Starting phenix.real_space_refine on Wed Aug 7 09:59:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xn9_38499/08_2024/8xn9_38499.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xn9_38499/08_2024/8xn9_38499.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xn9_38499/08_2024/8xn9_38499.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xn9_38499/08_2024/8xn9_38499.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xn9_38499/08_2024/8xn9_38499.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xn9_38499/08_2024/8xn9_38499.cif" } resolution = 1.99 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= 0.076 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 87 5.16 5 C 12301 2.51 5 N 3208 2.21 5 O 3877 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 260": "OD1" <-> "OD2" Residue "A TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 327": "OE1" <-> "OE2" Residue "A PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 354": "OE1" <-> "OE2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A GLU 441": "OE1" <-> "OE2" Residue "B TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 77": "OE1" <-> "OE2" Residue "B GLU 152": "OE1" <-> "OE2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 254": "OD1" <-> "OD2" Residue "B PHE 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 354": "OE1" <-> "OE2" Residue "B PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 95": "OE1" <-> "OE2" Residue "C GLU 152": "OE1" <-> "OE2" Residue "C GLU 156": "OE1" <-> "OE2" Residue "C TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 188": "OD1" <-> "OD2" Residue "C ASP 200": "OD1" <-> "OD2" Residue "C PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 287": "OE1" <-> "OE2" Residue "C TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 304": "OD1" <-> "OD2" Residue "C GLU 406": "OE1" <-> "OE2" Residue "D ASP 53": "OD1" <-> "OD2" Residue "D PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 83": "OD1" <-> "OD2" Residue "E GLU 84": "OE1" <-> "OE2" Residue "E TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 46": "OE1" <-> "OE2" Residue "G PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 6": "OE1" <-> "OE2" Residue "H TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 46": "OE1" <-> "OE2" Residue "I TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 73": "OD1" <-> "OD2" Residue "I PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 90": "OD1" <-> "OD2" Residue "I TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 161": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 19473 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3413 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 15, 'TRANS': 427} Chain breaks: 1 Chain: "B" Number of atoms: 3413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3413 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 15, 'TRANS': 427} Chain breaks: 1 Chain: "C" Number of atoms: 3413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3413 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 15, 'TRANS': 427} Chain breaks: 1 Chain: "D" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1552 Classifications: {'peptide': 211} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 197} Chain: "E" Number of atoms: 1540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1540 Classifications: {'peptide': 209} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 196} Chain: "G" Number of atoms: 1489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1489 Classifications: {'peptide': 196} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 181} Chain breaks: 2 Chain: "H" Number of atoms: 1502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1502 Classifications: {'peptide': 197} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 183} Chain breaks: 2 Chain: "F" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1552 Classifications: {'peptide': 211} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 197} Chain: "I" Number of atoms: 1515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1515 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 184} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "A" 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: "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: "C" 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: 11.12, per 1000 atoms: 0.57 Number of scatterers: 19473 At special positions: 0 Unit cell: (165.02, 159.84, 154.66, 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 87 16.00 O 3877 8.00 N 3208 7.00 C 12301 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=25, symmetry=0 Simple disulfide: pdb=" SG CYS A 71 " - pdb=" SG CYS A 192 " distance=2.04 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 340 " distance=2.04 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 363 " distance=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 392 " distance=2.03 Simple disulfide: pdb=" SG CYS A 394 " - pdb=" SG CYS A 417 " distance=2.04 Simple disulfide: pdb=" SG CYS B 71 " - pdb=" SG CYS B 192 " distance=2.04 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 340 " distance=2.04 Simple disulfide: pdb=" SG CYS B 355 " - pdb=" SG CYS B 363 " distance=2.03 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 392 " distance=2.04 Simple disulfide: pdb=" SG CYS B 394 " - pdb=" SG CYS B 417 " distance=2.04 Simple disulfide: pdb=" SG CYS C 71 " - pdb=" SG CYS C 192 " distance=2.06 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 340 " distance=2.04 Simple disulfide: pdb=" SG CYS C 355 " - pdb=" SG CYS C 363 " distance=2.03 Simple disulfide: pdb=" SG CYS C 387 " - pdb=" SG CYS C 392 " distance=2.03 Simple disulfide: pdb=" SG CYS C 394 " - pdb=" SG CYS C 417 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 89 " distance=2.05 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 89 " distance=2.05 Simple disulfide: pdb=" SG CYS E 138 " - pdb=" SG CYS E 197 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.06 Simple disulfide: pdb=" SG CYS G 153 " - pdb=" SG CYS G 209 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.06 Simple disulfide: pdb=" SG CYS H 153 " - pdb=" SG CYS H 209 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 89 " distance=2.05 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.06 Simple disulfide: pdb=" SG CYS I 153 " - pdb=" SG CYS I 209 " 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 601 " - " ASN A 99 " " NAG A 602 " - " ASN A 414 " " NAG B 601 " - " ASN B 99 " " NAG B 602 " - " ASN B 414 " " NAG C 601 " - " ASN C 99 " " NAG C 602 " - " ASN C 414 " Time building additional restraints: 6.69 Conformation dependent library (CDL) restraints added in 3.5 seconds 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4776 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 54 sheets defined 26.4% alpha, 39.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.89 Creating SS restraints... Processing helix chain 'A' and resid 29 through 36 removed outlier: 3.566A pdb=" N ILE A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 72 removed outlier: 3.708A pdb=" N SER A 69 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N GLN A 70 " --> pdb=" O ASN A 67 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR A 72 " --> pdb=" O SER A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 99 Proline residue: A 89 - end of helix removed outlier: 4.093A pdb=" N TYR A 97 " --> pdb=" O ALA A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 121 Processing helix chain 'A' and resid 125 through 145 removed outlier: 4.538A pdb=" N LYS A 139 " --> pdb=" O TYR A 135 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ASN A 140 " --> pdb=" O GLU A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 154 Processing helix chain 'A' and resid 175 through 182 Processing helix chain 'A' and resid 183 through 187 Processing helix chain 'A' and resid 191 through 215 removed outlier: 4.629A pdb=" N PHE A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N VAL A 213 " --> pdb=" O ASP A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 Processing helix chain 'A' and resid 233 through 236 Processing helix chain 'A' and resid 238 through 247 removed outlier: 3.640A pdb=" N LEU A 242 " --> pdb=" O ASN A 238 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY A 247 " --> pdb=" O LEU A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 328 through 331 Processing helix chain 'A' and resid 349 through 357 Processing helix chain 'A' and resid 359 through 363 Processing helix chain 'A' and resid 437 through 441 Processing helix chain 'A' and resid 452 through 476 removed outlier: 3.575A pdb=" N SER A 457 " --> pdb=" O LYS A 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.752A pdb=" N LYS B 35 " --> pdb=" O GLU B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 72 removed outlier: 3.623A pdb=" N SER B 69 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLN B 70 " --> pdb=" O ASN B 67 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR B 72 " --> pdb=" O SER B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 100 Proline residue: B 89 - end of helix removed outlier: 3.571A pdb=" N ILE B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N TYR B 97 " --> pdb=" O ALA B 93 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASN B 100 " --> pdb=" O ILE B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 121 Processing helix chain 'B' and resid 125 through 146 removed outlier: 4.378A pdb=" N LYS B 139 " --> pdb=" O TYR B 135 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ASN B 140 " --> pdb=" O GLU B 136 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASN B 143 " --> pdb=" O LYS B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 153 Processing helix chain 'B' and resid 175 through 182 Processing helix chain 'B' and resid 183 through 187 Processing helix chain 'B' and resid 191 through 215 removed outlier: 4.662A pdb=" N PHE B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N VAL B 213 " --> pdb=" O ASP B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 232 Processing helix chain 'B' and resid 233 through 236 Processing helix chain 'B' and resid 238 through 247 removed outlier: 3.732A pdb=" N LEU B 242 " --> pdb=" O ASN B 238 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU B 246 