Starting phenix.real_space_refine on Fri Feb 23 13:37:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sfw_25104/02_2024/7sfw_25104.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sfw_25104/02_2024/7sfw_25104.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sfw_25104/02_2024/7sfw_25104.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sfw_25104/02_2024/7sfw_25104.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sfw_25104/02_2024/7sfw_25104.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sfw_25104/02_2024/7sfw_25104.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 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 244 5.16 5 C 24444 2.51 5 N 6552 2.21 5 O 7380 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 97": "OD1" <-> "OD2" Residue "A ASP 112": "OD1" <-> "OD2" Residue "A GLU 345": "OE1" <-> "OE2" Residue "A PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 385": "OD1" <-> "OD2" Residue "B GLU 4": "OE1" <-> "OE2" Residue "B TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 94": "OD1" <-> "OD2" Residue "B GLU 173": "OE1" <-> "OE2" Residue "B ASP 241": "OD1" <-> "OD2" Residue "C GLU 176": "OE1" <-> "OE2" Residue "C TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 2": "OE1" <-> "OE2" Residue "D TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 97": "OD1" <-> "OD2" Residue "D ASP 212": "OD1" <-> "OD2" Residue "D ASP 311": "OD1" <-> "OD2" Residue "D GLU 345": "OE1" <-> "OE2" Residue "D GLU 348": "OE1" <-> "OE2" Residue "D ASP 385": "OD1" <-> "OD2" Residue "E ASP 94": "OD1" <-> "OD2" Residue "E PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 157": "OD1" <-> "OD2" Residue "E GLU 209": "OE1" <-> "OE2" Residue "E TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 108": "OD1" <-> "OD2" Residue "H PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 263": "OD1" <-> "OD2" Residue "J ASP 56": "OD1" <-> "OD2" Residue "J GLU 151": "OE1" <-> "OE2" Residue "J ASP 212": "OD1" <-> "OD2" Residue "J GLU 348": "OE1" <-> "OE2" Residue "J ASP 379": "OD1" <-> "OD2" Residue "K GLU 4": "OE1" <-> "OE2" Residue "K TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 56": "OD1" <-> "OD2" Residue "K ASP 157": "OD1" <-> "OD2" Residue "K ASP 175": "OD1" <-> "OD2" Residue "K ASP 192": "OD1" <-> "OD2" Residue "K ASP 263": "OD1" <-> "OD2" Residue "K TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 342": "OE1" <-> "OE2" Residue "L ASP 225": "OD1" <-> "OD2" Residue "N PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 82": "OD1" <-> "OD2" Residue "Q TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 50": "OD1" <-> "OD2" Residue "R ASP 92": "OD1" <-> "OD2" Residue "S PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 50": "OD1" <-> "OD2" Residue "T TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 38620 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 3351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3351 Classifications: {'peptide': 440} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 411} Chain: "B" Number of atoms: 3264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3264 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 30, 'TRANS': 387} Chain: "C" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1248 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 151} Chain: "D" Number of atoms: 3351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3351 Classifications: {'peptide': 440} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 411} Chain: "E" Number of atoms: 3264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3264 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 30, 'TRANS': 387} Chain: "F" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1248 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 151} Chain: "G" Number of atoms: 3351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3351 Classifications: {'peptide': 440} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 411} Chain: "H" Number of atoms: 3264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3264 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 30, 'TRANS': 387} Chain: "I" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1248 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 151} Chain: "J" Number of atoms: 3351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3351 Classifications: {'peptide': 440} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 411} Chain: "K" Number of atoms: 3264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3264 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 30, 'TRANS': 387} Chain: "L" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1248 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 151} Chain: "M" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 941 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "N" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 809 Classifications: {'peptide': 107} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 8, 'TRANS': 98} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "O" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 941 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "P" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 809 Classifications: {'peptide': 107} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 8, 'TRANS': 98} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 941 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "R" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 809 Classifications: {'peptide': 107} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 8, 'TRANS': 98} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 941 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "T" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 809 Classifications: {'peptide': 107} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 8, 'TRANS': 98} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 19.03, per 1000 atoms: 0.49 Number of scatterers: 38620 At special positions: 0 Unit cell: (224.05, 170.607, 249.743, 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 244 16.00 O 7380 8.00 N 6552 7.00 C 24444 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=60, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 114 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 94 " distance=2.03 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 271 " distance=2.03 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 376 " distance=2.03 Simple disulfide: pdb=" SG CYS A 306 " - pdb=" SG CYS A 380 " distance=2.03 Simple disulfide: pdb=" SG CYS A 328 " - pdb=" SG CYS A 370 " distance=2.02 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 123 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 27 " distance=2.03 Simple disulfide: pdb=" SG CYS B 90 " - pdb=" SG CYS B 104 " distance=2.03 Simple disulfide: pdb=" SG CYS B 151 " - pdb=" SG CYS B 266 " distance=2.03 Simple disulfide: pdb=" SG CYS B 200 " - pdb=" SG CYS B 226 " distance=2.04 Simple disulfide: pdb=" SG CYS B 202 " - pdb=" SG CYS B 220 " distance=2.03 Simple disulfide: pdb=" SG CYS D 49 " - pdb=" SG CYS D 114 " distance=2.03 Simple disulfide: pdb=" SG CYS D 62 " - pdb=" SG CYS D 94 " distance=2.03 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 259 " - pdb=" SG CYS D 271 " distance=2.03 Simple disulfide: pdb=" SG CYS D 301 " - pdb=" SG CYS D 376 " distance=2.03 Simple disulfide: pdb=" SG CYS D 306 " - pdb=" SG CYS D 380 " distance=2.03 Simple disulfide: pdb=" SG CYS D 328 " - pdb=" SG CYS D 370 " distance=2.03 Simple disulfide: pdb=" SG CYS E 19 " - pdb=" SG CYS E 123 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 27 " distance=2.03 Simple disulfide: pdb=" SG CYS E 90 " - pdb=" SG CYS E 104 " distance=2.03 Simple disulfide: pdb=" SG CYS E 151 " - pdb=" SG CYS E 266 " distance=2.03 Simple disulfide: pdb=" SG CYS E 200 " - pdb=" SG CYS E 226 " distance=2.04 Simple disulfide: pdb=" SG CYS E 202 " - pdb=" SG CYS E 220 " distance=2.03 Simple disulfide: pdb=" SG CYS G 49 " - pdb=" SG CYS G 114 " distance=2.03 Simple disulfide: pdb=" SG CYS G 62 " - pdb=" SG CYS G 94 " distance=2.03 Simple disulfide: pdb=" SG CYS G 63 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 259 " - pdb=" SG CYS G 271 " distance=2.03 Simple disulfide: pdb=" SG CYS G 301 " - pdb=" SG CYS G 376 " distance=2.03 Simple disulfide: pdb=" SG CYS G 306 " - pdb=" SG CYS G 380 " distance=2.03 Simple disulfide: pdb=" SG CYS G 328 " - pdb=" SG CYS G 370 " distance=2.03 Simple disulfide: pdb=" SG CYS H 19 " - pdb=" SG CYS H 123 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 27 " distance=2.01 Simple disulfide: pdb=" SG CYS H 90 " - pdb=" SG CYS H 104 " distance=2.03 Simple disulfide: pdb=" SG CYS H 151 " - pdb=" SG CYS H 266 " distance=2.03 Simple disulfide: pdb=" SG CYS H 200 " - pdb=" SG CYS H 226 " distance=2.04 Simple disulfide: pdb=" SG CYS H 202 " - pdb=" SG CYS H 220 " distance=2.03 Simple disulfide: pdb=" SG CYS J 49 " - pdb=" SG CYS J 114 " distance=2.03 Simple disulfide: pdb=" SG CYS J 62 " - pdb=" SG CYS J 94 " distance=2.03 Simple disulfide: pdb=" SG CYS J 63 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 259 " - pdb=" SG CYS J 271 " distance=2.03 Simple disulfide: pdb=" SG CYS J 301 " - pdb=" SG CYS J 376 " distance=2.03 Simple disulfide: pdb=" SG CYS J 306 " - pdb=" SG CYS J 380 " distance=2.03 Simple disulfide: pdb=" SG CYS J 328 " - pdb=" SG CYS J 370 " distance=2.03 Simple disulfide: pdb=" SG CYS K 19 " - pdb=" SG CYS K 123 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 27 " distance=2.02 Simple disulfide: pdb=" SG CYS K 90 " - pdb=" SG CYS K 104 " distance=2.03 Simple disulfide: pdb=" SG CYS K 151 " - pdb=" SG CYS K 266 " distance=2.03 Simple disulfide: pdb=" SG CYS K 200 " - pdb=" SG CYS K 226 " distance=2.03 Simple disulfide: pdb=" SG CYS K 202 " - pdb=" SG CYS K 220 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 96 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 88 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS T 22 " - pdb=" SG CYS T 88 " 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 NAG-ASN " NAG A 501 " - " ASN A 134 " " NAG B 502 " - " ASN B 318 " " NAG D 501 " - " ASN D 134 " " NAG G 501 " - " ASN G 134 " " NAG H 502 " - " ASN H 318 " " NAG J 501 " - " ASN J 134 " " NAG K 502 " - " ASN K 318 " Time building additional restraints: 13.14 Conformation dependent library (CDL) restraints added in 7.4 seconds 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9200 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 116 sheets defined 12.3% alpha, 40.