and resid 684 through 694 Processing helix chain 'F' and resid 702 through 711 removed outlier: 3.525A pdb=" N ALA F 705 " --> pdb=" O ARG F 702 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE F 708 " --> pdb=" O ALA F 705 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASP F 710 " --> pdb=" O VAL F 707 " (cutoff:3.500A) Processing helix chain 'F' and resid 714 through 722 removed outlier: 4.154A pdb=" N GLU F 719 " --> pdb=" O PRO F 715 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 40 removed outlier: 3.972A pdb=" N GLU G 40 " --> pdb=" O ARG G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 67 Processing helix chain 'G' and resid 84 through 96 removed outlier: 3.584A pdb=" N ILE G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 119 removed outlier: 3.589A pdb=" N ALA G 119 " --> pdb=" O PHE G 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 171 Processing helix chain 'G' and resid 175 through 182 Processing helix chain 'G' and resid 190 through 196 Processing helix chain 'H' and resid 33 through 40 removed outlier: 3.979A pdb=" N GLU H 40 " --> pdb=" O ARG H 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 67 Processing helix chain 'H' and resid 84 through 96 Processing helix chain 'H' and resid 111 through 119 removed outlier: 3.581A pdb=" N THR H 118 " --> pdb=" O PHE H 115 " (cutoff:3.500A) Processing helix chain 'H' and resid 146 through 171 Processing helix chain 'H' and resid 175 through 181 Processing helix chain 'H' and resid 190 through 196 Processing helix chain 'I' and resid 33 through 40 removed outlier: 3.747A pdb=" N GLU I 40 " --> pdb=" O ARG I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 51 through 67 Processing helix chain 'I' and resid 84 through 96 removed outlier: 3.753A pdb=" N SER I 89 " --> pdb=" O THR I 85 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ILE I 90 " --> pdb=" O ALA I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 112 through 119 removed outlier: 3.636A pdb=" N ALA I 119 " --> pdb=" O PHE I 115 " (cutoff:3.500A) Processing helix chain 'I' and resid 146 through 171 Processing helix chain 'I' and resid 175 through 182 Processing helix chain 'I' and resid 190 through 196 Processing helix chain 'J' and resid 33 through 40 removed outlier: 3.999A pdb=" N GLU J 40 " --> pdb=" O ARG J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 53 through 67 removed outlier: 5.338A pdb=" N ILE J 57 " --> pdb=" O ALA J 54 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL J 58 " --> pdb=" O ASN J 55 " (cutoff:3.500A) Processing helix chain 'J' and resid 84 through 96 removed outlier: 3.596A pdb=" N ILE J 90 " --> pdb=" O ALA J 86 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 119 removed outlier: 3.682A pdb=" N THR J 118 " --> pdb=" O PHE J 115 " (cutoff:3.500A) Processing helix chain 'J' and resid 146 through 171 Processing helix chain 'J' and resid 175 through 181 Processing helix chain 'J' and resid 190 through 196 Processing helix chain 'K' and resid 33 through 40 removed outlier: 3.958A pdb=" N GLU K 40 " --> pdb=" O ARG K 36 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 67 Processing helix chain 'K' and resid 84 through 96 removed outlier: 3.791A pdb=" N SER K 89 " --> pdb=" O THR K 85 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE K 90 " --> pdb=" O ALA K 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 119 Processing helix chain 'K' and resid 146 through 171 removed outlier: 3.518A pdb=" N ILE K 151 " --> pdb=" O THR K 147 " (cutoff:3.500A) Processing helix chain 'K' and resid 175 through 182 Processing helix chain 'K' and resid 190 through 196 Processing helix chain 'L' and resid 34 through 40 removed outlier: 3.964A pdb=" N GLU L 40 " --> pdb=" O ARG L 36 " (cutoff:3.500A) Processing helix chain 'L' and resid 51 through 67 Processing helix chain 'L' and resid 84 through 96 removed outlier: 3.621A pdb=" N ILE L 90 " --> pdb=" O ALA L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 112 through 119 removed outlier: 3.711A pdb=" N ALA L 119 " --> pdb=" O PHE L 115 " (cutoff:3.500A) Processing helix chain 'L' and resid 146 through 171 Processing helix chain 'L' and resid 175 through 182 Processing helix chain 'L' and resid 190 through 196 Processing helix chain 'M' and resid 33 through 40 removed outlier: 3.975A pdb=" N GLU M 40 " --> pdb=" O ARG M 36 " (cutoff:3.500A) Processing helix chain 'M' and resid 51 through 67 Processing helix chain 'M' and resid 84 through 96 removed outlier: 3.592A pdb=" N ILE M 90 " --> pdb=" O ALA M 86 " (cutoff:3.500A) Processing helix chain 'M' and resid 111 through 119 Processing helix chain 'M' and resid 146 through 171 Processing helix chain 'M' and resid 175 through 182 Processing helix chain 'M' and resid 190 through 196 Processing helix chain 'N' and resid 33 through 40 removed outlier: 3.940A pdb=" N GLU N 40 " --> pdb=" O ARG N 36 " (cutoff:3.500A) Processing helix chain 'N' and resid 51 through 67 removed outlier: 3.534A pdb=" N LEU N 56 " --> pdb=" O HIS N 52 " (cutoff:3.500A) Processing helix chain 'N' and resid 85 through 96 Processing helix chain 'N' and resid 112 through 119 removed outlier: 3.601A pdb=" N ALA N 119 " --> pdb=" O PHE N 115 " (cutoff:3.500A) Processing helix chain 'N' and resid 146 through 171 Processing helix chain 'N' and resid 175 through 182 Processing helix chain 'N' and resid 190 through 196 Processing helix chain 'O' and resid 33 through 40 removed outlier: 3.914A pdb=" N GLU O 40 " --> pdb=" O ARG O 36 " (cutoff:3.500A) Processing helix chain 