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLY B 247 " --> pdb=" O LEU B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 259 Processing helix chain 'B' and resid 328 through 331 Processing helix chain 'B' and resid 349 through 357 Processing helix chain 'B' and resid 359 through 363 Processing helix chain 'B' and resid 437 through 441 Processing helix chain 'B' and resid 452 through 476 removed outlier: 3.620A pdb=" N SER B 457 " --> pdb=" O LYS B 453 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR B 473 " --> pdb=" O GLN B 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 35 removed outlier: 3.709A pdb=" N LYS C 35 " --> pdb=" O GLU C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 72 removed outlier: 3.827A pdb=" N SER C 69 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N GLN C 70 " --> pdb=" O ASN C 67 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR C 72 " --> pdb=" O SER C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 99 removed outlier: 3.514A pdb=" N GLY C 85 " --> pdb=" O THR C 81 " (cutoff:3.500A) Proline residue: C 89 - end of helix removed outlier: 4.063A pdb=" N TYR C 97 " --> pdb=" O ALA C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 121 Processing helix chain 'C' and resid 125 through 146 removed outlier: 4.398A pdb=" N LYS C 139 " --> pdb=" O TYR C 135 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ASN C 140 " --> pdb=" O GLU C 136 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN C 143 " --> pdb=" O LYS C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 154 Processing helix chain 'C' and resid 175 through 182 Processing helix chain 'C' and resid 183 through 187 Processing helix chain 'C' and resid 191 through 215 removed outlier: 4.652A pdb=" N PHE C 212 " --> pdb=" O SER C 208 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N VAL C 213 " --> pdb=" O ASP C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 232 Processing helix chain 'C' and resid 233 through 236 Processing helix chain 'C' and resid 238 through 245 removed outlier: 3.696A pdb=" N LEU C 242 " --> pdb=" O ASN C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 259 Processing helix chain 'C' and resid 328 through 331 Processing helix chain 'C' and resid 349 through 357 Processing helix chain 'C' and resid 359 through 363 Processing helix chain 'C' and resid 437 through 441 Processing helix chain 'C' and resid 452 through 476 removed outlier: 3.726A pdb=" N SER C 457 " --> pdb=" O LYS C 453 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER C 470 " --> pdb=" O SER C 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 84 Processing helix chain 'D' and resid 125 through 131 Processing helix chain 'D' and resid 185 through 192 removed outlier: 3.690A pdb=" N HIS D 192 " --> pdb=" O GLN D 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 84 Processing helix chain 'E' and resid 125 through 131 Processing helix chain 'E' and resid 185 through 192 removed outlier: 3.741A pdb=" N TRP E 189 " --> pdb=" O THR E 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.671A pdb=" N TYR G 32 " --> pdb=" O ILE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 66 No H-bonds generated for 'chain 'G' and resid 64 through 66' Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.508A pdb=" N THR G 91 " --> pdb=" O ALA G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 171 No H-bonds generated for 'chain 'G' and resid 169 through 171' Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.705A pdb=" N TYR H 32 " --> pdb=" O ILE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 66 No H-bonds generated for 'chain 'H' and resid 64 through 66' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'F' and resid 80 through 84 removed outlier: 3.650A pdb=" N ASP F 83 " --> pdb=" O GLN F 80 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU F 84 " --> pdb=" O THR F 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 80 through 84' Processing helix chain 'F' and resid 125 through 131 removed outlier: 3.771A pdb=" N ALA F 131 " --> pdb=" O GLU F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 191 Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.880A pdb=" N TYR I 32 " --> pdb=" O ILE I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 66 removed outlier: 5.116A pdb=" N SER I 66 " --> pdb=" O SER I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'I' and resid 169 through 171 No H-bonds generated for 'chain 'I' and resid 169 through 171' Processing helix chain 'I' and resid 214 through 217 Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 162 removed outlier: 12.862A pdb=" N THR A 168 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N ASP A 56 " --> pdb=" O THR A 168 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N TYR A 170 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N VAL A 338 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LYS A 45 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N CYS A 340 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LYS A 47 " --> pdb=" O CYS A 340 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 226 through 227 removed outlier: 4.159A pdb=" N MET A 