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.14 Creating SS restraints... Processing helix chain 'A' and resid 238 through 246 Processing helix chain 'A' and resid 250 through 255 Processing helix chain 'A' and resid 256 through 259 Processing helix chain 'A' and resid 283 through 287 Processing helix chain 'A' and resid 403 through 439 removed outlier: 4.573A pdb=" N LEU A 413 " --> pdb=" O TRP A 409 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE A 421 " --> pdb=" O SER A 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 12 Processing helix chain 'B' and resid 351 through 362 Processing helix chain 'B' and resid 365 through 402 removed outlier: 3.806A pdb=" N LEU B 369 " --> pdb=" O MET B 365 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU B 371 " --> pdb=" O THR B 367 " (cutoff:3.500A) Proline residue: B 399 - end of helix removed outlier: 3.521A pdb=" N LEU B 402 " --> pdb=" O THR B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 415 Processing helix chain 'C' and resid 118 through 122 removed outlier: 3.992A pdb=" N LEU C 122 " --> pdb=" O MET C 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 118 through 122' Processing helix chain 'C' and resid 159 through 164 Processing helix chain 'C' and resid 181 through 187 removed outlier: 3.798A pdb=" N ALA C 186 " --> pdb=" O ASN C 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 246 Processing helix chain 'D' and resid 250 through 255 Processing helix chain 'D' and resid 256 through 259 Processing helix chain 'D' and resid 403 through 438 removed outlier: 4.463A pdb=" N GLY D 415 " --> pdb=" O THR D 411 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ALA D 418 " --> pdb=" O LEU D 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 12 removed outlier: 3.556A pdb=" N LEU E 11 " --> pdb=" O GLU E 8 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR E 12 " --> pdb=" O TYR E 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 8 through 12' Processing helix chain 'E' and resid 80 through 82 No H-bonds generated for 'chain 'E' and resid 80 through 82' Processing helix chain 'E' and resid 222 through 226 removed outlier: 3.527A pdb=" N CYS E 226 " --> pdb=" O LYS E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 362 Processing helix chain 'E' and resid 365 through 402 removed outlier: 3.828A pdb=" N LEU E 369 " --> pdb=" O MET E 365 " (cutoff:3.500A) Proline residue: E 399 - end of helix Processing helix chain 'E' and resid 408 through 415 removed outlier: 4.113A pdb=" N LEU E 412 " --> pdb=" O ILE E 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 123 removed outlier: 3.756A pdb=" N GLU F 123 " --> pdb=" O MET F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 165 Processing helix chain 'F' and resid 182 through 187 removed outlier: 3.630A pdb=" N ALA F 186 " --> pdb=" O ASN F 183 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP F 187 " --> pdb=" O MET F 184 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 246 Processing helix chain 'G' and resid 250 through 255 Processing helix chain 'G' and resid 256 through 259 Processing helix chain 'G' and resid 403 through 440 removed outlier: 3.876A pdb=" N SER G 417 " --> pdb=" O LEU G 413 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ALA G 418 " --> pdb=" O LEU G 414 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL G 419 " --> pdb=" O GLY G 415 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LYS G 440 " --> pdb=" O LEU G 436 " (cutoff:3.500A) Processing helix chain 'H' and resid 8 through 12 removed outlier: 3.559A pdb=" N THR H 12 " --> pdb=" O TYR H 9 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 82 No H-bonds generated for 'chain 'H' and resid 80 through 82' Processing helix chain 'H' and resid 222 through 224 No H-bonds generated for 'chain 'H' and resid 222 through 224' Processing helix chain 'H' and resid 351 through 362 Processing helix chain 'H' and resid 366 through 402 removed outlier: 3.506A pdb=" N GLY H 370 " --> pdb=" O SER H 366 " (cutoff:3.500A) Proline residue: H 399 - end of helix Processing helix chain 'H' and resid 408 through 415 removed outlier: 4.035A pdb=" N LEU H 412 " --> pdb=" O ILE H 408 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 122 removed outlier: 3.643A pdb=" N LYS I 121 " --> pdb=" O MET I 118 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU I 122 " --> pdb=" O VAL I 119 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 164 Processing helix chain 'I' and resid 181 through 185 Processing helix chain 'J' and resid 238 through 246 Processing helix chain 'J' and resid 250 through 255 removed outlier: 3.520A pdb=" N THR J 254 " --> pdb=" O SER J 250 " (cutoff:3.500A) Processing helix chain 'J' and resid 256 through 259 Processing helix chain 'J' and resid 289 through 293 Processing helix chain 'J' and resid 403 through 414 Processing helix chain 'J' and resid 415 through 437 removed outlier: 3.552A pdb=" N VAL J 419 " --> pdb=" O GLY J 415 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE J 420 " --> pdb=" O GLY J 416 " (cutoff:3.500A) Processing helix chain 'K' and resid 8 through 12 removed outlier: 3.714A pdb=" N THR K 12 " --> pdb=" O TYR K 9 " (cutoff:3.500A) Processing helix chain 'K' and resid 222 through 224 No H-bonds generated for 'chain 'K' and resid 222 through 224' Processing helix chain 'K' and resid 351 through 362 Processing helix chain 'K' and resid 369 through 402 Proline residue: K 399 - end of helix Processing helix chain 'K' and resid 408 through 415 removed outlier: 4.020A pdb=" N LEU K 412 " --> pdb=" O ILE K 408 " (cutoff:3.500A) Processing helix chain 'L' and resid 118 through 125 removed outlier: 3.802A pdb=" N LYS L 121 " --> pdb=" O MET L 118 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLU L 123 " --> pdb=" O MET L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 159 through 164 Processing helix chain 'M' and resid 87 through 91 Processing helix chain 'N' and resid 26 through 30 Processing helix chain 'N' and resid 79 through 83 Processing helix chain 'O' and resid 87 through 91 Processing helix chain 'P' and resid 26 through 30 Processing helix chain 'P' and resid 79 through 83 removed outlier: 3.658A pdb=" N ASP P 83 " --> pdb=" O ALA P 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 26 through 30 Processing helix chain 'R' and resid 79 through 83 Processing helix chain 'T' and resid 26 through 30 Processing helix chain 'T' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 8 Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 19 removed outlier: 7.086A pdb=" N ILE A 29 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL A 137 " --> pdb=" O ILE A 29 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE A 31 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ILE A 135 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU A 133 " --> pdb=" O PRO A 33 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LYS A 35 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ALA A 131 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LYS A 37 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N VAL A 129 " --> pdb=" O LYS A 37 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ILE A 39 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ALA A 127 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ALA A 121 " --> pdb=" O GLU A 45 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N VAL A 47 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ALA A 119 " --> pdb=" O VAL A 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 140 through 147 removed outlier: 6.421A pdb=" N ALA A 119 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N VAL A 47 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ALA A 121 " --> pdb=" O GLU A 45 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ALA A 127 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ILE A 39 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N VAL A 129 " --> pdb=" O LYS A 37 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LYS A 37 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ALA A 131 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LYS A 35 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU A 133 " --> pdb=" O PRO A 33 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ILE A 135 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE A 31 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL A 137 " --> pdb=" O ILE A 29 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ILE A 29 " --> pdb=" O VAL A 137 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 51 through 52 Processing sheet with id=AA5, first strand: chain 'A' and resid 59 through 61 Processing sheet with id=AA6, first strand: chain 'A' and resid 203 through 204 Processing sheet with id=AA7, first strand: chain 'A' and resid 220 through 221 removed outlier: 3.560A pdb=" N VAL A 220 " --> pdb=" O THR A 234 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 296 through 305 removed outlier: 5.038A pdb=" N ALA A 298 " --> pdb=" O SER A 321 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER A 321 " --> pdb=" O ALA A 298 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N ILE A 315 " --> pdb=" O ASN A 304 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 326 through 329 Processing sheet with id=AB1, first strand: chain 'A' and resid 365 through 368 Processing sheet with id=AB2, first strand: chain 'A' and resid 387 through 388 Processing sheet with id=AB3, first strand: chain 'B' and resid 17 through 19 Processing sheet with id=AB4, first strand: chain 'B' and resid 33 through 37 removed outlier: 8.280A pdb=" N ILE B 33 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N SER B 50 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS B 37 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 9.859A pdb=" N SER B 50 " --> pdb=" O ASP B 69 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ASP B 69 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY B 54 " --> pdb=" O THR B 65 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N THR B 65 " --> pdb=" O GLY B 54 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 33 through 37 removed outlier: 8.280A pdb=" N ILE B 33 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N SER B 50 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS B 37 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR B 49 " --> pdb=" O TYR B 98 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N TYR B 98 " --> pdb=" O THR B 49 " (cutoff:3.500A) removed outlier: 9.505A pdb=" N SER B 51 " --> pdb=" O HIS B 96 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N HIS B 96 " --> pdb=" O SER B 51 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N TYR B 53 " --> pdb=" O ASP B 94 " (cutoff:3.500A) removed outlier: 10.354A pdb=" N ASP B 94 " --> pdb=" O TYR B 53 " (cutoff:3.500A) removed outlier: 15.255A pdb=" N LEU B 55 " --> pdb=" O ILE B 92 " (cutoff:3.500A) removed outlier: 17.297A pdb=" N ILE B 92 " --> pdb=" O LEU B 55 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 83 through 85 Processing sheet with id=AB7, first strand: chain 'B' and resid 148 through 154 Processing sheet with id=AB8, first strand: chain 'B' and resid 237 through 238 Processing sheet with id=AB9, first strand: chain 'B' and resid 173 through 174 removed outlier: 3.810A pdb=" N SER B 195 " --> pdb=" O LEU B 231 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 179 through 182 Processing sheet with id=AC2, first strand: chain 'B' and resid 275 through 279 Processing sheet with id=AC3, first strand: chain 'C' and resid 156 through 157 removed outlier: 4.651A pdb=" N GLY C 138 " --> pdb=" O ILE C 130 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N LEU C 132 " --> pdb=" O ILE C 136 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ILE C 136 " --> pdb=" O LEU C 132 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 198 through 200 removed outlier: 5.090A pdb=" N PHE C 214 " --> pdb=" O LEU C 253 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VAL C 256 " --> pdb=" O VAL C 241 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N VAL C 241 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE C 230 " --> pdb=" O VAL C 238 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 198 through 200 removed outlier: 5.090A pdb=" N PHE C 214 " --> pdb=" O LEU C 253 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 2 through 8 Processing sheet with id=AC7, first strand: chain 'D' and resid 15 through 19 removed outlier: 5.471A pdb=" N ILE D 31 " --> pdb=" O THR D 136 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N THR D 136 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ASN D 134 " --> pdb=" O PRO D 33 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS D 35 " --> pdb=" O PHE D 132 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR D 41 " --> pdb=" O THR D 126 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N THR D 126 " --> pdb=" O THR D 41 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ASN D 43 " --> pdb=" O ALA D 124 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ALA D 124 " --> pdb=" O ASN D 43 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N GLU D 45 " --> pdb=" O TYR D 122 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N TYR D 122 " --> pdb=" O GLU D 45 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL D 47 " --> pdb=" O GLU D 120 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLU D 120 " --> pdb=" O VAL D 47 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 140 through 147 removed outlier: 6.722A pdb=" N GLU D 120 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL D 47 " --> pdb=" O GLU D 120 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N TYR D 122 " --> pdb=" O GLU D 45 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N GLU D 45 " --> pdb=" O TYR D 122 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ALA D 124 " --> pdb=" O ASN D 43 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ASN D 43 " --> pdb=" O ALA D 124 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N THR D 126 " --> pdb=" O THR D 41 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR D 41 " --> pdb=" O THR D 126 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS D 35 " --> pdb=" O PHE D 132 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ASN D 134 " --> pdb=" O PRO D 33 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N THR D 136 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N ILE D 31 " --> pdb=" O THR D 136 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 51 through 55 Processing sheet with id=AD1, first strand: chain 'D' and resid 51 through 55 Processing sheet with id=AD2, first strand: chain 'D' and resid 87 through 88 removed outlier: 3.602A pdb=" N GLY D 91 " --> pdb=" O MET D 88 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 203 through 204 Processing sheet with id=AD4, first strand: chain 'D' and resid 220 through 221 Processing sheet with id=AD5, first strand: chain 'D' and resid 296 through 305 removed outlier: 6.666A pdb=" N ALA D 299 " --> pdb=" O SER D 321 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N SER D 321 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N CYS D 301 " --> pdb=" O LYS D 319 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N LYS D 319 " --> pdb=" O CYS D 301 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N LEU D 303 " --> pdb=" O THR D 317 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N THR D 317 " --> pdb=" O LEU D 303 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 343 through 346 Processing sheet with id=AD7, first strand: chain 'D' and resid 387 through 388 Processing sheet with id=AD8, first strand: chain 'E' and resid 17 through 19 Processing sheet with id=AD9, first strand: chain 'E' and resid 33 through 37 removed outlier: 6.561A pdb=" N GLN E 48 " --> pdb=" O GLU E 34 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N VAL E 36 " --> pdb=" O ARG E 46 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ARG E 46 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 9.265A pdb=" N SER E 50 " --> pdb=" O ASP E 69 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ASP E 69 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N THR E 65 " --> pdb=" O GLY E 54 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 33 through 37 removed outlier: 6.561A pdb=" N GLN E 48 " --> pdb=" O GLU E 34 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N VAL E 36 " --> pdb=" O ARG E 46 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ARG E 46 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N TYR E 98 " --> pdb=" O THR E 49 " (cutoff:3.500A) removed outlier: 9.600A pdb=" N SER E 51 " --> pdb=" O HIS E 96 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N HIS E 96 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 8.701A pdb=" N TYR E 53 " --> pdb=" O ASP E 94 " (cutoff:3.500A) removed outlier: 10.599A pdb=" N ASP E 94 " --> pdb=" O TYR E 53 " (cutoff:3.500A) removed outlier: 14.616A pdb=" N LEU E 55 " --> pdb=" O ILE E 92 " (cutoff:3.500A) removed outlier: 17.058A pdb=" N ILE E 92 " --> pdb=" O LEU E 55 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 83 through 85 Processing sheet with id=AE3, first strand: chain 'E' and resid 147 through 154 Processing sheet with id=AE4, first strand: chain 'E' and resid 237 through 238 removed outlier: 3.524A pdb=" N GLY E 253 " --> pdb=" O MET E 167 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 173 through 174 removed outlier: 3.584A pdb=" N GLU E 173 " --> pdb=" O ARG E 230 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU E 231 " --> pdb=" O SER E 195 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N SER E 195 " --> pdb=" O LEU E 231 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 179 through 182 removed outlier: 3.728A pdb=" N VAL E 186 " --> pdb=" O PHE E 217 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 275 through 279 Processing sheet with id=AE8, first strand: chain 'F' and resid 156 through 157 removed outlier: 3.500A pdb=" N LYS F 156 " --> pdb=" O MET F 131 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 266 through 267 removed outlier: 3.818A pdb=" N LEU F 253 " --> pdb=" O PHE F 214 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N PHE F 214 " --> pdb=" O LEU F 253 " (cutoff:3.500A) removed outlier: 8.941A pdb=" N ALA F 206 " --> pdb=" O PRO F 217 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALA F 239 " --> pdb=" O ILE F 230 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY F 244 " --> pdb=" O GLU F 273 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU F 273 " --> pdb=" O GLY F 244 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 266 through 267 removed outlier: 6.377A pdb=" N VAL F 256 " --> pdb=" O VAL F 241 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N VAL F 241 " --> pdb=" O VAL F 256 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY F 244 " --> pdb=" O GLU F 273 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU F 273 " --> pdb=" O GLY F 244 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 2 through 8 Processing sheet with id=AF3, first strand: chain 'G' and resid 15 through 19 removed outlier: 5.526A pdb=" N ILE G 31 " --> pdb=" O THR G 136 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N THR G 136 " --> pdb=" O ILE G 31 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ASN G 134 " --> pdb=" O PRO G 33 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS G 35 " --> pdb=" O PHE G 132 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N THR G 126 " --> pdb=" O THR G 41 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N ASN G 43 " --> pdb=" O ALA G 124 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N ALA G 124 " --> pdb=" O ASN G 43 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N GLU G 45 " --> pdb=" O TYR G 122 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N TYR G 122 " --> pdb=" O GLU G 45 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL G 47 " --> pdb=" O GLU G 120 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLU G 120 " --> pdb=" O VAL G 47 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 140 through 147 removed outlier: 6.891A pdb=" N GLU G 120 " --> pdb=" O VAL G 47 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL G 47 " --> pdb=" O GLU G 120 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N TYR G 122 " --> pdb=" O GLU G 45 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N GLU G 45 " --> pdb=" O TYR G 122 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N ALA G 124 " --> pdb=" O ASN G 43 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N ASN G 43 " --> pdb=" O ALA G 124 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N THR G 126 " --> pdb=" O THR G 41 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS G 35 " --> pdb=" O PHE G 132 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ASN G 134 " --> pdb=" O PRO G 33 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N THR G 136 " --> pdb=" O ILE G 31 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N ILE G 31 " --> pdb=" O THR G 136 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 51 through 55 Processing sheet with id=AF6, first strand: chain 'G' and resid 51 through 55 Processing sheet with id=AF7, first strand: chain 'G' and resid 203 through 204 Processing sheet with id=AF8, first strand: chain 'G' and resid 220 through 221 Processing sheet with id=AF9, first strand: chain 'G' and resid 300 through 306 removed outlier: 3.622A pdb=" N ASN G 304 " --> pdb=" O ILE G 315 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE G 315 " --> pdb=" O ASN G 304 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'G' and resid 326 through 328 Processing sheet with id=AG2, first strand: chain 'G' and resid 364 through 368 Processing sheet with id=AG3, first strand: chain 'G' and resid 387 through 388 Processing sheet with id=AG4, first strand: chain 'H' and resid 17 through 19 Processing sheet with id=AG5, first strand: chain 'H' and resid 33 through 37 removed outlier: 6.584A pdb=" N GLN H 48 " --> pdb=" O GLU H 34 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N VAL H 36 " --> pdb=" O ARG H 46 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ARG H 46 " --> pdb=" O VAL H 36 " (cutoff:3.500A) removed outlier: 9.491A pdb=" N SER H 50 " --> pdb=" O ASP H 69 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ASP H 69 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N THR H 65 " --> pdb=" O GLY H 54 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'H' and resid 33 through 37 removed outlier: 6.584A pdb=" N GLN H 48 " --> pdb=" O GLU H 34 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N VAL H 36 " --> pdb=" O ARG H 46 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ARG H 46 " --> pdb=" O VAL H 36 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N TYR H 98 " --> pdb=" O THR H 49 " (cutoff:3.500A) removed outlier: 9.435A pdb=" N SER H 51 " --> pdb=" O HIS H 96 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N HIS H 96 " --> pdb=" O SER H 51 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N TYR H 53 " --> pdb=" O ASP H 94 " (cutoff:3.500A) removed outlier: 10.712A pdb=" N ASP H 94 " --> pdb=" O TYR H 53 " (cutoff:3.500A) removed outlier: 14.766A pdb=" N LEU H 55 " --> pdb=" O ILE H 92 " (cutoff:3.500A) removed outlier: 17.260A pdb=" N ILE H 92 " --> pdb=" O LEU H 55 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LEU H 84 " --> pdb=" O CYS H 90 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'H' and resid 147 through 154 Processing sheet with id=AG8, first strand: chain 'H' and resid 237 through 238 Processing sheet with id=AG9, first strand: chain 'H' and resid 173 through 174 removed outlier: 3.664A pdb=" N GLU H 173 " --> pdb=" O ARG H 230 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'H' and resid 179 through 182 removed outlier: 3.895A pdb=" N VAL H 186 " --> pdb=" O PHE H 217 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'H' and resid 275 through 279 Processing sheet with id=AH3, first strand: chain 'I' and resid 156 through 157 removed outlier: 4.460A pdb=" N GLY I 138 " --> pdb=" O ILE I 130 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU I 132 " --> pdb=" O ILE I 136 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N ILE I 136 " --> pdb=" O LEU I 132 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N TYR I 139 " --> pdb=" O PRO I 150 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'I' and resid 266 through 267 removed outlier: 6.602A pdb=" N VAL I 256 " --> pdb=" O VAL I 241 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N VAL I 241 " --> pdb=" O VAL I 256 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA I 239 " --> pdb=" O ILE I 230 " (cutoff:3.500A) removed outlier: 8.996A pdb=" N ALA I 206 " --> pdb=" O PRO I 217 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N PHE I 214 " --> pdb=" O LEU I 253 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'J' and resid 2 through 8 Processing sheet with id=AH6, first strand: chain 'J' and resid 15 through 19 removed outlier: 5.577A pdb=" N ILE J 31 " --> pdb=" O THR J 136 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N THR J 136 " --> pdb=" O ILE J 31 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ASN J 134 " --> pdb=" O PRO J 33 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS J 35 " --> pdb=" O PHE J 132 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR J 41 " --> pdb=" O THR J 126 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N THR J 126 " --> pdb=" O THR J 41 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ASN J 43 " --> pdb=" O ALA J 124 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ALA J 124 " --> pdb=" O ASN J 43 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N GLU J 45 " --> pdb=" O TYR J 122 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N TYR J 122 " --> pdb=" O GLU J 45 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL J 47 " --> pdb=" O GLU J 120 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLU J 120 " --> pdb=" O VAL J 47 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'J' and resid 140 through 147 removed outlier: 6.772A pdb=" N GLU J 120 " --> pdb=" O VAL J 47 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL J 47 " --> pdb=" O GLU J 120 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N TYR J 122 " --> pdb=" O GLU J 45 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N GLU J 45 " --> pdb=" O TYR J 122 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ALA J 124 " --> pdb=" O ASN J 43 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ASN