'O' and resid 51 through 67 Processing helix chain 'O' and resid 84 through 96 removed outlier: 3.546A pdb=" N ILE O 90 " --> pdb=" O ALA O 86 " (cutoff:3.500A) Processing helix chain 'O' and resid 112 through 119 removed outlier: 3.623A pdb=" N ALA O 119 " --> pdb=" O PHE O 115 " (cutoff:3.500A) Processing helix chain 'O' and resid 146 through 171 Processing helix chain 'O' and resid 175 through 182 Processing helix chain 'O' and resid 190 through 196 Processing helix chain 'P' and resid 33 through 40 removed outlier: 3.927A pdb=" N GLU P 40 " --> pdb=" O ARG P 36 " (cutoff:3.500A) Processing helix chain 'P' and resid 51 through 67 Processing helix chain 'P' and resid 84 through 96 removed outlier: 3.534A pdb=" N ILE P 90 " --> pdb=" O ALA P 86 " (cutoff:3.500A) Processing helix chain 'P' and resid 111 through 119 Processing helix chain 'P' and resid 146 through 171 Processing helix chain 'P' and resid 175 through 182 Processing helix chain 'P' and resid 190 through 196 Processing helix chain 'Q' and resid 33 through 40 removed outlier: 3.901A pdb=" N GLU Q 40 " --> pdb=" O ARG Q 36 " (cutoff:3.500A) Processing helix chain 'Q' and resid 51 through 67 Processing helix chain 'Q' and resid 85 through 96 Processing helix chain 'Q' and resid 112 through 119 removed outlier: 3.516A pdb=" N ALA Q 119 " --> pdb=" O PHE Q 115 " (cutoff:3.500A) Processing helix chain 'Q' and resid 146 through 171 removed outlier: 3.848A pdb=" N LEU Q 157 " --> pdb=" O ALA Q 153 " (cutoff:3.500A) Processing helix chain 'Q' and resid 175 through 181 Processing helix chain 'Q' and resid 190 through 196 Processing helix chain 'R' and resid 33 through 40 removed outlier: 3.892A pdb=" N GLU R 40 " --> pdb=" O ARG R 36 " (cutoff:3.500A) Processing helix chain 'R' and resid 51 through 67 Processing helix chain 'R' and resid 84 through 96 removed outlier: 3.863A pdb=" N SER R 89 " --> pdb=" O THR R 85 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE R 90 " --> pdb=" O ALA R 86 " (cutoff:3.500A) Processing helix chain 'R' and resid 111 through 119 removed outlier: 3.649A pdb=" N THR R 118 " --> pdb=" O PHE R 115 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 171 Processing helix chain 'R' and resid 175 through 182 Processing helix chain 'R' and resid 190 through 196 Processing helix chain 'S' and resid 33 through 40 removed outlier: 3.920A pdb=" N GLU S 40 " --> pdb=" O ARG S 36 " (cutoff:3.500A) Processing helix chain 'S' and resid 51 through 67 Processing helix chain 'S' and resid 84 through 96 removed outlier: 3.848A pdb=" N ILE S 90 " --> pdb=" O ALA S 86 " (cutoff:3.500A) Processing helix chain 'S' and resid 111 through 119 Processing helix chain 'S' and resid 146 through 171 removed outlier: 3.507A pdb=" N ILE S 151 " --> pdb=" O THR S 147 " (cutoff:3.500A) Processing helix chain 'S' and resid 175 through 182 Processing helix chain 'S' and resid 190 through 196 Processing helix chain 'T' and resid 33 through 40 removed outlier: 3.906A pdb=" N GLU T 40 " --> pdb=" O ARG T 36 " (cutoff:3.500A) Processing helix chain 'T' and resid 51 through 67 Processing helix chain 'T' and resid 84 through 96 removed outlier: 3.757A pdb=" N ILE T 90 " --> pdb=" O ALA T 86 " (cutoff:3.500A) Processing helix chain 'T' and resid 112 through 119 removed outlier: 3.615A pdb=" N ALA T 119 " --> pdb=" O PHE T 115 " (cutoff:3.500A) Processing helix chain 'T' and resid 146 through 171 Processing helix chain 'T' and resid 175 through 181 Processing helix chain 'T' and resid 190 through 196 Processing sheet with id= A, first strand: chain 'A' and resid 173 through 175 removed outlier: 6.477A pdb=" N ARG A 317 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N ILE A 284 " --> pdb=" O ARG A 317 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ILE A 319 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N GLN A 342 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL A 213 " --> pdb=" O GLN A 342 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ILE A 344 " --> pdb=" O VAL A 213 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 646 through 649 removed outlier: 3.676A pdb=" N ASN A 646 " --> pdb=" O SER A 490 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY A 489 " --> pdb=" O VAL A 599 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ALA A 559 " --> pdb=" O VAL A 600 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N VAL A 602 " --> pdb=" O ALA A 559 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU A 561 " --> pdb=" O VAL A 602 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N THR A 604 " --> pdb=" O LEU A 561 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N LEU A 563 " --> pdb=" O THR A 604 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLU A 515 " --> pdb=" O VAL A 560 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N LEU A 562 " --> pdb=" O GLU A 515 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU A 517 " --> pdb=" O LEU A 562 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ASP A 564 " --> pdb=" O LEU A 517 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N PHE A 519 " --> pdb=" O ASP A 564 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 585 through 587 Processing sheet with id= D, first strand: chain 'A' and resid 678 through 682 removed outlier: 6.752A pdb=" N GLY A 729 " --> pdb=" O SER A 679 " (cutoff:3.500A) removed outlier: 8.882A pdb=" N GLU A 681 " --> pdb=" O GLY A 729 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL A 731 " --> pdb=" O GLU A 681 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 