226 " --> pdb=" O GLY A 264 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR A 263 " --> pdb=" O TYR A 281 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE A 277 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N VAL A 269 " --> pdb=" O TYR A 275 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N TYR A 275 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ILE A 284 " --> pdb=" O ASN A 51 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N ASN A 51 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N THR A 286 " --> pdb=" O LYS A 49 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N LYS A 49 " --> pdb=" O THR A 286 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N GLU A 295 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N THR A 43 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE A 293 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N LYS A 45 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 8.564A pdb=" N ALA A 291 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N PHE A 315 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ILE A 326 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 102 Processing sheet with id=AA4, first strand: chain 'A' and resid 122 through 124 Processing sheet with id=AA5, first strand: chain 'A' and resid 301 through 303 Processing sheet with id=AA6, first strand: chain 'A' and resid 410 through 412 Processing sheet with id=AA7, first strand: chain 'A' and resid 392 through 394 removed outlier: 6.841A pdb=" N ILE A 426 " --> pdb=" O MET C 115 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 158 through 162 removed outlier: 12.905A pdb=" N THR B 168 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ASP B 56 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N TYR B 170 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N VAL B 338 " --> pdb=" O THR B 43 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LYS B 45 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N CYS B 340 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LYS B 47 " --> pdb=" O CYS B 340 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 226 through 227 removed outlier: 4.250A pdb=" N MET B 226 " --> pdb=" O GLY B 264 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE B 277 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N VAL B 269 " --> pdb=" O TYR B 275 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N TYR B 275 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ILE B 284 " --> pdb=" O ASN B 51 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ASN B 51 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N THR B 286 " --> pdb=" O LYS B 49 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N LYS B 49 " --> pdb=" O THR B 286 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N GLU B 295 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N THR B 43 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE B 293 " --> pdb=" O THR B 43 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N LYS B 45 " --> pdb=" O ALA B 291 " (cutoff:3.500A) removed outlier: 8.521A pdb=" N ALA B 291 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N PHE B 315 " --> pdb=" O ILE B 326 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ILE B 326 " --> pdb=" O PHE B 315 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 101 through 102 removed outlier: 6.900A pdb=" N MET B 115 " --> pdb=" O SER C 428 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N CYS C 392 " --> pdb=" O ILE C 401 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 122 through 124 Processing sheet with id=AB3, first strand: chain 'B' and resid 301 through 303 Processing sheet with id=AB4, first strand: chain 'C' and resid 158 through 162 removed outlier: 12.760A pdb=" N THR C 168 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N ASP C 56 " --> pdb=" O THR C 168 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N TYR C 170 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N VAL C 338 " --> pdb=" O THR C 43 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LYS C 45 " --> pdb=" O VAL C 338 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N CYS C 340 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LYS C 47 " --> pdb=" O CYS C 340 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 226 through 227 removed outlier: 4.200A pdb=" N MET C 226 " --> pdb=" O GLY C 264 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE C 277 " --> pdb=" O ILE C 267 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N VAL C 269 " --> pdb=" O TYR C 275 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N TYR C 275 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE C 284 " --> pdb=" O ASN C 51 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ASN C 51 " --> pdb=" O ILE C 284 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N THR C 286 " --> pdb=" O LYS C 49 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N LYS C 49 " --> pdb=" O THR C 286 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N GLU C 295 " --> pdb=" O GLY C 41 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N THR C 43 " --> pdb=" O ILE C 293 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE C 293 " --> pdb=" O THR C 43 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N LYS C 45 " --> pdb=" O ALA C 291 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N ALA C 291 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N PHE C 315 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ILE C 326 " --> pdb=" O PHE C 315 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 301 through 302 Processing sheet with id=AB7, first strand: chain 'D' and resid 9 through 13 removed outlier: 6.579A pdb=" N ALA D 10 " --> pdb=" O THR D 108 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N LEU D 110 " --> pdb=" O ALA D 10 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLU D 12 " --> pdb=" O LEU D 110 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL D 34 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N SER D 50 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 9 through 13 removed outlier: 6.579A pdb=" N ALA D 10 " --> pdb=" O THR D 108 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N LEU D 110 " --> pdb=" O ALA D 10 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLU D 12 " --> pdb=" O LEU D 110 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY D 98 " --> pdb=" O ASP D 93 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 18 through 23 Processing sheet with id=AC1, first strand: chain 'D' and resid 118 through 122 removed outlier: 3.572A pdb=" N VAL D 137 " --> pdb=" O PHE D 122 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ALA D 134 " --> pdb=" O LEU D 184 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER D 180 " --> pdb=" O CYS D 138 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 118 through 122 removed outlier: 3.572A pdb=" N VAL D 137 " --> pdb=" O PHE D 122 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ALA D 134 " --> pdb=" O LEU D 184 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER D 180 " --> pdb=" O CYS D 138 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 157 through 159 removed outlier: 4.551A pdb=" N TRP D 152 " --> pdb=" O VAL D 159 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 9 through 13 removed outlier: 6.545A pdb=" N ALA E 10 " --> pdb=" O THR E 108 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N LEU E 110 " --> pdb=" O ALA E 10 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLU E 12 " --> pdb=" O LEU E 110 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA E 85 " --> pdb=" O LEU E 107 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL E 34 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N SER E 50 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 9 through 13 removed outlier: 6.545A pdb=" N ALA E 10 " --> pdb=" O THR E 108 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N LEU E 110 " --> pdb=" O ALA E 10 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLU E 12 " --> pdb=" O LEU E 110 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA E 85 " --> pdb=" O LEU E 107 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 18 through 23 Processing sheet with id=AC7, first strand: chain 'E' and resid 118 through 122 removed outlier: 3.815A pdb=" N ALA E 134 " --> pdb=" O LEU E 184 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU E 184 " --> pdb=" O ALA E 134 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N TYR E 176 " --> pdb=" O ASP E 142 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 118 through 122 removed outlier: 3.815A pdb=" N ALA E 134 " --> pdb=" O LEU E 184 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU E 184 " --> pdb=" O ALA E 134 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N TYR E 176 " --> pdb=" O ASP E 142 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 157 through 159 removed outlier: 4.126A pdb=" N TRP E 152 " --> pdb=" O VAL E 159 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AD2, first strand: chain 'G' and resid 57 through 60 removed outlier: 5.504A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL G 115 " --> pdb=" O ARG G 98 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 57 through 60 removed outlier: 5.504A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 101 through 103 Processing sheet with id=AD5, first strand: chain 'G' and resid 133 through 135 removed outlier: 5.711A pdb=" N LEU G 154 " --> pdb=" O SER G 193 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N SER G 193 " --> pdb=" O LEU G 154 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N LYS G 156 " --> pdb=" O LEU G 191 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N LEU G 191 " --> pdb=" O LYS G 156 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 133 through 135 removed outlier: 5.711A pdb=" N LEU G 154 " --> pdb=" O SER G 193 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N SER G 193 " --> pdb=" O LEU G 154 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N LYS G 156 " --> pdb=" O LEU G 191 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N LEU G 191 " --> pdb=" O LYS G 156 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 164 through 167 Processing sheet with