J 43 " --> pdb=" O ALA J 124 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N THR J 126 " --> pdb=" O THR J 41 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR J 41 " --> pdb=" O THR J 126 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS J 35 " --> pdb=" O PHE J 132 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ASN J 134 " --> pdb=" O PRO J 33 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N THR J 136 " --> pdb=" O ILE J 31 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N ILE J 31 " --> pdb=" O THR J 136 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'J' and resid 51 through 55 Processing sheet with id=AH9, first strand: chain 'J' and resid 51 through 55 Processing sheet with id=AI1, first strand: chain 'J' and resid 87 through 88 Processing sheet with id=AI2, first strand: chain 'J' and resid 203 through 204 Processing sheet with id=AI3, first strand: chain 'J' and resid 220 through 221 Processing sheet with id=AI4, first strand: chain 'J' and resid 296 through 297 removed outlier: 3.541A pdb=" N SER J 321 " --> pdb=" O SER J 297 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR J 317 " --> pdb=" O LEU J 303 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N LEU J 303 " --> pdb=" O THR J 317 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N LYS J 319 " --> pdb=" O CYS J 301 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N CYS J 301 " --> pdb=" O LYS J 319 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'J' and resid 296 through 297 removed outlier: 3.541A pdb=" N SER J 321 " --> pdb=" O SER J 297 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'J' and resid 343 through 346 Processing sheet with id=AI7, first strand: chain 'J' and resid 387 through 388 Processing sheet with id=AI8, first strand: chain 'K' and resid 17 through 19 Processing sheet with id=AI9, first strand: chain 'K' and resid 33 through 37 removed outlier: 8.347A pdb=" N ILE K 33 " --> pdb=" O SER K 50 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N SER K 50 " --> pdb=" O ILE K 33 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA K 35 " --> pdb=" O GLN K 48 " (cutoff:3.500A) removed outlier: 9.640A pdb=" N SER K 50 " --> pdb=" O ASP K 69 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ASP K 69 " --> pdb=" O SER K 50 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N THR K 65 " --> pdb=" O GLY K 54 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'K' and resid 33 through 37 removed outlier: 8.347A pdb=" N ILE K 33 " --> pdb=" O SER K 50 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N SER K 50 " --> pdb=" O ILE K 33 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA K 35 " --> pdb=" O GLN K 48 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N TYR K 98 " --> pdb=" O THR K 49 " (cutoff:3.500A) removed outlier: 9.481A pdb=" N SER K 51 " --> pdb=" O HIS K 96 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N HIS K 96 " --> pdb=" O SER K 51 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N TYR K 53 " --> pdb=" O ASP K 94 " (cutoff:3.500A) removed outlier: 10.279A pdb=" N ASP K 94 " --> pdb=" O TYR K 53 " (cutoff:3.500A) removed outlier: 14.954A pdb=" N LEU K 55 " --> pdb=" O ILE K 92 " (cutoff:3.500A) removed outlier: 17.327A pdb=" N ILE K 92 " --> pdb=" O LEU K 55 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'K' and resid 82 through 85 Processing sheet with id=AJ3, first strand: chain 'K' and resid 147 through 154 Processing sheet with id=AJ4, first strand: chain 'K' and resid 237 through 238 Processing sheet with id=AJ5, first strand: chain 'K' and resid 173 through 174 removed outlier: 3.556A pdb=" N GLU K 173 " --> pdb=" O ARG K 230 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'K' and resid 179 through 181 Processing sheet with id=AJ7, first strand: chain 'K' and resid 275 through 279 Processing sheet with id=AJ8, first strand: chain 'L' and resid 156 through 157 removed outlier: 6.106A pdb=" N PHE L 128 " --> pdb=" O TYR L 139 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N TYR L 139 " --> pdb=" O PHE L 128 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ILE L 130 " --> pdb=" O ASN L 137 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N TYR L 139 " --> pdb=" O PRO L 150 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'L' and resid 198 through 200 removed outlier: 5.130A pdb=" N PHE L 214 " --> pdb=" O LEU L 253 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL L 256 " --> pdb=" O VAL L 241 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N VAL L 241 " --> pdb=" O VAL L 256 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'L' and resid 229 through 231 removed outlier: 4.249A pdb=" N ALA L 239 " --> pdb=" O ILE L 230 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N VAL L 241 " --> pdb=" O VAL L 256 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL L 256 " --> pdb=" O VAL L 241 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'M' and resid 3 through 6 Processing sheet with id=AK3, first strand: chain 'M' and resid 46 through 52 removed outlier: 5.670A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY M 49 " --> pdb=" O TRP M 36 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'N' and resid 9 through 12 removed outlier: 3.725A pdb=" N VAL N 12 " --> pdb=" O THR N 107 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N TRP N 34 " --> pdb=" O VAL N 46 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'N' and resid 9 through 12 removed outlier: 3.725A pdb=" N VAL N 12 " --> pdb=" O THR N 107 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'N' and resid 18 through 23 Processing sheet with id=AK7, first strand: chain 'O' and resid 3 through 6 Processing sheet with id=AK8, first strand: chain 'O' and resid 3 through 6 removed outlier: 3.666A pdb=" N ALA O 78 " --> pdb=" O ASP O 73 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'O' and resid 10 through 11 removed outlier: 4.180A pdb=" N THR O 119 " --> pdb=" O GLU O 10 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE O 34 " --> pdb=" O TRP O 50 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N TRP O 50 " --> pdb=" O ILE O 34 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N TRP O 36 " --> pdb=" O MET O 48 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'O' and resid 10 through 11 removed outlier: 4.180A pdb=" N THR O 119 " --> pdb=" O GLU O 10 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR O 98 " --> pdb=" O TYR O 111 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'P' and resid 9 through 11 removed outlier: 7.100A pdb=" N VAL P 10 " --> pdb=" O THR P 107 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR P 86 " --> pdb=" O THR P 104 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N TRP P 34 " --> pdb=" O VAL P 46 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'P' and resid 9 through 11 removed outlier: 7.100A pdb=" N VAL P 10 " --> pdb=" O THR P 107 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR P 86 " --> pdb=" O THR P 104 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'P' and resid 18 through 23 Processing sheet with id=AL5, first strand: chain 'Q' and resid 3 through 6 Processing sheet with id=AL6, first strand: chain 'Q' and resid 3 through 6 removed outlier: 3.626A pdb=" N ALA Q 78 " --> pdb=" O ASP Q 73 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP Q 73 " --> pdb=" O ALA Q 78 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'Q' and resid 58 through 60 removed outlier: 3.735A pdb=" N LYS Q 59 " --> pdb=" O TRP Q 50 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TRP Q 50 " --> pdb=" O LYS Q 59 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N TRP Q 47 " --> pdb=" O ARG Q 38 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ARG Q 38 " --> pdb=" O TRP Q 47 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'R' and resid 11 through 12 removed outlier: 3.991A pdb=" N ALA R 84 " --> pdb=" O VAL R 106 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N TRP R 34 " --> pdb=" O VAL R 46 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'R' and resid 11 through 12 removed outlier: 3.991A pdb=" N ALA R 84 " --> pdb=" O VAL R 106 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'R' and resid 17 through 23 Processing sheet with id=AM2, first strand: chain 'S' and resid 10 through 11 removed outlier: 3.882A pdb=" N THR S 119 " --> pdb=" O GLU S 10 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'S' and resid 10 through 11 removed outlier: 3.882A pdb=" N THR S 119 " --> pdb=" O GLU S 10 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'S' and resid 18 through 23 removed outlier: 3.912A pdb=" N GLU S 82 " --> pdb=" O SER S 69 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER S 69 " --> pdb=" O GLU S 82 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'S' and resid 18 through 23 removed outlier: 3.692A pdb=" N ALA S 78 " --> pdb=" O ASP S 73 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP S 73 " --> pdb=" O ALA S 78 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'T' and resid 9 through 12 removed outlier: 6.549A pdb=" N TRP T 34 " --> pdb=" O VAL T 46 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'T' and resid 9 through 12 Processing sheet with id=AM8, first strand: chain 'T' and resid 18 through 23 1493 hydrogen bonds defined for protein. 3723 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: 17.00 Time building geometry restraints manager: 14.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12433 1.34 - 1.47: 9784 1.47 - 1.59: 17066 1.59 - 1.71: 1 1.71 - 1.83: 328 Bond restraints: 39612 Sorted by residual: bond pdb=" CB CYS K 27 " pdb=" SG CYS K 27 " ideal model delta sigma weight residual 1.808 1.734 0.074 3.30e-02 9.18e+02 5.02e+00 bond pdb=" CB PRO M 41 " pdb=" CG PRO M 41 " ideal model delta sigma weight residual 1.492 1.599 -0.107 5.00e-02 4.00e+02 4.56e+00 bond pdb=" C THR G 152 " pdb=" N PRO G 153 " ideal model delta sigma weight residual 1.330 1.351 -0.021 1.22e-02 6.72e+03 3.04e+00 bond pdb=" CB CYS H 27 " pdb=" SG CYS H 27 " ideal model delta sigma weight residual 1.808 1.755 0.053 3.30e-02 9.18e+02 2.62e+00 bond pdb=" C1 NAG D 501 " pdb=" O5 NAG D 501 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.20e+00 ... (remaining 39607 not shown) Histogram of bond angle deviations from ideal: 98.20 - 105.40: 977 105.40 - 112.61: 20988 112.61 - 119.81: 12556 119.81 - 127.02: 18827 127.02 - 134.23: 576 Bond angle restraints: 53924 Sorted by residual: angle pdb=" CA PRO M 41 " pdb=" N PRO M 41 " pdb=" CD PRO M 41 " ideal model delta sigma weight residual 112.00 105.80 6.20 1.40e+00 5.10e-01 1.96e+01 angle pdb=" N VAL C 238 " pdb=" CA VAL C 238 " pdb=" C VAL C 238 " ideal model delta sigma weight residual 112.96 108.96 4.00 1.00e+00 1.00e+00 1.60e+01 angle pdb=" N VAL G 148 " pdb=" CA VAL G 148 " pdb=" C VAL G 148 " ideal model delta sigma weight residual 111.91 108.37 3.54 8.90e-01 1.26e+00 1.58e+01 angle pdb=" CA MET C 151 " pdb=" CB MET C 151 " pdb=" CG MET C 151 " ideal model delta sigma weight residual 114.10 121.71 -7.61 2.00e+00 2.50e-01 1.45e+01 angle pdb=" N VAL B 198 " pdb=" CA VAL B 198 " pdb=" C VAL B 198 " ideal model delta sigma weight residual 106.72 112.51 -5.79 1.59e+00 3.96e-01 1.33e+01 ... (remaining 53919 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.48: 22039 21.48 - 42.97: 1509 42.97 - 64.45: 187 64.45 - 85.93: 70 85.93 - 107.42: 39 Dihedral angle restraints: 23844 sinusoidal: 9416 harmonic: 14428 Sorted by residual: dihedral pdb=" CB CYS A 62 " pdb=" SG CYS A 62 " pdb=" SG CYS A 94 " pdb=" CB CYS A 94 " ideal model delta sinusoidal sigma weight residual -86.00 -173.21 87.21 1 1.00e+01 1.00e-02 9.13e+01 dihedral pdb=" CB CYS E 151 " pdb=" SG CYS E 151 " pdb=" SG CYS E 266 " pdb=" CB CYS E 266 " ideal model delta sinusoidal sigma weight residual -86.00 -172.21 86.21 1 1.00e+01 1.00e-02 8.97e+01 dihedral pdb=" CB CYS H 151 " pdb=" SG CYS H 151 " pdb=" SG CYS H 266 " pdb=" CB CYS H 266 " ideal model delta sinusoidal sigma weight residual -86.00 -171.07 85.07 1 1.00e+01 1.00e-02 8.78e+01 ... (remaining 23841 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 4689 0.050 - 0.100: 1051 0.100 - 0.151: 257 0.151 - 0.201: 8 0.201 - 0.251: 2 Chirality restraints: 6007 Sorted by residual: chirality pdb=" C1 NAG H 502 " pdb=" ND2 ASN H 318 " pdb=" C2 NAG H 502 " pdb=" O5 NAG H 502 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" C1 