734 through 736 Processing sheet with id= F, first strand: chain 'B' and resid 173 through 175 Processing sheet with id= G, first strand: chain 'B' and resid 342 through 346 removed outlier: 6.610A pdb=" N GLY B 320 " --> pdb=" O LEU B 212 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N GLY B 214 " --> pdb=" O GLY B 320 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N THR B 322 " --> pdb=" O GLY B 214 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 646 through 650 removed outlier: 3.558A pdb=" N ASN B 646 " --> pdb=" O SER B 490 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY B 489 " --> pdb=" O VAL B 599 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ALA B 559 " --> pdb=" O VAL B 600 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N VAL B 602 " --> pdb=" O ALA B 559 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU B 561 " --> pdb=" O VAL B 602 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N THR B 604 " --> pdb=" O LEU B 561 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N LEU B 563 " --> pdb=" O THR B 604 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLU B 515 " --> pdb=" O VAL B 560 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N LEU B 562 " --> pdb=" O GLU B 515 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LEU B 517 " --> pdb=" O LEU B 562 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N ASP B 564 " --> pdb=" O LEU B 517 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N PHE B 519 " --> pdb=" O ASP B 564 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 585 through 587 Processing sheet with id= J, first strand: chain 'B' and resid 679 through 682 removed outlier: 3.715A pdb=" N ALA B 734 " --> pdb=" O THR B 743 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 173 through 175 removed outlier: 3.612A pdb=" N SER C 321 " --> pdb=" O ILE C 284 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N GLN C 342 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N VAL C 213 " --> pdb=" O GLN C 342 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ILE C 344 " --> pdb=" O VAL C 213 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 646 through 649 removed outlier: 3.766A pdb=" N ASN C 646 " --> pdb=" O SER C 490 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLY C 489 " --> pdb=" O VAL C 599 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ALA C 559 " --> pdb=" O VAL C 600 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N VAL C 602 " --> pdb=" O ALA C 559 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LEU C 561 " --> pdb=" O VAL C 602 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N THR C 604 " --> pdb=" O LEU C 561 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LEU C 563 " --> pdb=" O THR C 604 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N GLU C 515 " --> pdb=" O VAL C 560 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N LEU C 562 " --> pdb=" O GLU C 515 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU C 517 " --> pdb=" O LEU C 562 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ASP C 564 " --> pdb=" O LEU C 517 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N PHE C 519 " --> pdb=" O ASP C 564 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 585 through 587 Processing sheet with id= N, first strand: chain 'C' and resid 680 through 682 removed outlier: 6.505A pdb=" N VAL C 731 " --> pdb=" O GLU C 681 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'D' and resid 173 through 175 removed outlier: 6.775A pdb=" N ARG D 317 " --> pdb=" O LEU D 282 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 342 through 346 removed outlier: 6.775A pdb=" N GLY D 320 " --> pdb=" O LEU D 212 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N GLY D 214 " --> pdb=" O GLY D 320 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N THR D 322 " --> pdb=" O GLY D 214 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 646 through 649 removed outlier: 4.028A pdb=" N ASN D 646 " --> pdb=" O SER D 490 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLY D 489 " --> pdb=" O VAL D 599 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ALA D 559 " --> pdb=" O VAL D 600 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N VAL D 602 " --> pdb=" O ALA D 559 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N LEU D 561 " --> pdb=" O VAL D 602 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N THR D 604 " --> pdb=" O LEU D 561 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU D 563 " --> pdb=" O THR D 604 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N GLU D 515 " --> pdb=" O VAL D 560 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N LEU D 562 " --> pdb=" O GLU D 515 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU D 517 " --> pdb=" O LEU D 562 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ASP D 564 " --> pdb=" O LEU D 517 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N PHE D 519 " --> pdb=" O ASP D 564 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 585 through 587 Processing sheet with id= S, first strand: chain 'E' and resid 173 through 175 removed outlier: 6.566A pdb=" N ARG E 317 " --> pdb=" O LEU E 282 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N ILE E 284 " --> pdb=" O ARG E 317 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE E 319 " --> pdb=" O ILE E 284 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 646 through 650 removed outlier: 4.151A pdb=" N GLY E 489 " --> pdb=" O VAL E 599 