Starting phenix.real_space_refine on Sat Mar 16 07:06:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pm5_20388/03_2024/6pm5_20388.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pm5_20388/03_2024/6pm5_20388.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/6pm5_20388/03_2024/6pm5_20388.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pm5_20388/03_2024/6pm5_20388.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pm5_20388/03_2024/6pm5_20388.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pm5_20388/03_2024/6pm5_20388.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= 0.065 sd= 3.206 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 9120 2.51 5 N 2275 2.21 5 O 2480 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 45": "NH1" <-> "NH2" Residue "A ARG 81": "NH1" <-> "NH2" Residue "A ARG 88": "NH1" <-> "NH2" Residue "A ARG 229": "NH1" <-> "NH2" Residue "A ARG 325": "NH1" <-> "NH2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B ARG 81": "NH1" <-> "NH2" Residue "B ARG 88": "NH1" <-> "NH2" Residue "B ARG 229": "NH1" <-> "NH2" Residue "B ARG 325": "NH1" <-> "NH2" Residue "C ARG 45": "NH1" <-> "NH2" Residue "C ARG 81": "NH1" <-> "NH2" Residue "C ARG 88": "NH1" <-> "NH2" Residue "C ARG 229": "NH1" <-> "NH2" Residue "C ARG 325": "NH1" <-> "NH2" Residue "D ARG 45": "NH1" <-> "NH2" Residue "D ARG 81": "NH1" <-> "NH2" Residue "D ARG 88": "NH1" <-> "NH2" Residue "D ARG 229": "NH1" <-> "NH2" Residue "D ARG 325": "NH1" <-> "NH2" Residue "E ARG 45": "NH1" <-> "NH2" Residue "E ARG 81": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E ARG 229": "NH1" <-> "NH2" Residue "E ARG 325": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13975 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2751 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'HIS:plan': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 39 Chain: "B" Number of atoms: 2751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2751 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'HIS:plan': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 39 Chain: "C" Number of atoms: 2751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2751 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'HIS:plan': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 39 Chain: "D" Number of atoms: 2751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2751 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'HIS:plan': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 39 Chain: "E" Number of atoms: 2751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2751 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'HIS:plan': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 39 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 8.08, per 1000 atoms: 0.58 Number of scatterers: 13975 At special positions: 0 Unit cell: (106.167, 106.167, 134.972, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 100 16.00 O 2480 8.00 N 2275 7.00 C 9120 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 225 " distance=2.03 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 225 " distance=2.03 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 225 " distance=2.03 Simple disulfide: pdb=" SG CYS D 214 " - pdb=" SG CYS D 225 " distance=2.03 Simple disulfide: pdb=" SG CYS E 214 " - pdb=" SG CYS E 225 " distance=2.03 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 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG F 1 " - " ASN A 54 " " NAG G 1 " - " ASN B 54 " " NAG H 1 " - " ASN C 54 " " NAG I 1 " - " ASN D 54 " " NAG J 1 " - " ASN E 54 " Time building additional restraints: 5.53 Conformation dependent library (CDL) restraints added in 2.4 seconds 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3320 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 20 sheets defined 40.3% alpha, 33.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 25 through 35 removed outlier: 3.533A pdb=" N ASP A 31 " --> pdb=" O SER A 27 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 40 removed outlier: 3.834A pdb=" N GLY A 39 " --> pdb=" O LYS A 36 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR A 40 " --> pdb=" O VAL A 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 36 through 40' Processing helix chain 'A' and resid 87 through 90 removed outlier: 3.542A pdb=" N ALA A 90 " --> pdb=" O PRO A 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 87 through 90' Processing helix chain 'A' and resid 102 through 107 removed outlier: 3.642A pdb=" N ASP A 107 " --> pdb=" O PRO A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 243 Processing helix chain 'A' and resid 244 through 256 removed outlier: 3.774A pdb=" N VAL A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 264 through 286 removed outlier: 3.506A pdb=" N THR A 275 