NAG K 502 " pdb=" ND2 ASN K 318 " pdb=" C2 NAG K 502 " pdb=" O5 NAG K 502 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA TRP A 409 " pdb=" N TRP A 409 " pdb=" C TRP A 409 " pdb=" CB TRP A 409 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.95e-01 ... (remaining 6004 not shown) Planarity restraints: 6919 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR G 152 " -0.091 5.00e-02 4.00e+02 1.40e-01 3.12e+01 pdb=" N PRO G 153 " 0.241 5.00e-02 4.00e+02 pdb=" CA PRO G 153 " -0.078 5.00e-02 4.00e+02 pdb=" CD PRO G 153 " -0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA M 40 " 0.079 5.00e-02 4.00e+02 1.16e-01 2.14e+01 pdb=" N PRO M 41 " -0.200 5.00e-02 4.00e+02 pdb=" CA PRO M 41 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO M 41 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE L 128 " 0.068 5.00e-02 4.00e+02 1.03e-01 1.71e+01 pdb=" N PRO L 129 " -0.179 5.00e-02 4.00e+02 pdb=" CA PRO L 129 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO L 129 " 0.055 5.00e-02 4.00e+02 ... (remaining 6916 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 921 2.69 - 3.24: 36387 3.24 - 3.79: 59288 3.79 - 4.35: 80003 4.35 - 4.90: 134436 Nonbonded interactions: 311035 Sorted by model distance: nonbonded pdb=" O SER E 184 " pdb=" ND2 ASN O 31 " model vdw 2.133 2.520 nonbonded pdb=" OG1 THR D 358 " pdb=" OD1 ASN D 360 " model vdw 2.173 2.440 nonbonded pdb=" OD1 ASN Q 106 " pdb=" N GLY Q 107 " model vdw 2.178 2.520 nonbonded pdb=" NH2 ARG S 44 " pdb=" OE2 GLU T 3 " model vdw 2.184 2.520 nonbonded pdb=" OG SER J 291 " pdb=" OE1 GLU J 292 " model vdw 2.194 2.440 ... (remaining 311030 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 'D' selection = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' } ncs_group { reference = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' } 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: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.770 Check model and map are aligned: 0.530 Set scattering table: 0.310 Process input model: 100.880 Find NCS groups from input model: 2.570 Set up NCS constraints: 0.400 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 39612 Z= 0.238 Angle : 0.618 9.572 53924 Z= 0.325 Chirality : 0.045 0.251 6007 Planarity : 0.005 0.140 6912 Dihedral : 14.960 107.418 14464 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.05 % Allowed : 0.43 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.12), residues: 4944 helix: 1.22 (0.26), residues: 461 sheet: -0.01 (0.12), residues: 1708 loop : -0.58 (0.12), residues: 2775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 36 HIS 0.006 0.001 HIS J 230 PHE 0.025 0.001 PHE S 29 TYR 0.046 0.001 TYR E 53 ARG 0.013 0.000 ARG I 185 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 648 time to evaluate : 4.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 390 HIS cc_start: 0.6618 (m-70) cc_final: 0.6347 (m-70) REVERT: D 434 TYR cc_start: 0.8598 (t80) cc_final: 0.8355 (t80) REVERT: E 199 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7414 (mm-30) REVERT: E 201 GLU cc_start: 0.8083 (tm-30) cc_final: 0.7775 (tm-30) REVERT: E 365 MET cc_start: 0.6571 (tpp) cc_final: 0.6320 (tmm) REVERT: I 174 ASP cc_start: 0.8324 (t70) cc_final: 0.8067 (t0) REVERT: I 191 TYR cc_start: 0.7927 (p90) cc_final: 0.7219 (p90) REVERT: I 208 GLN cc_start: 0.8137 (pt0) cc_final: 0.7774 (pt0) REVERT: J 24 TYR cc_start: 0.8310 (m-80) cc_final: 0.8061 (m-10) REVERT: L 184 MET cc_start: 0.8378 (ptm) cc_final: 0.8081 (ptt) REVERT: N 104 THR cc_start: 0.8611 (m) cc_final: 0.8325 (t) REVERT: O 32 TYR cc_start: 0.4662 (m-80) cc_final: 0.3232 (m-80) REVERT: P 44 VAL cc_start: 0.9039 (t) cc_final: 0.8679 (p) REVERT: R 34 TRP cc_start: 0.8344 (m100) cc_final: 0.8092 (m100) REVERT: T 4 LEU cc_start: 0.8591 (mt) cc_final: 0.8005 (mt) REVERT: T 97 GLU cc_start: 0.7536 (pm20) cc_final: 0.7322 (pm20) outliers start: 2 outliers final: 1 residues processed: 649 average time/residue: 0.4823 time to fit residues: 516.5091 Evaluate side-chains 541 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 540 time to evaluate : 3.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 232 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 412 optimal weight: 6.9990 chunk 369 optimal weight: 4.9990 chunk 205 optimal weight: 5.9990 chunk 126 optimal weight: 0.9990 chunk 249 optimal weight: 0.6980 chunk 197 optimal weight: 0.8980 chunk 382 optimal weight: 10.0000 chunk 148 optimal weight: 4.9990 chunk 232 optimal weight: 20.0000 chunk 284 optimal weight: 0.0000 chunk 443 optimal weight: 5.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 332 ASN C 197 GLN ** D 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 361 HIS G 264 ASN H 159 GLN H 212 ASN H 341 GLN H 361 HIS ** I 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 60 ASN ** M 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 114 GLN P 37 GLN Q 55 ASN S 106 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.0758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 39612 Z= 0.235 Angle : 0.590 10.350 53924 Z= 0.302 Chirality : 0.045 0.244 6007 Planarity : 0.005 0.077 6912 Dihedral : 7.830 76.233 5663 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.43 % Favored : 95.55 % Rotamer: Outliers : 1.24 % Allowed : 7.93 % Favored : 90.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.12), residues: 4944 helix: 1.23 (0.26), residues: 473 sheet: -0.02 (0.12), residues: 1727 loop : -0.50 (0.12), residues: 2744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP P 34 HIS 0.006 0.001 HIS J 230 PHE 0.018 0.001 PHE A 365 TYR 0.017 0.001 TYR G 308 ARG 0.007 0.000 ARG I 185 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 571 time to evaluate : 4.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 311 ILE cc_start: 0.8073 (pt) cc_final: 0.7844 (pt) REVERT: D 385 ASP cc_start: 0.7670 (p0) cc_final: 0.7452 (p0) REVERT: E 201 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7348 (tm-30) REVERT: E 365 MET cc_start: 0.6517 (tpp) cc_final: 0.6206 (tmm) REVERT: F 151 MET cc_start: 0.8155 (tpp) cc_final: 0.7797 (tpp) REVERT: I 191 TYR cc_start: 0.7933 (p90) cc_final: 0.7207 (p90) REVERT: J 24 TYR cc_start: 0.8336 (m-80) cc_final: 0.8129 (m-80) REVERT: J 142 ILE cc_start: 0.8089 (tt) cc_final: 0.7865 (tp) REVERT: L 184 MET cc_start: 0.8451 (ptm) cc_final: 0.8216 (ptt) REVERT: P 44 VAL cc_start: 0.9168 (t) cc_final: 0.8921 (p) REVERT: T 4 LEU cc_start: 0.8592 (mt) cc_final: 0.8110 (mt) REVERT: T 97 GLU cc_start: 0.7563 (pm20) cc_final: 0.7299 (pm20) outliers start: 52 outliers final: 34 residues processed: 590 average time/residue: 0.4900 time to fit residues: 478.4947 Evaluate side-chains 563 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 529 time to evaluate : 4.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain B residue 232 GLN Chi-restraints excluded: chain B residue 302 ASP Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 263 ASP Chi-restraints excluded: chain E residue 374 CYS Chi-restraints excluded: chain G residue 396 GLN Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 192 ASP Chi-restraints excluded: chain J residue 55 MET Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain J residue 315 ILE Chi-restraints excluded: chain J residue 361 ILE Chi-restraints excluded: chain J residue 374 VAL Chi-restraints excluded: chain J residue 397 THR Chi-restraints excluded: chain J residue 436 LEU Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain K residue 277 THR Chi-restraints excluded: chain O residue 101 MET Chi-restraints excluded: chain Q residue 48 MET Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain T residue 32 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 246 optimal weight: 0.5980 chunk 137 optimal weight: 4.9990 chunk 368 optimal weight: 3.9990 chunk 301 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 443 optimal weight: 4.9990 chunk 479 optimal weight: 0.1980 chunk 395 optimal weight: 0.0770 chunk 440 optimal weight: 20.0000 chunk 151 optimal weight: 0.9980 chunk 356 optimal weight: 7.9990 overall best weight: 1.1740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 232 GLN C 197 GLN D 77 GLN D 438 ASN E 361 HIS G 264 ASN H 361 HIS I 152 HIS I 208 GLN M 35 HIS M 106 ASN N 30 GLN ** O 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 114 GLN Q 100 GLN S 55 ASN S 57 ASN S 106 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.0979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 39612 Z= 0.193 Angle : 0.555 7.933 53924 Z= 0.283 Chirality : 0.044 0.238 6007 Planarity : 0.004 0.060 6912 Dihedral : 6.012 76.193 5663 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.64 % Allowed : 10.98 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.12), residues: 4944 helix: 1.36 (0.26), residues: 473 sheet: 0.07 (0.12), residues: 1723 loop : -0.48 (0.12), residues: 2748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP O 36 HIS 0.005 0.001 HIS J 230 PHE 0.016 0.001 PHE A 365 TYR 0.016 0.001 TYR G 308 ARG 0.004 0.000 ARG D 289 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 548 time to evaluate : 4.860 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: B 21 ARG cc_start: 0.7912 (tpt90) cc_final: 0.7453 (mmm160) REVERT: B 70 MET cc_start: 0.7833 (mmm) cc_final: 0.7586 (tpt) REVERT: B 311 ILE cc_start: 0.8056 (pt) cc_final: 0.7835 (pt) REVERT: D 385 ASP cc_start: 0.7701 (p0) cc_final: 0.7389 (p0) REVERT: E 201 GLU cc_start: 0.7801 (tm-30) cc_final: 0.7213 (tm-30) REVERT: F 151 MET cc_start: 0.8289 (tpp) cc_final: 0.7937 (tpp) REVERT: I 169 LYS cc_start: 0.8881 (mptt) cc_final: 0.8557 (mmtt) REVERT: I 191 TYR cc_start: 0.7947 (p90) cc_final: 0.7213 (p90) REVERT: J 24 TYR cc_start: 0.8423 (m-80) cc_final: 0.8162 (m-80) REVERT: L 125 ASP cc_start: 0.6318 (OUTLIER) cc_final: 0.6037 (t0) REVERT: P 44 VAL cc_start: 0.9216 (t) cc_final: 0.8849 (p) REVERT: T 4 LEU cc_start: 0.8620 (mt) cc_final: 0.8133 (mt) REVERT: T 87 TYR cc_start: 0.8320 (m-80) cc_final: 0.7883 (m-80) REVERT: T 97 GLU cc_start: 0.7534 (pm20) cc_final: 0.7278 (pm20) outliers start: 69 outliers final: 48 residues processed: 578 average time/residue: 0.4772 time to fit residues: 455.7154 Evaluate side-chains 570 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 521 time to evaluate : 3.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 222 LYS Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 348 GLU Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 263 ASP Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 396 GLN Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 128 GLU Chi-restraints excluded: chain H residue 192 ASP Chi-restraints excluded: chain H residue 241 ASP Chi-restraints excluded: chain H residue 297 THR Chi-restraints excluded: chain I residue 256 VAL Chi-restraints excluded: chain J residue 55 MET Chi-restraints excluded: chain J residue 167 SER Chi-restraints excluded: chain J residue 246 ASP Chi-restraints excluded: chain J residue 315 ILE Chi-restraints excluded: chain J residue 374 VAL Chi-restraints excluded: chain J residue 397 THR Chi-restraints excluded: chain J residue 436 LEU Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain K residue 277 THR Chi-restraints excluded: chain L residue 125 ASP Chi-restraints excluded: chain M residue 108 ASP Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain Q residue 48 MET Chi-restraints excluded: chain R residue 27 LEU Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain T residue 29 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 438 optimal weight: 4.9990 chunk 333 optimal weight: 2.9990 chunk 230 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 211 optimal weight: 5.9990 chunk 298 optimal weight: 9.9990 chunk 445 optimal weight: 4.9990 chunk 471 optimal weight: 10.0000 chunk 232 optimal weight: 20.0000 chunk 422 optimal weight: 9.9990 chunk 127 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 ASN B 332 ASN B 361 HIS ** C 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 GLN D 157 ASN ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 GLN E 81 GLN ** E 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 230 HIS G 264 ASN H 216 GLN H 361 HIS J 368 GLN ** K 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 225 GLN O 52 ASN O 114 GLN ** Q 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 106 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.132 39612 Z= 0.536 Angle : 0.702 11.651 53924 Z= 0.357 Chirality : 0.049 0.267 6007 Planarity : 0.005 0.058 6912 Dihedral : 5.897 77.401 5660 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.21 % Allowed : 13.29 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.48 (0.12), residues: 4944 helix: 0.92 (0.25), residues: 491 sheet: -0.09 (0.12), residues: 1729 loop : -0.66 (0.12), residues: 2724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP O 36 HIS 0.015 0.002 HIS J 230 PHE 0.023 0.002 PHE A 365 TYR 0.027 0.002 TYR G 308 ARG 0.007 0.001 ARG H 362 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 524 time to evaluate : 4.