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLY E 495 " --> pdb=" O THR E 605 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ALA E 559 " --> pdb=" O VAL E 600 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N VAL E 602 " --> pdb=" O ALA E 559 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LEU E 561 " --> pdb=" O VAL E 602 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N THR E 604 " --> pdb=" O LEU E 561 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LEU E 563 " --> pdb=" O THR E 604 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 585 through 587 Processing sheet with id= V, first strand: chain 'E' and resid 678 through 682 removed outlier: 6.819A pdb=" N GLY E 729 " --> pdb=" O SER E 679 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N GLU E 681 " --> pdb=" O GLY E 729 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL E 731 " --> pdb=" O GLU E 681 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 173 through 175 removed outlier: 3.717A pdb=" N ILE F 281 " --> pdb=" O THR F 244 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ARG F 317 " --> pdb=" O LEU F 282 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 341 through 345 removed outlier: 6.853A pdb=" N ASN F 209 " --> pdb=" O GLN F 342 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N ILE F 344 " --> pdb=" O ASN F 209 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU F 211 " --> pdb=" O ILE F 344 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N GLY F 320 " --> pdb=" O LEU F 212 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N GLY F 214 " --> pdb=" O GLY F 320 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N THR F 322 " --> pdb=" O GLY F 214 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'F' and resid 646 through 650 removed outlier: 3.518A pdb=" N ASN F 646 " --> pdb=" O SER F 490 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR F 605 " --> pdb=" O PHE F 493 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY F 495 " --> pdb=" O THR F 605 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'F' and resid 585 through 587 Processing sheet with id= AA, first strand: chain 'F' and resid 678 through 682 removed outlier: 6.753A pdb=" N GLY F 729 " --> pdb=" O SER F 679 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N GLU F 681 " --> pdb=" O GLY F 729 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL F 731 " --> pdb=" O GLU F 681 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'G' and resid 19 through 21 Processing sheet with id= AC, first strand: chain 'G' and resid 42 through 46 removed outlier: 6.436A pdb=" N TYR G 74 " --> pdb=" O ILE G 43 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N LEU G 45 " --> pdb=" O TYR G 74 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TYR G 76 " --> pdb=" O LEU G 45 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'G' and resid 108 through 110 removed outlier: 6.757A pdb=" N ARG G 132 " --> pdb=" O ALA G 109 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'G' and resid 126 through 128 removed outlier: 6.621A pdb=" N SER G 201 " --> pdb=" O CYS G 127 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain 'H' and resid 19 through 21 Processing sheet with id= AG, first strand: chain 'H' and resid 42 through 46 removed outlier: 6.352A pdb=" N TYR H 74 " --> pdb=" O ILE H 43 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N LEU H 45 " --> pdb=" O TYR H 74 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N TYR H 76 " --> pdb=" O LEU H 45 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'H' and resid 108 through 110 removed outlier: 6.842A pdb=" N ARG H 132 " --> pdb=" O ALA H 109 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'H' and resid 126 through 128 removed outlier: 6.638A pdb=" N SER H 201 " --> pdb=" O CYS H 127 " (cutoff:3.500A) No H-bonds generated for sheet with id= AI Processing sheet with id= AJ, first strand: chain 'I' and resid 19 through 21 Processing sheet with id= AK, first strand: chain 'I' and resid 42 through 46 removed outlier: 6.443A pdb=" N TYR I 74 " --> pdb=" O ILE I 43 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N LEU I 45 " --> pdb=" O TYR I 74 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N TYR I 76 " --> pdb=" O LEU I 45 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'I' and resid 108 through 110 removed outlier: 6.794A pdb=" N ARG I 132 " --> pdb=" O ALA I 109 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'I' and resid 126 through 128 removed outlier: 6.578A pdb=" N SER I 201 " --> pdb=" O CYS I 127 " (cutoff:3.500A) No H-bonds generated for sheet with id= AM Processing sheet with id= AN, first strand: chain 'J' and resid 19 through 22 removed outlier: 4.110A pdb=" N ARG J 29 " --> pdb=" O GLU J 22 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'J' and resid 42 through 46 removed outlier: 6.302A pdb=" N TYR J 74 " --> pdb=" O ILE J 43 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N LEU J 45 " --> pdb=" O TYR J 74 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N TYR J 76 " --> pdb=" O LEU J 45 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'J' and resid 108 through 110 removed outlier: 6.843A pdb=" N ARG J 132 " --> pdb=" O ALA J 109 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'J' and resid 126 through 128 removed outlier: 6.613A pdb=" N SER J 201 " --> pdb=" O CYS J 127 " (cutoff:3.500A) No H-bonds generated for sheet with id= AQ Processing sheet with id= AR, first strand: chain 'K' and resid 19 through 21 