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N VAL A 276 " --> pdb=" O GLY A 272 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR A 278 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N MET A 279 " --> pdb=" O THR A 275 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR A 280 " --> pdb=" O VAL A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 327 removed outlier: 3.610A pdb=" N ILE A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TRP A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU A 314 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS A 327 " --> pdb=" O ILE A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 428 removed outlier: 3.608A pdb=" N ILE A 396 " --> pdb=" O ARG A 392 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N SER A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP A 403 " --> pdb=" O ALA A 399 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG A 407 " --> pdb=" O ASP A 403 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL A 408 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE A 410 " --> pdb=" O SER A 406 " (cutoff:3.500A) Proline residue: A 411 - end of helix removed outlier: 3.719A pdb=" N LEU A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TRP A 422 " --> pdb=" O ASN A 418 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR A 424 " --> pdb=" O PHE A 420 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE A 427 " --> pdb=" O ILE A 423 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE A 428 " --> pdb=" O THR A 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 35 removed outlier: 3.534A pdb=" N ASP B 31 " --> pdb=" O SER B 27 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 40 removed outlier: 3.834A pdb=" N GLY B 39 " --> pdb=" O LYS B 36 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR B 40 " --> pdb=" O VAL B 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 36 through 40' Processing helix chain 'B' and resid 87 through 90 removed outlier: 3.542A pdb=" N ALA B 90 " --> pdb=" O PRO B 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 87 through 90' Processing helix chain 'B' and resid 102 through 107 removed outlier: 3.641A pdb=" N ASP B 107 " --> pdb=" O PRO B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 243 Processing helix chain 'B' and resid 244 through 256 removed outlier: 3.774A pdb=" N VAL B 251 " --> pdb=" O SER B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 259 No H-bonds generated for 'chain 'B' and resid 257 through 259' Processing helix chain 'B' and resid 264 through 286 removed outlier: 3.506A pdb=" N THR B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N VAL B 276 " --> pdb=" O GLY B 272 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR B 278 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N MET B 279 " --> pdb=" O THR B 275 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR B 280 " --> pdb=" O VAL B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 327 removed outlier: 3.609A pdb=" N ILE B 301 " --> pdb=" O LYS B 297 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TRP B 302 " --> pdb=" O ALA B 298 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU B 314 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS B 327 " --> pdb=" O ILE B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 428 removed outlier: 3.607A pdb=" N ILE B 396 " --> pdb=" O ARG B 392 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N SER B 397 " --> pdb=" O LYS B 393 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP B 403 " --> pdb=" O ALA B 399 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG B 407 " --> pdb=" O ASP B 403 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL B 408 " --> pdb=" O THR B 404 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE B 410 " --> pdb=" O SER B 406 " (cutoff:3.500A) Proline residue: B 411 - end of helix removed outlier: 3.719A pdb=" N LEU B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TRP B 422 " --> pdb=" O ASN B 418 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR B 424 " --> pdb=" O PHE B 420 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE B 427 " --> pdb=" O ILE B 423 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE B 428 " --> pdb=" O THR B 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 35 removed outlier: 3.533A pdb=" N ASP C 31 " --> pdb=" O SER C 27 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS C 32 " --> pdb=" O GLU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 40 removed outlier: 3.834A pdb=" N GLY C 39 " --> pdb=" O LYS C 36 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR C 40 " --> pdb=" O VAL C 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 36 through 40' Processing helix chain 'C' and resid 87 through 90 removed outlier: 3.542A pdb=" N ALA C 90 " --> pdb=" O PRO C 