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 114 PHE cc_start: 0.8227 (OUTLIER) cc_final: 0.7827 (t80) REVERT: B 239 ASN cc_start: 0.8295 (t0) cc_final: 0.7943 (t0) REVERT: C 118 MET cc_start: 0.5880 (mmm) cc_final: 0.5452 (mmm) REVERT: C 211 ASN cc_start: 0.8322 (t0) cc_final: 0.7860 (t0) REVERT: D 145 THR cc_start: 0.8569 (OUTLIER) cc_final: 0.8324 (p) REVERT: D 385 ASP cc_start: 0.7843 (p0) cc_final: 0.7439 (p0) REVERT: E 201 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7626 (tm-30) REVERT: F 151 MET cc_start: 0.8344 (tpp) cc_final: 0.8004 (tpp) REVERT: I 169 LYS cc_start: 0.8929 (mptt) cc_final: 0.8482 (mmtt) REVERT: I 191 TYR cc_start: 0.8091 (p90) cc_final: 0.7477 (p90) REVERT: J 364 GLU cc_start: 0.7303 (mm-30) cc_final: 0.7062 (mm-30) REVERT: K 232 GLN cc_start: 0.7942 (OUTLIER) cc_final: 0.7654 (mp10) REVERT: O 32 TYR cc_start: 0.5401 (m-80) cc_final: 0.4668 (m-80) REVERT: Q 106 ASN cc_start: 0.7510 (t0) cc_final: 0.7280 (t0) REVERT: T 4 LEU cc_start: 0.8729 (mt) cc_final: 0.8067 (mt) REVERT: T 87 TYR cc_start: 0.8352 (m-80) cc_final: 0.7871 (m-80) REVERT: T 97 GLU cc_start: 0.7565 (pm20) cc_final: 0.7299 (pm20) outliers start: 135 outliers final: 90 residues processed: 614 average time/residue: 0.4983 time to fit residues: 506.1225 Evaluate side-chains 599 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 506 time to evaluate : 4.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 376 CYS Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 114 PHE Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 199 TYR Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 348 GLU Chi-restraints excluded: chain D residue 368 GLN Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 263 ASP Chi-restraints excluded: chain E residue 324 LYS Chi-restraints excluded: chain E residue 374 CYS Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 225 ASP Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 128 GLU Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 192 ASP Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain H residue 241 ASP Chi-restraints excluded: chain H residue 297 THR Chi-restraints excluded: chain I residue 230 ILE Chi-restraints excluded: chain I residue 245 VAL Chi-restraints excluded: chain I residue 256 VAL Chi-restraints excluded: chain I residue 265 VAL Chi-restraints excluded: chain J residue 55 MET Chi-restraints excluded: chain J residue 137 VAL Chi-restraints excluded: chain J residue 167 SER Chi-restraints excluded: chain J residue 246 ASP Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain J residue 315 ILE Chi-restraints excluded: chain J residue 361 ILE Chi-restraints excluded: chain J residue 374 VAL Chi-restraints excluded: chain J residue 397 THR Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain K residue 232 GLN Chi-restraints excluded: chain K residue 277 THR Chi-restraints excluded: chain K residue 329 VAL Chi-restraints excluded: chain L residue 192 THR Chi-restraints excluded: chain L residue 265 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 55 SER Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain Q residue 34 ILE Chi-restraints excluded: chain Q residue 48 MET Chi-restraints excluded: chain Q residue 99 LEU Chi-restraints excluded: chain R residue 27 LEU Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 75 ILE Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain S residue 28 THR Chi-restraints excluded: chain S residue 37 VAL Chi-restraints excluded: chain T residue 29 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 392 optimal weight: 8.9990 chunk 267 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 351 optimal weight: 0.7980 chunk 194 optimal weight: 6.9990 chunk 402 optimal weight: 0.9980 chunk 326 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 240 optimal weight: 9.9990 chunk 423 optimal weight: 0.1980 chunk 119 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 332 ASN C 197 GLN D 50 HIS D 368 GLN G 43 ASN G 264 ASN H 361 HIS ** I 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 361 HIS ** O 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 114 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 39612 Z= 0.166 Angle : 0.556 10.437 53924 Z= 0.285 Chirality : 0.044 0.251 6007 Planarity : 0.004 0.060 6912 Dihedral : 5.359 76.451 5660 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.24 % Allowed : 15.21 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.12), residues: 4944 helix: 1.34 (0.26), residues: 473 sheet: -0.06 (0.13), residues: 1710 loop : -0.52 (0.12), residues: 2761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP O 36 HIS 0.004 0.001 HIS G 3 PHE 0.015 0.001 PHE S 64 TYR 0.016 0.001 TYR F 209 ARG 0.009 0.000 ARG I 185 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 528 time to evaluate : 4.221 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: A 260 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.6355 (mp0) REVERT: B 311 ILE cc_start: 0.8193 (pt) cc_final: 0.7842 (pt) REVERT: C 211 ASN cc_start: 0.8351 (t0) cc_final: 0.7993 (t0) REVERT: D 385 ASP cc_start: 0.7776 (p0) cc_final: 0.7395 (p0) REVERT: F 151 MET cc_start: 0.8347 (tpp) cc_final: 0.8067 (tpp) REVERT: F 208 GLN cc_start: 0.6919 (pm20) cc_final: 0.6627 (pm20) REVERT: H 287 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.8769 (mt) REVERT: H 365 MET cc_start: 0.5930 (pmm) cc_final: 0.5711 (pmm) REVERT: I 191 TYR cc_start: 0.8024 (p90) cc_final: 0.7360 (p90) REVERT: J 166 LEU cc_start: 0.8532 (tp) cc_final: 0.8185 (mp) REVERT: L 184 MET cc_start: 0.7967 (ptt) cc_final: 0.7747 (ptt) REVERT: O 47 TRP cc_start: 0.8392 (t60) cc_final: 0.7563 (t60) REVERT: P 30 GLN cc_start: 0.7742 (mm-40) cc_final: 0.6892 (mt0) REVERT: Q 106 ASN cc_start: 0.6962 (t0) cc_final: 0.6689 (t0) REVERT: S 111 TYR cc_start: 0.4800 (t80) cc_final: 0.4373 (t80) REVERT: T 87 TYR cc_start: 0.8305 (m-80) cc_final: 0.7736 (m-80) REVERT: T 97 GLU cc_start: 0.7596 (pm20) cc_final: 0.7269 (pm20) outliers start: 94 outliers final: 60 residues processed: 582 average time/residue: 0.4882 time to fit residues: 468.5285 Evaluate side-chains 560 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 498 time to evaluate : 4.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 222 LYS Chi-restraints excluded: chain B residue 226 CYS Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 302 ASP Chi-restraints excluded: chain C residue 199 TYR Chi-restraints excluded: chain C residue 218 LYS Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 348 GLU Chi-restraints excluded: chain D residue 368 GLN Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain E residue 167 MET Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 263 ASP Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 192 ASP Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain H residue 241 ASP Chi-restraints excluded: chain H residue 287 LEU Chi-restraints excluded: chain H residue 297 THR Chi-restraints excluded: chain I residue 120 MET Chi-restraints excluded: chain I residue 230 ILE Chi-restraints excluded: chain I residue 256 VAL Chi-restraints excluded: chain J residue 55 MET Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 167 SER Chi-restraints excluded: chain J residue 315 ILE Chi-restraints excluded: chain J residue 374 VAL Chi-restraints excluded: chain J residue 397 THR Chi-restraints excluded: chain J residue 436 LEU Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain L residue 161 VAL Chi-restraints excluded: chain L residue 207 VAL Chi-restraints excluded: chain L residue 230 ILE Chi-restraints excluded: chain O residue 2 VAL Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain Q residue 34 ILE Chi-restraints excluded: chain Q residue 48 MET Chi-restraints excluded: chain R residue 27 LEU Chi-restraints excluded: chain R residue 108 VAL Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain T residue 29 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 158 optimal weight: 0.5980 chunk 424 optimal weight: 7.9990 chunk 93 optimal weight: 9.9990 chunk 276 optimal weight: 5.9990 chunk 116 optimal weight: 5.9990 chunk 472 optimal weight: 10.0000 chunk 391 optimal weight: 10.0000 chunk 218 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 156 optimal weight: 0.5980 chunk 247 optimal weight: 5.9990 overall best weight: 1.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN ** C 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 264 ASN H 361 HIS ** I 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 239 ASN ** O 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 114 GLN S 106 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 39612 Z= 0.251 Angle : 0.569 10.869 53924 Z= 0.290 Chirality : 0.045 0.254 6007 Planarity : 0.004 0.059 6912 Dihedral : 5.309 76.762 5660 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.57 % Allowed : 15.62 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.12), residues: 4944 helix: 1.34 (0.25), residues: 473 sheet: -0.08 (0.12), residues: 1734 loop : -0.51 (0.12), residues: 2737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP O 36 HIS 0.006 0.001 HIS J 230 PHE 0.016 0.001 PHE A 365 TYR 0.018 0.001 TYR G 308 ARG 0.010 0.000 ARG I 185 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 506 time to evaluate : 3.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.8002 (mmm) cc_final: 0.7599 (mtt) REVERT: A 260 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.6401 (mp0) REVERT: B 114 PHE cc_start: 0.8066 (OUTLIER) cc_final: 0.7734 (t80) REVERT: B 311 ILE cc_start: 0.8267 (pt) cc_final: 0.7915 (pt) REVERT: C 211 ASN cc_start: 0.8336 (t0) cc_final: 0.7921 (t0) REVERT: D 385 ASP cc_start: 0.7783 (p0) cc_final: 0.7408 (p0) REVERT: F 151 MET cc_start: 0.8402 (tpp) cc_final: 0.8097 (tpp) REVERT: H 287 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.8790 (mt) REVERT: I 191 TYR cc_start: 0.8027 (p90) cc_final: 0.7407 (p90) REVERT: J 346 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7755 (mp) REVERT: P 30 GLN cc_start: 0.7724 (mm-40) cc_final: 0.6900 (mt0) REVERT: Q 106 ASN cc_start: 0.7059 (t0) cc_final: 0.6810 (t0) REVERT: S 111 TYR cc_start: 0.4858 (t80) cc_final: 0.4364 (t80) REVERT: T 4 LEU cc_start: 0.8651 (mp) cc_final: 0.8438 (mt) REVERT: T 87 TYR cc_start: 0.8287 (m-80) cc_final: 0.7727 (m-80) REVERT: T 97 GLU cc_start: 0.7591 (pm20) cc_final: 0.7266 (pm20) outliers start: 108 outliers final: 78 residues processed: 573 average time/residue: 0.4882 time to fit residues: 461.8047 Evaluate side-chains 585 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 503 time to evaluate : 4.