Processing sheet with id= AS, first strand: chain 'K' and resid 42 through 46 removed outlier: 6.338A pdb=" N TYR K 74 " --> pdb=" O ILE K 43 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N LEU K 45 " --> pdb=" O TYR K 74 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N TYR K 76 " --> pdb=" O LEU K 45 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'K' and resid 108 through 110 removed outlier: 6.873A pdb=" N ARG K 132 " --> pdb=" O ALA K 109 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'K' and resid 126 through 128 removed outlier: 6.597A pdb=" N SER K 201 " --> pdb=" O CYS K 127 " (cutoff:3.500A) No H-bonds generated for sheet with id= AU Processing sheet with id= AV, first strand: chain 'L' and resid 42 through 46 removed outlier: 6.413A pdb=" N TYR L 74 " --> pdb=" O ILE L 43 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N LEU L 45 " --> pdb=" O TYR L 74 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N TYR L 76 " --> pdb=" O LEU L 45 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'L' and resid 108 through 110 removed outlier: 6.815A pdb=" N ARG L 132 " --> pdb=" O ALA L 109 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'L' and resid 126 through 128 removed outlier: 6.613A pdb=" N SER L 201 " --> pdb=" O CYS L 127 " (cutoff:3.500A) No H-bonds generated for sheet with id= AX Processing sheet with id= AY, first strand: chain 'M' and resid 42 through 46 removed outlier: 6.451A pdb=" N TYR M 74 " --> pdb=" O ILE M 43 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N LEU M 45 " --> pdb=" O TYR M 74 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N TYR M 76 " --> pdb=" O LEU M 45 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'M' and resid 108 through 110 removed outlier: 6.760A pdb=" N ARG M 132 " --> pdb=" O ALA M 109 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'M' and resid 126 through 128 removed outlier: 6.595A pdb=" N SER M 201 " --> pdb=" O CYS M 127 " (cutoff:3.500A) No H-bonds generated for sheet with id= BA Processing sheet with id= BB, first strand: chain 'N' and resid 19 through 22 removed outlier: 4.014A pdb=" N ARG N 29 " --> pdb=" O GLU N 22 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'N' and resid 42 through 46 removed outlier: 6.423A pdb=" N TYR N 74 " --> pdb=" O ILE N 43 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N LEU N 45 " --> pdb=" O TYR N 74 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N TYR N 76 " --> pdb=" O LEU N 45 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'N' and resid 108 through 110 removed outlier: 6.800A pdb=" N ARG N 132 " --> pdb=" O ALA N 109 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'N' and resid 126 through 128 removed outlier: 6.648A pdb=" N SER N 201 " --> pdb=" O CYS N 127 " (cutoff:3.500A) No H-bonds generated for sheet with id= BE Processing sheet with id= BF, first strand: chain 'O' and resid 19 through 21 Processing sheet with id= BG, first strand: chain 'O' and resid 42 through 46 removed outlier: 6.444A pdb=" N TYR O 74 " --> pdb=" O ILE O 43 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N LEU O 45 " --> pdb=" O TYR O 74 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N TYR O 76 " --> pdb=" O LEU O 45 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'O' and resid 108 through 110 removed outlier: 6.747A pdb=" N ARG O 132 " --> pdb=" O ALA O 109 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'O' and resid 126 through 128 removed outlier: 6.607A pdb=" N SER O 201 " --> pdb=" O CYS O 127 " (cutoff:3.500A) No H-bonds generated for sheet with id= BI Processing sheet with id= BJ, first strand: chain 'P' and resid 19 through 21 Processing sheet with id= BK, first strand: chain 'P' and resid 42 through 46 removed outlier: 6.460A pdb=" N TYR P 74 " --> pdb=" O ILE P 43 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N LEU P 45 " --> pdb=" O TYR P 74 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N TYR P 76 " --> pdb=" O LEU P 45 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'P' and resid 108 through 110 removed outlier: 6.788A pdb=" N ARG P 132 " --> pdb=" O ALA P 109 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'P' and resid 126 through 128 removed outlier: 6.665A pdb=" N SER P 201 " --> pdb=" O CYS P 127 " (cutoff:3.500A) No H-bonds generated for sheet with id= BM Processing sheet with id= BN, first strand: chain 'Q' and resid 19 through 21 Processing sheet with id= BO, first strand: chain 'Q' and resid 42 through 46 removed outlier: 6.397A pdb=" N TYR Q 74 " --> pdb=" O ILE Q 43 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N LEU Q 45 " --> pdb=" O TYR Q 74 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N TYR Q 76 " --> pdb=" O LEU Q 45 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'Q' and resid 108 through 110 removed outlier: 6.838A pdb=" N ARG Q 132 " --> pdb=" O ALA Q 109 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'Q' and resid 126 through 128 removed outlier: 6.595A pdb=" N SER Q 201 " --> pdb=" O CYS Q 127 " (cutoff:3.500A) No H-bonds generated for sheet with id= BQ Processing sheet with id= BR, first strand: chain 'R' and resid 19 through 22 removed outlier: 4.096A pdb=" N ARG R 29 " --> pdb=" O GLU R 22 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'R' and resid 42 through 46 removed outlier: 6.382A pdb=" N TYR R 74 " --> pdb=" O ILE R 43 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N LEU R 45 " --> pdb=" O TYR R 74 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N TYR