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 87 through 90' Processing helix chain 'C' and resid 102 through 107 removed outlier: 3.643A pdb=" N ASP C 107 " --> pdb=" O PRO C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 243 Processing helix chain 'C' and resid 244 through 256 removed outlier: 3.773A pdb=" N VAL C 251 " --> pdb=" O SER C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 259 No H-bonds generated for 'chain 'C' and resid 257 through 259' Processing helix chain 'C' and resid 264 through 286 removed outlier: 3.505A pdb=" N THR C 275 " --> pdb=" O LEU C 271 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N VAL C 276 " --> pdb=" O GLY C 272 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR C 278 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N MET C 279 " --> pdb=" O THR C 275 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR C 280 " --> pdb=" O VAL C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 327 removed outlier: 3.611A pdb=" N ILE C 301 " --> pdb=" O LYS C 297 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TRP C 302 " --> pdb=" O ALA C 298 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU C 314 " --> pdb=" O VAL C 310 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS C 327 " --> pdb=" O ILE C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 428 removed outlier: 3.608A pdb=" N ILE C 396 " --> pdb=" O ARG C 392 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N SER C 397 " --> pdb=" O LYS C 393 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASP C 403 " --> pdb=" O ALA C 399 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG C 407 " --> pdb=" O ASP C 403 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL C 408 " --> pdb=" O THR C 404 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE C 410 " --> pdb=" O SER C 406 " (cutoff:3.500A) Proline residue: C 411 - end of helix removed outlier: 3.720A pdb=" N LEU C 415 " --> pdb=" O PRO C 411 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TRP C 422 " --> pdb=" O ASN C 418 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR C 424 " --> pdb=" O PHE C 420 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE C 427 " --> pdb=" O ILE C 423 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE C 428 " --> pdb=" O THR C 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 35 removed outlier: 3.533A pdb=" N ASP D 31 " --> pdb=" O SER D 27 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS D 32 " --> pdb=" O GLU D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 40 removed outlier: 3.834A pdb=" N GLY D 39 " --> pdb=" O LYS D 36 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR D 40 " --> pdb=" O VAL D 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 36 through 40' Processing helix chain 'D' and resid 87 through 90 removed outlier: 3.542A pdb=" N ALA D 90 " --> pdb=" O PRO D 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 87 through 90' Processing helix chain 'D' and resid 102 through 107 removed outlier: 3.642A pdb=" N ASP D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 243 Processing helix chain 'D' and resid 244 through 256 removed outlier: 3.774A pdb=" N VAL D 251 " --> pdb=" O SER D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 259 No H-bonds generated for 'chain 'D' and resid 257 through 259' Processing helix chain 'D' and resid 264 through 286 removed outlier: 3.506A pdb=" N THR D 275 " --> pdb=" O LEU D 271 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N VAL D 276 " --> pdb=" O GLY D 272 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR D 278 " --> pdb=" O THR D 274 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N MET D 279 " --> pdb=" O THR D 275 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR D 280 " --> pdb=" O VAL D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 327 removed outlier: 3.610A pdb=" N ILE D 301 " --> pdb=" O LYS D 297 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TRP D 302 " --> pdb=" O ALA D 298 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU D 314 " --> pdb=" O VAL D 310 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS D 327 " --> pdb=" O ILE D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 428 removed outlier: 3.607A pdb=" N ILE D 396 " --> pdb=" O ARG D 392 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N SER D 397 " --> pdb=" O LYS D 393 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASP D 403 " --> pdb=" O ALA D 399 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG D 407 " --> pdb=" O ASP D 403 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL D 408 " --> pdb=" O THR D 404 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE D 410 " --> pdb=" O SER D 406 " (cutoff:3.500A) Proline residue: D 411 - end of helix removed outlier: 3.718A pdb=" N LEU D 415 " --> pdb=" O