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 376 CYS Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 114 PHE Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 222 LYS Chi-restraints excluded: chain B residue 226 CYS Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 199 TYR Chi-restraints excluded: chain C residue 218 LYS Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 348 GLU Chi-restraints excluded: chain E residue 167 MET Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain E residue 200 CYS Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 263 ASP Chi-restraints excluded: chain E residue 324 LYS Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 192 ASP Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain H residue 241 ASP Chi-restraints excluded: chain H residue 287 LEU Chi-restraints excluded: chain H residue 297 THR Chi-restraints excluded: chain I residue 120 MET Chi-restraints excluded: chain I residue 230 ILE Chi-restraints excluded: chain I residue 256 VAL Chi-restraints excluded: chain I residue 265 VAL Chi-restraints excluded: chain J residue 55 MET Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 167 SER Chi-restraints excluded: chain J residue 246 ASP Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain J residue 315 ILE Chi-restraints excluded: chain J residue 346 LEU Chi-restraints excluded: chain J residue 374 VAL Chi-restraints excluded: chain J residue 397 THR Chi-restraints excluded: chain J residue 436 LEU Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 267 THR Chi-restraints excluded: chain L residue 161 VAL Chi-restraints excluded: chain L residue 199 TYR Chi-restraints excluded: chain L residue 207 VAL Chi-restraints excluded: chain L residue 230 ILE Chi-restraints excluded: chain L residue 265 VAL Chi-restraints excluded: chain O residue 2 VAL Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain Q residue 34 ILE Chi-restraints excluded: chain Q residue 48 MET Chi-restraints excluded: chain Q residue 99 LEU Chi-restraints excluded: chain R residue 27 LEU Chi-restraints excluded: chain R residue 75 ILE Chi-restraints excluded: chain R residue 108 VAL Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain T residue 29 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 455 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 269 optimal weight: 2.9990 chunk 344 optimal weight: 6.9990 chunk 267 optimal weight: 0.6980 chunk 397 optimal weight: 5.9990 chunk 263 optimal weight: 0.3980 chunk 470 optimal weight: 3.9990 chunk 294 optimal weight: 10.0000 chunk 286 optimal weight: 9.9990 chunk 217 optimal weight: 3.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 361 HIS ** C 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 GLN ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 264 ASN H 361 HIS ** I 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 114 GLN S 106 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 39612 Z= 0.318 Angle : 0.602 11.406 53924 Z= 0.306 Chirality : 0.046 0.262 6007 Planarity : 0.004 0.057 6912 Dihedral : 5.368 77.293 5660 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.76 % Allowed : 15.93 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.12), residues: 4944 helix: 1.42 (0.26), residues: 461 sheet: -0.20 (0.12), residues: 1795 loop : -0.51 (0.12), residues: 2688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP O 36 HIS 0.008 0.001 HIS J 230 PHE 0.016 0.002 PHE A 365 TYR 0.021 0.001 TYR G 308 ARG 0.011 0.000 ARG I 185 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 514 time to evaluate : 4.735 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: A 260 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.6521 (mp0) REVERT: B 114 PHE cc_start: 0.8113 (OUTLIER) cc_final: 0.7763 (t80) REVERT: C 211 ASN cc_start: 0.8375 (t0) cc_final: 0.7961 (t0) REVERT: D 385 ASP cc_start: 0.7812 (p0) cc_final: 0.7386 (p0) REVERT: E 81 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.8200 (mt0) REVERT: F 151 MET cc_start: 0.8406 (tpp) cc_final: 0.8116 (tpp) REVERT: H 287 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.8800 (mt) REVERT: I 191 TYR cc_start: 0.8069 (p90) cc_final: 0.7430 (p90) REVERT: J 346 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7734 (mp) REVERT: O 47 TRP cc_start: 0.8409 (t60) cc_final: 0.7583 (t60) REVERT: Q 106 ASN cc_start: 0.7223 (t0) cc_final: 0.6976 (t0) REVERT: S 111 TYR cc_start: 0.5015 (t80) cc_final: 0.4512 (t80) REVERT: T 4 LEU cc_start: 0.8695 (mp) cc_final: 0.8469 (mt) REVERT: T 87 TYR cc_start: 0.8288 (m-80) cc_final: 0.7681 (m-80) REVERT: T 97 GLU cc_start: 0.7584 (pm20) cc_final: 0.7267 (pm20) outliers start: 116 outliers final: 90 residues processed: 590 average time/residue: 0.4879 time to fit residues: 479.6612 Evaluate side-chains 596 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 501 time to evaluate : 4.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 376 CYS Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 114 PHE Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 222 LYS Chi-restraints excluded: chain B residue 226 CYS Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 199 TYR Chi-restraints excluded: chain C residue 218 LYS Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 348 GLU Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 167 MET Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain E residue 200 CYS Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 263 ASP Chi-restraints excluded: chain E residue 324 LYS Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 192 ASP Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain H residue 241 ASP Chi-restraints excluded: chain H residue 287 LEU Chi-restraints excluded: chain H residue 297 THR Chi-restraints excluded: chain I residue 230 ILE Chi-restraints excluded: chain I residue 256 VAL Chi-restraints excluded: chain I residue 265 VAL Chi-restraints excluded: chain J residue 55 MET Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 167 SER Chi-restraints excluded: chain J residue 246 ASP Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain J residue 315 ILE Chi-restraints excluded: chain J residue 346 LEU Chi-restraints excluded: chain J residue 374 VAL Chi-restraints excluded: chain J residue 397 THR Chi-restraints excluded: chain J residue 436 LEU Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 267 THR Chi-restraints excluded: chain K residue 277 THR Chi-restraints excluded: chain L residue 161 VAL Chi-restraints excluded: chain L residue 199 TYR Chi-restraints excluded: chain L residue 207 VAL Chi-restraints excluded: chain L residue 265 VAL Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain O residue 2 VAL Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain Q residue 34 ILE Chi-restraints excluded: chain Q residue 99 LEU Chi-restraints excluded: chain R residue 27 LEU Chi-restraints excluded: chain R residue 75 ILE Chi-restraints excluded: chain R residue 108 VAL Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain T residue 29 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 290 optimal weight: 0.5980 chunk 187 optimal weight: 0.7980 chunk 280 optimal weight: 6.9990 chunk 141 optimal weight: 5.9990 chunk 92 optimal weight: 8.9990 chunk 91 optimal weight: 8.9990 chunk 299 optimal weight: 6.9990 chunk 320 optimal weight: 4.9990 chunk 232 optimal weight: 20.0000 chunk 43 optimal weight: 10.0000 chunk 369 optimal weight: 3.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 361 HIS ** C 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 239 ASN G 264 ASN H 361 HIS ** I 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 361 HIS O 114 GLN S 6 GLN T 36 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 39612 Z= 0.413 Angle : 0.644 12.155 53924 Z= 0.327 Chirality : 0.047 0.269 6007 Planarity : 0.005 0.058 6912 Dihedral : 5.524 77.799 5660 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 3.12 % Allowed : 16.50 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.12), residues: 4944 helix: 1.22 (0.25), residues: 473 sheet: -0.25 (0.12), residues: 1792 loop : -0.60 (0.12), residues: 2679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP O 36 HIS 0.010 0.001 HIS J 230 PHE 0.019 0.002 PHE A 365 TYR 0.023 0.002 TYR G 308 ARG 0.012 0.001 ARG I 185 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 503 time to evaluate : 4.111 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: A 260 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.6601 (mp0) REVERT: B 114 PHE cc_start: 0.8196 (OUTLIER) cc_final: 0.7806 (t80) REVERT: B 127 TYR cc_start: 0.8464 (m-80) cc_final: 0.8117 (m-80) REVERT: C 211 ASN cc_start: 0.8410 (t0) cc_final: 0.8001 (t0) REVERT: D 385 ASP cc_start: 0.7803 (p0) cc_final: 0.7402 (p0) REVERT: E 81 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.8194 (mt0) REVERT: F 220 VAL cc_start: 0.8263 (t) cc_final: 0.8025 (p) REVERT: H 287 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.8817 (mt) REVERT: I 191 TYR cc_start: 0.8114 (p90) cc_final: 0.7444 (p90) REVERT: J 24 TYR cc_start: 0.8538 (m-80) cc_final: 0.8332 (m-80) REVERT: J 120 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8501 (pt0) REVERT: J 346 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7663 (mp) REVERT: Q 55 ASN cc_start: 0.8950 (t0) cc_final: 0.8455 (t0) REVERT: Q 106 ASN cc_start: 0.7477 (t0) cc_final: 0.7253 (t0) REVERT: S 111 TYR cc_start: 0.5047 (t80) cc_final: 0.4561 (t80) REVERT: T 4 LEU cc_start: 0.8733 (mp) cc_final: 0.8492 (mt) REVERT: T 87 TYR cc_start: 0.8297 (m-80) cc_final: 0.7677 (m-80) REVERT: T 97 GLU cc_start: 0.7578 (pm20) cc_final: 0.7237 (pm20) outliers start: 131 outliers final: 102 residues processed: 591 average time/residue: 0.4963 time to fit residues: 484.1897 Evaluate side-chains 603 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 495 time to evaluate : 4.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 376 CYS Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 114 PHE Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 226 CYS Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 302 ASP Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 199 TYR Chi-restraints excluded: chain C residue 218 LYS Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain E residue 167 MET Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain E residue 200 CYS Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 263 ASP Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain G residue 43 ASN Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 192 ASP Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain H residue 241 ASP Chi-restraints excluded: chain H residue 287 LEU Chi-restraints excluded: chain H residue 297 THR Chi-restraints excluded: chain I residue 230 ILE Chi-restraints excluded: chain I residue 245 VAL Chi-restraints excluded: chain I residue 256 VAL Chi-restraints excluded: chain I residue 265 VAL Chi-restraints excluded: chain J residue 55 MET Chi-restraints excluded: chain J residue 63 CYS Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 120 GLU Chi-restraints excluded: chain J residue 167 SER Chi-restraints excluded: chain J residue 246 ASP Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain J residue 315 ILE Chi-restraints excluded: chain J residue 346 LEU Chi-restraints excluded: chain J residue 370 CYS Chi-restraints excluded: chain J residue 374 VAL Chi-restraints excluded: chain J residue 397 THR Chi-restraints excluded: chain J residue 436 LEU Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 267 THR Chi-restraints excluded: chain K residue 277 THR Chi-restraints excluded: chain K residue 329 VAL Chi-restraints excluded: chain L residue 161 VAL Chi-restraints excluded: chain L residue 192 THR Chi-restraints excluded: chain L residue 199 TYR Chi-restraints excluded: chain L residue 207 VAL Chi-restraints excluded: chain L residue 265 VAL Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain O residue 2 VAL Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain Q residue 24 SER Chi-restraints excluded: chain Q residue 34 ILE Chi-restraints excluded: chain Q residue 48 MET Chi-restraints excluded: chain Q residue 99 LEU Chi-restraints excluded: chain R residue 27 LEU Chi-restraints excluded: chain R residue 75 ILE Chi-restraints excluded: chain R residue 108 VAL Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain S residue 28 THR Chi-restraints excluded: chain S residue 48 MET Chi-restraints excluded: chain T residue 29 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 427 optimal weight: 9.9990 chunk 450 optimal weight: 5.9990 chunk 411 optimal weight: 2.9990 chunk 438 optimal weight: 10.0000 chunk 263 optimal weight: 6.9990 chunk 190 optimal weight: 9.9990 chunk 344 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 chunk 396 optimal weight: 1.9990 chunk 414 optimal weight: 6.9990 chunk 436 optimal weight: 20.