R 76 " --> pdb=" O LEU R 45 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain 'R' and resid 108 through 110 removed outlier: 6.843A pdb=" N ARG R 132 " --> pdb=" O ALA R 109 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'R' and resid 126 through 128 removed outlier: 6.588A pdb=" N SER R 201 " --> pdb=" O CYS R 127 " (cutoff:3.500A) No H-bonds generated for sheet with id= BU Processing sheet with id= BV, first strand: chain 'S' and resid 19 through 21 Processing sheet with id= BW, first strand: chain 'S' and resid 42 through 46 removed outlier: 6.400A pdb=" N TYR S 74 " --> pdb=" O ILE S 43 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N LEU S 45 " --> pdb=" O TYR S 74 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N TYR S 76 " --> pdb=" O LEU S 45 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 'S' and resid 108 through 110 removed outlier: 6.787A pdb=" N ARG S 132 " --> pdb=" O ALA S 109 " (cutoff:3.500A) Processing sheet with id= BY, first strand: chain 'S' and resid 126 through 128 removed outlier: 6.639A pdb=" N SER S 201 " --> pdb=" O CYS S 127 " (cutoff:3.500A) No H-bonds generated for sheet with id= BY Processing sheet with id= BZ, first strand: chain 'T' and resid 19 through 21 Processing sheet with id= CA, first strand: chain 'T' and resid 42 through 46 removed outlier: 6.397A pdb=" N TYR T 74 " --> pdb=" O ILE T 43 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N LEU T 45 " --> pdb=" O TYR T 74 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N TYR T 76 " --> pdb=" O LEU T 45 " (cutoff:3.500A) Processing sheet with id= CB, first strand: chain 'T' and resid 108 through 110 removed outlier: 6.808A pdb=" N ARG T 132 " --> pdb=" O ALA T 109 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain 'T' and resid 126 through 128 removed outlier: 6.616A pdb=" N SER T 201 " --> pdb=" O CYS T 127 " (cutoff:3.500A) No H-bonds generated for sheet with id= CC 1991 hydrogen bonds defined for protein. 5454 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 22.69 Time building geometry restraints manager: 19.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 11030 1.32 - 1.45: 14983 1.45 - 1.59: 22724 1.59 - 1.73: 154 1.73 - 1.87: 385 Bond restraints: 49276 Sorted by residual: bond pdb=" C3' AGS D 802 " pdb=" C4' AGS D 802 " ideal model delta sigma weight residual 1.526 1.361 0.165 1.10e-02 8.26e+03 2.25e+02 bond pdb=" C3' AGS C 801 " pdb=" C4' AGS C 801 " ideal model delta sigma weight residual 1.526 1.362 0.164 1.10e-02 8.26e+03 2.23e+02 bond pdb=" C3' AGS B 802 " pdb=" C4' AGS B 802 " ideal model delta sigma weight residual 1.526 1.362 0.164 1.10e-02 8.26e+03 2.21e+02 bond pdb=" C3' AGS B 801 " pdb=" C4' AGS B 801 " ideal model delta sigma weight residual 1.526 1.365 0.161 1.10e-02 8.26e+03 2.14e+02 bond pdb=" C3' AGS E 802 " pdb=" C4' AGS E 802 " ideal model delta sigma weight residual 1.526 1.366 0.160 1.10e-02 8.26e+03 2.11e+02 ... (remaining 49271 not shown) Histogram of bond angle deviations from ideal: 94.63 - 103.35: 608 103.35 - 112.07: 22876 112.07 - 120.79: 29065 120.79 - 129.51: 13770 129.51 - 138.23: 236 Bond angle restraints: 66555 Sorted by residual: angle pdb=" C5 AGS C 802 " pdb=" N7 AGS C 802 " pdb=" C8 AGS C 802 " ideal model delta sigma weight residual 103.67 109.27 -5.60 4.26e-01 5.51e+00 1.73e+02 angle pdb=" C5 AGS B 802 " pdb=" N7 AGS B 802 " pdb=" C8 AGS B 802 " ideal model delta sigma weight residual 103.67 109.03 -5.36 4.26e-01 5.51e+00 1.58e+02 angle pdb=" N VAL B 414 " pdb=" CA VAL B 414 " pdb=" C VAL B 414 " ideal model delta sigma weight residual 113.53 101.41 12.12 9.80e-01 1.04e+00 1.53e+02 angle pdb=" C5 AGS E 802 " pdb=" N7 AGS E 802 " pdb=" C8 AGS E 802 " ideal model delta sigma weight residual 103.67 108.90 -5.23 4.26e-01 5.51e+00 1.51e+02 angle pdb=" C5 AGS D 801 " pdb=" N7 AGS D 801 " pdb=" C8 AGS D 801 " ideal model delta sigma weight residual 103.67 108.73 -5.06 4.26e-01 5.51e+00 1.41e+02 ... (remaining 66550 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.91: 29726 34.91 - 69.82: 372 69.82 - 104.72: 37 104.72 - 139.63: 19 139.63 - 174.54: 5 Dihedral angle restraints: 30159 sinusoidal: 12463 harmonic: 17696 Sorted by residual: dihedral pdb=" C2' ADP A 801 " pdb=" C1' ADP A 801 " pdb=" N9 ADP A 801 " pdb=" C4 ADP A 801 " ideal model delta sinusoidal sigma weight residual 91.55 -82.99 174.54 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C5' ADP A 801 " pdb=" O5' ADP A 801 " pdb=" PA ADP A 801 " pdb=" O2A ADP A 801 " ideal model delta sinusoidal sigma weight residual 300.00 133.98 166.02 1 2.00e+01 2.50e-03 4.73e+01 dihedral pdb=" O1B ADP E 801 " pdb=" O3A ADP E 801 " pdb=" PB ADP E 801 " pdb=" PA ADP E 801 " ideal model delta sinusoidal sigma weight residual 300.00 153.98 146.01 1 2.00e+01 2.50e-03 4.39e+01 ... (remaining 30156 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.069: 7587 1.069 - 2.139: 0 2.139 - 3.208: 0 3.208 - 4.277: 0 4.277 - 5.347: 27 Chirality restraints: 7614 Sorted by residual: chirality pdb=" C3' ADP A 801 " pdb=" C2' ADP A 801 " pdb=" C4' ADP A 801 " pdb=" O3' ADP A 801 " both_signs ideal model delta sigma weight residual False -2.51 2.84 -5.35 2.00e-01 2.50e+01 7.15e+02 chirality pdb=" C3' ADP F 802 " pdb=" C2' ADP F 802 " pdb=" C4' ADP F 802 " pdb=" O3' ADP F 802 " both_signs ideal model delta sigma weight residual False -2.51 2.80 -5.31 2.00e-01 2.50e+01 7.04e+02 chirality pdb=" C3' ADP F 801 " pdb=" C2' ADP F 801 " pdb=" C4' ADP F 801 " pdb=" O3' ADP F 801 " both_signs ideal model delta sigma weight residual