PRO D 411 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TRP D 422 " --> pdb=" O ASN D 418 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR D 424 " --> pdb=" O PHE D 420 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE D 427 " --> pdb=" O ILE D 423 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE D 428 " --> pdb=" O THR D 424 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 35 removed outlier: 3.533A pdb=" N ASP E 31 " --> pdb=" O SER E 27 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS E 32 " --> pdb=" O GLU E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 40 removed outlier: 3.834A pdb=" N GLY E 39 " --> pdb=" O LYS E 36 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR E 40 " --> pdb=" O VAL E 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 36 through 40' Processing helix chain 'E' and resid 87 through 90 removed outlier: 3.542A pdb=" N ALA E 90 " --> pdb=" O PRO E 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 87 through 90' Processing helix chain 'E' and resid 102 through 107 removed outlier: 3.642A pdb=" N ASP E 107 " --> pdb=" O PRO E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 243 Processing helix chain 'E' and resid 244 through 256 removed outlier: 3.774A pdb=" N VAL E 251 " --> pdb=" O SER E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 259 No H-bonds generated for 'chain 'E' and resid 257 through 259' Processing helix chain 'E' and resid 264 through 286 removed outlier: 3.506A pdb=" N THR E 275 " --> pdb=" O LEU E 271 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N VAL E 276 " --> pdb=" O GLY E 272 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR E 278 " --> pdb=" O THR E 274 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N MET E 279 " --> pdb=" O THR E 275 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR E 280 " --> pdb=" O VAL E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 327 removed outlier: 3.610A pdb=" N ILE E 301 " --> pdb=" O LYS E 297 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TRP E 302 " --> pdb=" O ALA E 298 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU E 314 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS E 327 " --> pdb=" O ILE E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 391 through 428 removed outlier: 3.609A pdb=" N ILE E 396 " --> pdb=" O ARG E 392 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N SER E 397 " --> pdb=" O LYS E 393 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASP E 403 " --> pdb=" O ALA E 399 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG E 407 " --> pdb=" O ASP E 403 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL E 408 " --> pdb=" O THR E 404 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE E 410 " --> pdb=" O SER E 406 " (cutoff:3.500A) Proline residue: E 411 - end of helix removed outlier: 3.719A pdb=" N LEU E 415 " --> pdb=" O PRO E 411 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TRP E 422 " --> pdb=" O ASN E 418 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR E 424 " --> pdb=" O PHE E 420 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE E 427 " --> pdb=" O ILE E 423 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE E 428 " --> pdb=" O THR E 424 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 99 through 100 removed outlier: 3.683A pdb=" N LEU A 99 " --> pdb=" O ILE A 136 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE A 136 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ASP A 73 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N SER A 66 " --> pdb=" O ASP A 73 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N VAL A 53 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N GLU A 185 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL A 55 " --> pdb=" O GLU A 185 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 122 through 123 removed outlier: 3.727A pdb=" N ASN A 123 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ASP A 73 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N SER A 66 " --> pdb=" O ASP A 73 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 114 through 116 removed outlier: 3.566A pdb=" N ARG A 212 " --> pdb=" O GLU A 227 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N HIS A 231 " --> pdb=" O GLU A 208 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLU A 208 " --> pdb=" O HIS A 231 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 216 through 217 removed outlier: 3.807A pdb=" N LYS A 216 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE A 223 " --> pdb=" O LYS A 216 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 99 through 100 removed outlier: 3.683A pdb=" N LEU B 99 " --> pdb=" O ILE B 136 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE B 136 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ASP