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 361 HIS ** C 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 GLN ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 264 ASN ** H 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 361 HIS ** I 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 361 HIS O 114 GLN Q 57 ASN S 3 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.125 39612 Z= 0.510 Angle : 0.695 13.092 53924 Z= 0.353 Chirality : 0.049 0.278 6007 Planarity : 0.005 0.059 6912 Dihedral : 5.725 78.317 5660 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.93 % Allowed : 16.93 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.12), residues: 4944 helix: 0.93 (0.25), residues: 493 sheet: -0.25 (0.12), residues: 1716 loop : -0.76 (0.12), residues: 2735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP P 34 HIS 0.012 0.001 HIS J 230 PHE 0.019 0.002 PHE E 328 TYR 0.026 0.002 TYR G 308 ARG 0.012 0.001 ARG I 185 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 501 time to evaluate : 4.656 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: A 260 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.6641 (mp0) REVERT: B 114 PHE cc_start: 0.8252 (OUTLIER) cc_final: 0.7846 (t80) REVERT: B 127 TYR cc_start: 0.8471 (m-80) cc_final: 0.8131 (m-80) REVERT: C 211 ASN cc_start: 0.8438 (t0) cc_final: 0.8032 (t0) REVERT: D 385 ASP cc_start: 0.7882 (p0) cc_final: 0.7469 (p0) REVERT: E 81 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.8200 (mt0) REVERT: F 220 VAL cc_start: 0.8261 (t) cc_final: 0.7950 (p) REVERT: F 257 MET cc_start: 0.7856 (ptp) cc_final: 0.7620 (ptp) REVERT: H 287 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.8801 (mt) REVERT: I 191 TYR cc_start: 0.8151 (p90) cc_final: 0.7440 (p90) REVERT: J 24 TYR cc_start: 0.8671 (m-80) cc_final: 0.8359 (m-80) REVERT: J 95 PHE cc_start: 0.7826 (p90) cc_final: 0.7607 (p90) REVERT: J 120 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8524 (pt0) REVERT: J 346 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7770 (mp) REVERT: L 211 ASN cc_start: 0.8821 (t0) cc_final: 0.8496 (t0) REVERT: O 2 VAL cc_start: 0.5081 (OUTLIER) cc_final: 0.4824 (m) REVERT: P 53 ARG cc_start: 0.8397 (ptt-90) cc_final: 0.7958 (ptt-90) REVERT: Q 81 MET cc_start: 0.7496 (tmm) cc_final: 0.7120 (tmm) REVERT: Q 106 ASN cc_start: 0.7580 (t0) cc_final: 0.7363 (t0) REVERT: S 111 TYR cc_start: 0.5235 (t80) cc_final: 0.4821 (t80) REVERT: T 4 LEU cc_start: 0.8761 (mp) cc_final: 0.8500 (mt) REVERT: T 87 TYR cc_start: 0.8337 (m-80) cc_final: 0.7706 (m-80) REVERT: T 97 GLU cc_start: 0.7590 (pm20) cc_final: 0.7269 (pm20) outliers start: 123 outliers final: 100 residues processed: 587 average time/residue: 0.5167 time to fit residues: 497.5732 Evaluate side-chains 599 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 492 time to evaluate : 4.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 376 CYS Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 114 PHE Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 226 CYS Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 199 TYR Chi-restraints excluded: chain C residue 218 LYS Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 370 CYS Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain E residue 167 MET Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 200 CYS Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain G residue 43 ASN Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 192 ASP Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain H residue 241 ASP Chi-restraints excluded: chain H residue 287 LEU Chi-restraints excluded: chain H residue 297 THR Chi-restraints excluded: chain I residue 230 ILE Chi-restraints excluded: chain I residue 245 VAL Chi-restraints excluded: chain I residue 256 VAL Chi-restraints excluded: chain I residue 265 VAL Chi-restraints excluded: chain J residue 55 MET Chi-restraints excluded: chain J residue 63 CYS Chi-restraints excluded: chain J residue 120 GLU Chi-restraints excluded: chain J residue 167 SER Chi-restraints excluded: chain J residue 246 ASP Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain J residue 315 ILE Chi-restraints excluded: chain J residue 346 LEU Chi-restraints excluded: chain J residue 361 ILE Chi-restraints excluded: chain J residue 370 CYS Chi-restraints excluded: chain J residue 374 VAL Chi-restraints excluded: chain J residue 397 THR Chi-restraints excluded: chain J residue 436 LEU Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain K residue 267 THR Chi-restraints excluded: chain K residue 277 THR Chi-restraints excluded: chain K residue 329 VAL Chi-restraints excluded: chain L residue 161 VAL Chi-restraints excluded: chain L residue 192 THR Chi-restraints excluded: chain L residue 199 TYR Chi-restraints excluded: chain L residue 207 VAL Chi-restraints excluded: chain L residue 265 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain O residue 2 VAL Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain Q residue 24 SER Chi-restraints excluded: chain Q residue 34 ILE Chi-restraints excluded: chain Q residue 48 MET Chi-restraints excluded: chain Q residue 99 LEU Chi-restraints excluded: chain R residue 27 LEU Chi-restraints excluded: chain R residue 75 ILE Chi-restraints excluded: chain R residue 108 VAL Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain S residue 28 THR Chi-restraints excluded: chain T residue 29 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 287 optimal weight: 8.9990 chunk 463 optimal weight: 5.9990 chunk 282 optimal weight: 9.9990 chunk 219 optimal weight: 2.9990 chunk 322 optimal weight: 0.7980 chunk 486 optimal weight: 5.9990 chunk 447 optimal weight: 8.9990 chunk 387 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 chunk 299 optimal weight: 4.9990 chunk 237 optimal weight: 5.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 361 HIS ** C 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 208 GLN ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 264 ASN ** H 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 361 HIS ** I 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 394 HIS ** K 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 233 ASN K 361 HIS O 114 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.118 39612 Z= 0.505 Angle : 0.693 10.987 53924 Z= 0.353 Chirality : 0.049 0.276 6007 Planarity : 0.005 0.059 6912 Dihedral : 5.770 79.248 5660 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.79 % Allowed : 17.21 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.12), residues: 4944 helix: 0.88 (0.25), residues: 493 sheet: -0.29 (0.12), residues: 1694 loop : -0.83 (0.12), residues: 2757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP P 34 HIS 0.012 0.001 HIS J 230 PHE 0.019 0.002 PHE E 328 TYR 0.025 0.002 TYR G 308 ARG 0.013 0.001 ARG I 185 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 504 time to evaluate : 4.487 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: A 260 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.6642 (mp0) REVERT: B 114 PHE cc_start: 0.8259 (OUTLIER) cc_final: 0.7850 (t80) REVERT: B 127 TYR cc_start: 0.8486 (m-80) cc_final: 0.8145 (m-80) REVERT: C 211 ASN cc_start: 0.8448 (t0) cc_final: 0.8035 (t0) REVERT: D 385 ASP cc_start: 0.7911 (p0) cc_final: 0.7491 (p0) REVERT: E 81 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.8199 (mt0) REVERT: E 207 ILE cc_start: 0.8400 (mm) cc_final: 0.8122 (mm) REVERT: F 220 VAL cc_start: 0.8274 (t) cc_final: 0.7999 (p) REVERT: F 228 ARG cc_start: 0.8696 (mmt90) cc_final: 0.8358 (mtp85) REVERT: F 257 MET cc_start: 0.7888 (ptp) cc_final: 0.7644 (ptp) REVERT: H 287 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.8805 (mt) REVERT: I 191 TYR cc_start: 0.8203 (p90) cc_final: 0.7476 (p90) REVERT: J 120 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8510 (pt0) REVERT: J 346 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7789 (mp) REVERT: L 211 ASN cc_start: 0.8822 (t0) cc_final: 0.8513 (t0) REVERT: O 2 VAL cc_start: 0.5037 (OUTLIER) cc_final: 0.4665 (m) REVERT: P 53 ARG cc_start: 0.8388 (ptt-90) cc_final: 0.8164 (ptt90) REVERT: Q 81 MET cc_start: 0.7521 (tmm) cc_final: 0.7141 (tmm) REVERT: Q 106 ASN cc_start: 0.7795 (t0) cc_final: 0.7576 (t0) REVERT: S 111 TYR cc_start: 0.5267 (t80) cc_final: 0.4866 (t80) REVERT: T 4 LEU cc_start: 0.8774 (mp) cc_final: 0.8503 (mt) REVERT: T 87 TYR cc_start: 0.8338 (m-80) cc_final: 0.7781 (m-80) REVERT: T 97 GLU cc_start: 0.7667 (pm20) cc_final: 0.7313 (pm20) outliers start: 117 outliers final: 107 residues processed: 581 average time/residue: 0.5118 time to fit residues: 487.8120 Evaluate side-chains 606 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 492 time to evaluate : 4.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 376 CYS Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 114 PHE Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 226 CYS Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 199 TYR Chi-restraints excluded: chain C residue 218 LYS Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 370 CYS Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain E residue 167 MET Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 200 CYS Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 263 ASP Chi-restraints excluded: chain F residue 199 TYR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain G residue 43 ASN Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 192 ASP Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain H residue 241 ASP Chi-restraints excluded: chain H residue 287 LEU Chi-restraints excluded: chain H residue 297 THR Chi-restraints excluded: chain I residue 230 ILE Chi-restraints excluded: chain I residue 245 VAL Chi-restraints excluded: chain I residue 256 VAL Chi-restraints excluded: chain I residue 265 VAL Chi-restraints excluded: chain J residue 55 MET Chi-restraints excluded: chain J residue 63 CYS Chi-restraints excluded: chain J residue 120 GLU Chi-restraints excluded: chain J residue 167 SER Chi-restraints excluded: chain J residue 246 ASP Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain J residue 315 ILE Chi-restraints excluded: chain J residue 346 LEU Chi-restraints excluded: chain J residue 361 ILE Chi-restraints excluded: chain J residue 370 CYS Chi-restraints excluded: chain J residue 374 VAL Chi-restraints excluded: chain J residue 397 THR Chi-restraints excluded: chain J residue 436 LEU Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain K residue 267 THR Chi-restraints excluded: chain K residue 277 THR Chi-restraints excluded: chain K residue 329 VAL Chi-restraints excluded: chain L residue 125 ASP Chi-restraints excluded: chain L residue 161 VAL Chi-restraints excluded: chain L residue 192 THR Chi-restraints excluded: chain L residue 199 TYR Chi-restraints excluded: chain L residue 207 VAL Chi-restraints excluded: chain L residue 265 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain O residue 2 VAL Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain Q residue 24 SER Chi-restraints excluded: chain Q residue 34 ILE Chi-restraints excluded: chain Q residue 48 MET Chi-restraints excluded: chain Q residue 99 LEU Chi-restraints excluded: chain R residue 27 LEU Chi-restraints excluded: chain R residue 75 ILE Chi-restraints excluded: chain R residue 108 VAL Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain S residue 28 THR Chi-restraints excluded: chain T residue 29 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 307 optimal weight: 0.0170 chunk 412 optimal weight: 4.9990 chunk 118 optimal weight: 0.8980 chunk 356 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 387 optimal weight: 9.9990 chunk 162 optimal weight: 2.9990 chunk 398 optimal weight: 10.0000 chunk 49 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 overall best weight: 0.9422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN C 197 GLN C 208 GLN ** E 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 264 ASN ** H 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 361 HIS ** I 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 233 ASN K 361 HIS O 65 GLN O 114 GLN ** S 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.167664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.107709 restraints weight = 48297.055| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 1.76 r_work: 0.2848 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 39612 Z= 0.196 Angle : 0.586 10.589 53924 Z= 0.300 Chirality : 0.044 0.259 6007 Planarity : 0.004 0.059 6912 Dihedral : 5.341 78.254 5660 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.29 % Allowed : 17.93 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.12), residues: 4944 helix: 1.29 (0.25), residues: 481 sheet: -0.23 (0.12), residues: 1730 loop : -0.64 (0.12), residues: 2733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP O 36 HIS 0.004 0.001 HIS J 230 PHE 0.015 0.001 PHE D 365 TYR 0.016 0.001 TYR G 308 ARG 0.013 0.000 ARG I 185 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10401.16 seconds wall clock time: 190 minutes 35.30 seconds (11435.30 seconds total)