False -2.51 2.72 -5.23 2.00e-01 2.50e+01 6.84e+02 ... (remaining 7611 not shown) Planarity restraints: 8616 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE D 746 " -0.038 2.00e-02 2.50e+03 7.60e-02 5.77e+01 pdb=" C PHE D 746 " 0.131 2.00e-02 2.50e+03 pdb=" O PHE D 746 " -0.047 2.00e-02 2.50e+03 pdb=" OXT PHE D 746 " -0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG I 206 " -0.034 2.00e-02 2.50e+03 6.85e-02 4.69e+01 pdb=" C ARG I 206 " 0.118 2.00e-02 2.50e+03 pdb=" O ARG I 206 " -0.043 2.00e-02 2.50e+03 pdb=" OXT ARG I 206 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG Q 206 " 0.033 2.00e-02 2.50e+03 6.62e-02 4.39e+01 pdb=" C ARG Q 206 " -0.115 2.00e-02 2.50e+03 pdb=" O ARG Q 206 " 0.041 2.00e-02 2.50e+03 pdb=" OXT ARG Q 206 " 0.041 2.00e-02 2.50e+03 ... (remaining 8613 not shown) Histogram of nonbonded interaction distances: 1.21 - 1.95: 36 1.95 - 2.69: 4509 2.69 - 3.43: 68367 3.43 - 4.16: 120679 4.16 - 4.90: 209800 Nonbonded interactions: 403391 Sorted by model distance: nonbonded pdb=" O GLU F 215 " pdb=" O2B ADP F 801 " model vdw 1.215 3.040 nonbonded pdb=" OG1 THR E 221 " pdb=" O2A ADP E 801 " model vdw 1.249 2.440 nonbonded pdb=" O GLY D 294 " pdb=" OD1 ASP D 302 " model vdw 1.255 3.040 nonbonded pdb=" O GLY A 694 " pdb=" O GLY A 700 " model vdw 1.364 3.040 nonbonded pdb=" CB ALA C 293 " pdb=" OD2 ASP C 302 " model vdw 1.382 3.460 ... (remaining 403386 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 169 through 746) selection = (chain 'B' and resid 169 through 746) selection = (chain 'C' and resid 169 through 746) selection = (chain 'D' and resid 169 through 746) selection = (chain 'E' and resid 169 through 746) selection = (chain 'F' and resid 169 through 746) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } ncs_group { reference = chain 'X' selection = chain 'Y' } 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: 25.080 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: 0.000 Extract box with map and model: 49.090 Check model and map are aligned: 0.870 Set scattering table: 0.480 Process input model: 125.970 Find NCS groups from input model: 4.170 Set up NCS constraints: 0.660 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:3.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 209.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5511 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 : 0.024 0.215 49276 Z= 1.616 Angle : 1.783 20.753 66555 Z= 1.217 Chirality : 0.318 5.347 7614 Planarity : 0.009 0.088 8616 Dihedral : 12.243 174.538 18759 Min Nonbonded Distance : 1.215 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.64 % Allowed : 3.29 % Favored : 96.08 % Rotamer: Outliers : 0.48 % Allowed : 1.10 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.30 % 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: -0.41 (0.10), residues: 6116 helix: -0.53 (0.08), residues: 3050 sheet: 1.21 (0.16), residues: 960 loop : -0.32 (0.13), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.006 TRP B 689 HIS 0.008 0.002 HIS H 152 PHE 0.035 0.004 PHE E 746 TYR 0.067 0.007 TYR B 695 ARG 0.009 0.001 ARG A 641 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12232 Ramachandran restraints generated. 6116 Oldfield, 0 Emsley, 6116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12232 Ramachandran restraints generated. 6116 Oldfield, 0 Emsley, 6116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 817 residues out of total 5178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 792 time to evaluate : 5.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 24 THR cc_start: 0.7673 (p) cc_final: 0.7235 (p) REVERT: I 100 ASP cc_start: 0.8671 (m-30) cc_final: 0.8375 (m-30) REVERT: K 200 ASP cc_start: 0.8360 (m-30) cc_final: 0.8143 (m-30) REVERT: L 23 GLN cc_start: 0.8061 (mm-40) cc_final: 0.7782 (mm-40) REVERT: L 85 THR cc_start: 0.8826 (m) cc_final: 0.8447 (p) REVERT: L 112 MET cc_start: 0.8822 (tpt) cc_final: 0.8526 (tpt) REVERT: M 85 THR cc_start: 0.8923 (m) cc_final: 0.8616 (p) REVERT: M 88 MET cc_start: 0.8654 (mmm) cc_final: 0.8369 (mmt) REVERT: O 39 LYS cc_start: 0.9041 (tttt) cc_final: 0.8511 (mttt) REVERT: Q 200 ASP cc_start: 0.8528 (m-30) cc_final: 0.8186 (m-30) REVERT: R 167 MET cc_start: 0.8921 (mmm) cc_final: 0.8574 (mmt) REVERT: T 71 LYS cc_start: 0.8580 (mtpt) cc_final: 0.8378 (mtpp) outliers start: 25 outliers final: 9 residues processed: 806 average time/residue: 0.7019 time to fit residues: 873.7707 Evaluate side-chains 453 residues out of total 5178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 444 time to evaluate : 5.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 491 PHE Chi-restraints excluded: chain A residue 699 MET Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain I residue 126 PHE Chi-restraints excluded: chain K residue 126 PHE Chi-restraints excluded: chain L residue 126 PHE Chi-restraints excluded: chain Q residue 126 PHE Chi-restraints excluded: chain S residue 126 PHE Chi-restraints excluded: chain T residue 126 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 513 optimal weight: 1.9990 chunk 460 optimal weight: 0.6980 chunk 255 optimal weight: 5.9990 chunk 157 optimal weight: 0.7980 chunk 310 optimal weight: 8.9990 chunk 246 optimal weight: 6.9990 chunk 476 optimal weight: 0.9980 chunk 184 optimal weight: 4.9990 chunk 289 optimal weight: 5.9990 chunk 354 optimal weight: 1.9990 chunk 552 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 485 HIS B 288 HIS ** B 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 HIS B 393 HIS B 579 GLN C 273 GLN C 288 HIS ** C 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 485 HIS C 711 ASN D 200 GLN ** F 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 55 ASN H 55 ASN I 55 ASN K 55 ASN K 143 GLN K 205 HIS L 55 ASN M 55 ASN N 55 ASN N 205 HIS P 55 ASN P 205 HIS Q 55 ASN ** Q 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 48 GLN R 55 ASN S 55 ASN T 55 ASN T 60 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5491 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 49276 Z= 0.278 Angle : 0.712 15.236 66555 Z= 0.374 Chirality : 0.059 3.228 7614 Planarity : 0.004 0.056 8616 Dihedral : 9.944 179.502 6919 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.73 % Favored : 97.16 % Rotamer: Outliers : 0.87 % Allowed : 4.91 % Favored : 94.