B 73 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N SER B 66 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N VAL B 53 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N GLU B 185 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL B 55 " --> pdb=" O GLU B 185 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 122 through 123 removed outlier: 3.727A pdb=" N ASN B 123 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ASP B 73 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N SER B 66 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 114 through 116 removed outlier: 3.567A pdb=" N ARG B 212 " --> pdb=" O GLU B 227 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N HIS B 231 " --> pdb=" O GLU B 208 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLU B 208 " --> pdb=" O HIS B 231 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 216 through 217 removed outlier: 3.807A pdb=" N LYS B 216 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE B 223 " --> pdb=" O LYS B 216 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 99 through 100 removed outlier: 3.681A pdb=" N LEU C 99 " --> pdb=" O ILE C 136 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE C 136 " --> pdb=" O LEU C 99 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ASP C 73 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N SER C 66 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL C 53 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N GLU C 185 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N VAL C 55 " --> pdb=" O GLU C 185 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 122 through 123 removed outlier: 3.727A pdb=" N ASN C 123 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ASP C 73 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N SER C 66 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 114 through 116 removed outlier: 3.566A pdb=" N ARG C 212 " --> pdb=" O GLU C 227 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N HIS C 231 " --> pdb=" O GLU C 208 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLU C 208 " --> pdb=" O HIS C 231 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 216 through 217 removed outlier: 3.807A pdb=" N LYS C 216 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE C 223 " --> pdb=" O LYS C 216 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'D' and resid 99 through 100 removed outlier: 3.682A pdb=" N LEU D 99 " --> pdb=" O ILE D 136 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE D 136 " --> pdb=" O LEU D 99 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ASP D 73 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N SER D 66 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL D 53 " --> pdb=" O ILE D 183 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N GLU D 185 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL D 55 " --> pdb=" O GLU D 185 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 122 through 123 removed outlier: 3.727A pdb=" N ASN D 123 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ASP D 73 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N SER D 66 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 114 through 116 removed outlier: 3.566A pdb=" N ARG D 212 " --> pdb=" O GLU D 227 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N HIS D 231 " --> pdb=" O GLU D 208 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLU D 208 " --> pdb=" O HIS D 231 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 216 through 217 removed outlier: 3.807A pdb=" N LYS D 216 " --> pdb=" O PHE D 223 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE D 223 " --> pdb=" O LYS D 216 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'E' and resid 99 through 100 removed outlier: 3.682A pdb=" N LEU E 99 " --> pdb=" O ILE E 136 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE E 136 " --> pdb=" O LEU E 99 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ASP E 73 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N SER E 66 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N VAL E 53 " --> pdb=" O ILE E 183 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N GLU E 185 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL E 55 " --> pdb=" O GLU E 185 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 122 through 123 removed outlier: 3.727A pdb=" N ASN E 123 " --> pdb=" O THR E 149 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ASP E 73 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N SER E 66 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 114 through 116 removed outlier: 3.566A pdb=" N ARG E 212 " --> pdb=" O GLU E 227 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N HIS E 231 " --> pdb=" O GLU E 208 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLU E 208 " --> pdb=" O HIS E 231 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 216 through 217 removed outlier: 3.807A pdb=" N LYS E 216 " --> pdb=" O PHE E 223 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE E 223 " --> pdb=" O LYS E 216 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 645 hydrogen bonds defined for protein. 1935 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: 4.19 Time building geometry restraints manager: 5.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4285 1.34 - 1.46: 3522 1.46 - 1.58: 6343 1.58 - 1.70: 0 1.70 - 1.81: 170 Bond restraints: 14320 Sorted by residual: bond pdb=" C1 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.84e+00 bond pdb=" C1 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.82e+00 bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.82e+00 bond pdb=" C1 NAG I 1 " pdb=" O5 NAG I 1 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.77e+00 bond pdb=" C1 NAG H 1 " pdb=" O5 NAG H 1 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.74e+00 ... (remaining 14315 not shown) Histogram of bond angle deviations from ideal: 100.64 - 107.31: 544 107.31 - 113.98: 8111 113.98 - 120.65: 5662 120.65 - 127.32: 4973 127.32 - 134.00: 160 Bond angle restraints: 19450 Sorted by residual: angle pdb=" C3 BMA F 3 " pdb=" C2 BMA F 3 " pdb=" O2 BMA F 3 " ideal model delta sigma weight residual 112.95 106.74 6.21 3.00e+00 1.11e-01 4.29e+00 angle pdb=" C3 BMA I 3 " pdb=" C2 BMA I 3 " pdb=" O2 BMA I 3 " ideal model delta sigma weight residual 112.95 106.76 6.19 3.00e+00 1.11e-01 4.26e+00 angle pdb=" C3 BMA J 3 " pdb=" C2 BMA J 3 " pdb=" O2 BMA J 3 " ideal model delta sigma weight residual 112.95 106.77 6.18 3.00e+00 1.11e-01 4.25e+00 angle pdb=" C3 BMA G 3 " pdb=" C2 BMA G 3 " pdb=" O2 BMA G 3 " ideal model delta sigma weight residual 112.95 106.78 6.17 3.00e+00 1.11e-01 4.23e+00 angle pdb=" C3 BMA H 3 " pdb=" C2 BMA H 3 " pdb=" O2 BMA H 3 " ideal model delta sigma weight residual 112.95 106.79 6.16 3.00e+00 1.11e-01 4.22e+00 ... (remaining 19445 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.72: 8540 21.72 - 43.44: 120 43.44 - 65.16: 0 65.16 - 86.88: 30 86.88 - 108.60: 20 Dihedral angle restraints: 8710 sinusoidal: 3595 harmonic: 5115 Sorted by residual: dihedral pdb=" O4 BMA J 3 " pdb=" C4 BMA J 3 " pdb=" C5 BMA J 3 " pdb=" O5 BMA J 3 " ideal model delta sinusoidal sigma weight residual -71.29 -179.89 108.60 1 3.00e+01 1.11e-03 1.41e+01 dihedral pdb=" O4 BMA H 3 " pdb=" C4 BMA H 3 " pdb=" C5 BMA H 3 " pdb=" O5 BMA H 3 " ideal model delta sinusoidal sigma weight residual -71.29 -179.87 108.58 1 3.00e+01 1.11e-03 1.41e+01 dihedral pdb=" O4 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C5 BMA I 3 " pdb=" O5 BMA I 3 " ideal model delta sinusoidal sigma weight residual -71.29 -179.86 108.57 1 3.00e+01 1.11e-03 1.41e+01 ... (remaining 8707 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.197: 2245 0.197 - 0.393: 5 0.393 - 0.590: 0 0.590 - 0.787: 0 0.787 - 0.984: 5 Chirality restraints: 2255 Sorted by residual: chirality pdb=" C1 BMA J 3 " pdb=" O4 NAG J 2 " pdb=" C2 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.42 -0.98 2.00e-02 2.50e+03 2.42e+03 chirality pdb=" C1 BMA H 3 " pdb=" O4 NAG H 2 " pdb=" C2 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.42 -0.98 2.00e-02 2.50e+03 2.42e+03 chirality pdb=" C1 BMA G 3 " pdb=" O4 NAG G 2 " pdb=" C2 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.42 -0.98 2.00e-02 2.50e+03 2.42e+03 ... (remaining 2252 not shown) Planarity restraints: 2405 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 102 " -0.020 5.00e-02 4.00e+02 3.07e-02 1.51e+00 pdb=" N PRO E 103 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO E 103 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO E 103 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 102 " -0.020 5.00e-02 4.00e+02 3.07e-02 1.51e+00 pdb=" N PRO D 103 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 410 " 0.020 5.00e-02 4.00e+02 3.06e-02 1.50e+00 pdb=" N PRO C 411 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO C 411 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 411 " 0.017 5.00e-02 4.00e+02 ... (remaining 2402 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3735 2.80 - 3.33: 12281 3.33 - 3.85: 21877 3.85 - 4.38: 26629 4.38 - 4.90: 45304 Nonbonded interactions: 109826 Sorted by model distance: nonbonded pdb=" OG1 THR E 178 " pdb=" OD1 ASN E 180 " model vdw 2.275 2.440 nonbonded pdb=" OG1 THR B 178 " pdb=" OD1 ASN B 180 " model vdw 2.276 2.440 nonbonded pdb=" OG1 THR D 178 " pdb=" OD1 ASN D 180 " model vdw 2.276 2.440 nonbonded pdb=" OG1 THR A 178 " pdb=" OD1 ASN A 180 " model vdw 2.276 2.440 nonbonded pdb=" OG1 THR C 178 " pdb=" OD1 ASN C 180 " model vdw 2.276 2.440 ... (remaining 109821 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.490 