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.10), residues: 6116 helix: 0.76 (0.09), residues: 3072 sheet: 0.87 (0.16), residues: 994 loop : -0.61 (0.13), residues: 2050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP F 649 HIS 0.017 0.001 HIS B 393 PHE 0.040 0.002 PHE B 331 TYR 0.020 0.002 TYR A 388 ARG 0.006 0.001 ARG O 29 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12232 Ramachandran restraints generated. 6116 Oldfield, 0 Emsley, 6116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12232 Ramachandran restraints generated. 6116 Oldfield, 0 Emsley, 6116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 5178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 529 time to evaluate : 5.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 167 MET cc_start: 0.8685 (mmt) cc_final: 0.8151 (mmt) REVERT: K 32 ASP cc_start: 0.7459 (p0) cc_final: 0.7215 (p0) REVERT: K 55 ASN cc_start: 0.8325 (t0) cc_final: 0.7939 (t0) REVERT: K 85 THR cc_start: 0.9064 (m) cc_final: 0.8702 (p) REVERT: L 55 ASN cc_start: 0.8330 (t0) cc_final: 0.7863 (t0) REVERT: L 112 MET cc_start: 0.8486 (tpt) cc_final: 0.8284 (tpt) REVERT: N 48 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.7687 (mp10) REVERT: N 67 GLU cc_start: 0.7632 (tt0) cc_final: 0.7426 (tt0) REVERT: O 39 LYS cc_start: 0.8957 (tttt) cc_final: 0.8422 (mttt) REVERT: O 55 ASN cc_start: 0.8874 (t0) cc_final: 0.8357 (t0) REVERT: Q 106 MET cc_start: 0.8046 (ptt) cc_final: 0.7839 (ptp) REVERT: Q 200 ASP cc_start: 0.8406 (m-30) cc_final: 0.8166 (m-30) REVERT: R 88 MET cc_start: 0.8390 (mmt) cc_final: 0.7745 (mmt) REVERT: S 55 ASN cc_start: 0.8253 (t0) cc_final: 0.7966 (t0) outliers start: 45 outliers final: 19 residues processed: 558 average time/residue: 0.6107 time to fit residues: 561.1868 Evaluate side-chains 444 residues out of total 5178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 424 time to evaluate : 5.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain C residue 544 ASP Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain E residue 319 ILE Chi-restraints excluded: chain E residue 603 MET Chi-restraints excluded: chain F residue 393 HIS Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain I residue 51 ASP Chi-restraints excluded: chain M residue 204 THR Chi-restraints excluded: chain N residue 48 GLN Chi-restraints excluded: chain O residue 17 VAL Chi-restraints excluded: chain P residue 21 ILE Chi-restraints excluded: chain P residue 204 THR Chi-restraints excluded: chain S residue 204 THR Chi-restraints excluded: chain T residue 31 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.8484 > 50: distance: 106 - 111: 18.669 distance: 112 - 113: 17.164 distance: 112 - 115: 22.314 distance: 113 - 114: 11.934 distance: 113 - 123: 6.956 distance: 115 - 116: 9.038 distance: 116 - 117: 6.017 distance: 116 - 118: 14.567 distance: 117 - 119: 9.603 distance: 118 - 120: 12.985 distance: 119 - 121: 6.041 distance: 120 - 121: 12.111 distance: 121 - 122: 31.435 distance: 123 - 124: 17.809 distance: 123 - 211: 26.070 distance: 124 - 125: 20.154 distance: 124 - 127: 46.190 distance: 125 - 126: 20.623 distance: 125 - 131: 5.190 distance: 126 - 221: 27.437 distance: 127 - 128: 26.432 distance: 128 - 129: 42.229 distance: 128 - 130: 12.543 distance: 131 - 132: 16.091 distance: 132 - 133: 11.345 distance: 132 - 135: 32.700 distance: 133 - 134: 13.196 distance: 133 - 143: 18.953 distance: 135 - 136: 16.961 distance: 136 - 137: 19.310 distance: 136 - 138: 13.401 distance: 137 - 139: 14.814 distance: 138 - 140: 34.782 distance: 139 - 141: 21.651 distance: 140 - 141: 13.410 distance: 141 - 142: 33.282 distance: 143 - 144: 22.552 distance: 143 - 224: 23.172 distance: 144 - 145: 15.575 distance: 144 - 147: 5.237 distance: 145 - 146: 10.423 distance: 145 - 151: 34.477 distance: 147 - 148: 53.582 distance: 147 - 149: 18.744 distance: 148 - 150: 43.516 distance: 151 - 152: 9.585 distance: 152 - 153: 33.379 distance: 152 - 155: 29.354 distance: 153 - 154: 13.281 distance: 153 - 159: 35.167 distance: 155 - 156: 11.391 distance: 156 - 158: 40.466 distance: 159 - 160: 13.010 distance: 160 - 161: 15.575 distance: 160 - 163: 10.407 distance: 161 - 162: 18.160 distance: 161 - 165: 7.713 distance: 163 - 164: 15.391 distance: 165 - 171: 57.421 distance: 166 - 167: 39.798 distance: 167 - 172: 27.503 distance: 169 - 170: 56.840 distance: 172 - 173: 41.485 distance: 173 - 174: 3.925 distance: 174 - 175: 36.992 distance: 176 - 177: 39.497 distance: 177 - 178: 50.195 distance: 178 - 179: 9.874 distance: 178 - 180: 12.627 distance: 180 - 181: 30.446 distance: 181 - 182: 12.173 distance: 181 - 184: 36.234 distance: 182 - 183: 13.308 distance: 182 - 187: 28.887 distance: 184 - 185: 7.402 distance: 184 - 186: 39.312