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: 0.010 Extract box with map and model: 7.520 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 38.640 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.120 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: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 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 : 0.002 0.027 14320 Z= 0.125 Angle : 0.490 6.666 19450 Z= 0.238 Chirality : 0.063 0.984 2255 Planarity : 0.003 0.031 2400 Dihedral : 11.101 108.604 5375 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % 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: -4.42 (0.15), residues: 1710 helix: -3.74 (0.12), residues: 535 sheet: -2.45 (0.21), residues: 380 loop : -2.45 (0.18), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP D 422 HIS 0.001 0.000 HIS A 125 PHE 0.003 0.001 PHE A 203 TYR 0.004 0.000 TYR D 74 ARG 0.001 0.000 ARG C 135 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 354 time to evaluate : 1.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.6039 (mmp) cc_final: 0.5671 (ppp) REVERT: A 185 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7652 (mt-10) REVERT: A 210 ASP cc_start: 0.7649 (m-30) cc_final: 0.7280 (m-30) REVERT: A 303 MET cc_start: 0.8856 (mmt) cc_final: 0.8599 (mmt) REVERT: A 398 ARG cc_start: 0.7194 (ttm170) cc_final: 0.6366 (mmp80) REVERT: B 105 MET cc_start: 0.6130 (mmp) cc_final: 0.5608 (ppp) REVERT: B 210 ASP cc_start: 0.7667 (m-30) cc_final: 0.7249 (m-30) REVERT: B 303 MET cc_start: 0.8915 (mmt) cc_final: 0.8556 (mmt) REVERT: B 390 GLU cc_start: 0.5402 (mp0) cc_final: 0.4918 (mp0) REVERT: B 398 ARG cc_start: 0.7322 (ttm170) cc_final: 0.6380 (mmp80) REVERT: C 105 MET cc_start: 0.6194 (mmp) cc_final: 0.5614 (ppp) REVERT: C 185 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7485 (mt-10) REVERT: C 210 ASP cc_start: 0.7695 (m-30) cc_final: 0.7494 (m-30) REVERT: C 398 ARG cc_start: 0.7401 (ttm170) cc_final: 0.6614 (mmp80) REVERT: D 105 MET cc_start: 0.5942 (mmp) cc_final: 0.5610 (ppp) REVERT: D 106 LEU cc_start: 0.7783 (tm) cc_final: 0.7406 (tp) REVERT: D 163 MET cc_start: 0.7048 (mpp) cc_final: 0.6787 (mpp) REVERT: D 210 ASP cc_start: 0.7557 (m-30) cc_final: 0.7068 (m-30) REVERT: D 398 ARG cc_start: 0.7451 (ttm170) cc_final: 0.6811 (mmp80) REVERT: E 185 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7667 (mt-10) REVERT: E 210 ASP cc_start: 0.7581 (m-30) cc_final: 0.7154 (m-30) REVERT: E 303 MET cc_start: 0.8951 (mmt) cc_final: 0.8744 (mmt) REVERT: E 398 ARG cc_start: 0.7388 (ttm170) cc_final: 0.6551 (mmp80) outliers start: 0 outliers final: 0 residues processed: 354 average time/residue: 0.2979 time to fit residues: 146.9703 Evaluate side-chains 263 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 263 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- 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: 63.0398 > 50: distance: 20 - 22: 9.930 distance: 22 - 23: 28.731 distance: 23 - 24: 25.961 distance: 23 - 26: 31.930 distance: 27 - 28: 17.498 distance: 28 - 29: 8.880 distance: 28 - 31: 34.724 distance: 29 - 30: 14.993 distance: 29 - 35: 12.971 distance: 30 - 131: 24.849 distance: 31 - 32: 23.248 distance: 32 - 33: 7.704 distance: 35 - 36: 18.689 distance: 36 - 37: 17.198 distance: 36 - 39: 18.295 distance: 37 - 38: 19.661 distance: 37 - 46: 10.382 distance: 39 - 40: 8.816 distance: 40 - 41: 10.354 distance: 40 - 42: 7.340 distance: 41 - 43: 10.021 distance: 42 - 44: 5.965 distance: 43 - 45: 9.065 distance: 44 - 45: 11.381 distance: 46 - 47: 7.996 distance: 47 - 48: 15.800 distance: 47 - 50: 17.960 distance: 48 - 49: 25.097 distance: 48 - 56: 29.160 distance: 50 - 51: 19.167 distance: 51 - 52: 39.900 distance: 51 - 53: 38.727 distance: 52 - 54: 36.044 distance: 53 - 55: 15.099 distance: 54 - 55: 45.521 distance: 56 - 57: 40.022 distance: 57 - 58: 16.743 distance: 57 - 60: 40.861 distance: 58 - 59: 20.447 distance: 58 - 61: 4.155 distance: 61 - 62: 20.355 distance: 62 - 63: 17.738 distance: 62 - 65: 14.259 distance: 63 - 64: 4.346 distance: 63 - 68: 15.041 distance: 65 - 66: 40.810 distance: 65 - 67: 45.290 distance: 68 - 69: 20.421 distance: 69 - 70: 32.218 distance: 69 - 72: 20.435 distance: 70 - 71: 17.230 distance: 70 - 75: 20.325 distance: 72 - 73: 31.500 distance: 72 - 74: 46.658 distance: 75 - 76: 20.153 distance: 76 - 77: 26.236 distance: 76 - 79: 16.744 distance: 77 - 78: 19.057 distance: 77 - 82: 14.449 distance: 79 - 80: 26.077 distance: 79 - 81: 33.321 distance: 82 - 83: 26.308 distance: 83 - 84: 18.913 distance: 83 - 86: 24.562 distance: 84 - 85: 13.721 distance: 84 - 87: 10.613 distance: 87 - 88: 26.202 distance: 88 - 89: 21.376 distance: 88 - 91: 9.005 distance: 89 - 90: 16.097 distance: 89 - 95: 8.851 distance: 91 - 92: 8.925 distance: 92 - 93: 5.557 distance: 92 - 94: 26.917