id=AD8, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AD9, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.584A pdb=" N TRP H 34 " --> pdb=" O ASP H 50 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ASP H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.996A pdb=" N VAL H 115 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 101 through 103 Processing sheet with id=AE3, first strand: chain 'H' and resid 155 through 158 removed outlier: 5.359A pdb=" N LYS H 156 " --> pdb=" O LEU H 191 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N LEU H 191 " --> pdb=" O LYS H 156 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER H 190 " --> pdb=" O VAL H 182 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 164 through 167 removed outlier: 3.515A pdb=" N THR H 164 " --> pdb=" O ASN H 212 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN H 212 " --> pdb=" O THR H 164 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS H 222 " --> pdb=" O CYS H 209 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL H 211 " --> pdb=" O VAL H 220 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 176 through 178 Processing sheet with id=AE6, first strand: chain 'F' and resid 9 through 13 removed outlier: 6.416A pdb=" N ALA F 10 " --> pdb=" O THR F 108 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N LEU F 110 " --> pdb=" O ALA F 10 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLU F 12 " --> pdb=" O LEU F 110 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL F 34 " --> pdb=" O SER F 50 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N SER F 50 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N TRP F 36 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 9 through 13 removed outlier: 6.416A pdb=" N ALA F 10 " --> pdb=" O THR F 108 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N LEU F 110 " --> pdb=" O ALA F 10 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLU F 12 " --> pdb=" O LEU F 110 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY F 98 " --> pdb=" O ASP F 93 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 18 through 23 Processing sheet with id=AE9, first strand: chain 'F' and resid 118 through 122 removed outlier: 3.706A pdb=" N SER F 141 " --> pdb=" O SER F 118 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL F 137 " --> pdb=" O PHE F 122 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA F 134 " --> pdb=" O LEU F 184 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N TYR F 176 " --> pdb=" O ASP F 142 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 118 through 122 removed outlier: 3.706A pdb=" N SER F 141 " --> pdb=" O SER F 118 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL F 137 " --> pdb=" O PHE F 122 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA F 134 " --> pdb=" O LEU F 184 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N TYR F 176 " --> pdb=" O ASP F 142 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 157 through 159 removed outlier: 4.425A pdb=" N TRP F 152 " --> pdb=" O VAL F 159 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AF4, first strand: chain 'I' and resid 11 through 12 removed outlier: 6.635A pdb=" N TRP I 34 " --> pdb=" O ASP I 50 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ASP I 50 " --> pdb=" O TRP I 34 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 11 through 12 removed outlier: 4.041A pdb=" N VAL I 115 " --> pdb=" O ARG I 98 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 101 through 103 Processing sheet with id=AF7, first strand: chain 'I' and resid 133 through 135 removed outlier: 3.565A pdb=" N SER I 133 " --> pdb=" O LYS I 156 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LYS I 156 " --> pdb=" O SER I 133 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N TYR I 189 " --> pdb=" O ASP I 157 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 164 through 167 removed outlier: 3.861A pdb=" N LYS I 222 " --> pdb=" O CYS I 209 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL I 211 " --> pdb=" O VAL I 220 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 176 through 178 942 hydrogen bonds defined for protein. 2385 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: 7.49 Time building geometry restraints manager: 7.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 6226 1.35 - 1.48: 4940 1.48 - 1.62: 8560 1.62 - 1.76: 1 1.76 - 1.90: 119 Bond restraints: 19846 Sorted by residual: bond pdb=" CB CYS C 71 " pdb=" SG CYS C 71 " ideal model delta sigma weight residual 1.808 1.895 -0.087 3.30e-02 9.18e+02 6.96e+00 bond pdb=" C ILE B 36 " pdb=" O ILE B 36 " ideal model delta sigma weight residual 1.236 1.216 0.020 1.19e-02 7.06e+03 2.93e+00 bond pdb=" CA VAL C 373 " pdb=" CB VAL C 373 " ideal model delta sigma weight residual 1.537 1.558 -0.021 1.29e-02 6.01e+03 2.63e+00 bond pdb=" CB CYS C 192 " pdb=" SG CYS C 192 " ideal model delta sigma weight residual 1.808 1.755 0.053 3.30e-02 9.18e+02 2.56e+00 bond pdb=" C2 NAG C 602 " pdb=" N2 NAG C 602 " ideal model delta sigma weight residual 1.439 1.471 -0.032 2.00e-02 2.50e+03 2.49e+00 ... (remaining 19841 not shown) Histogram of bond angle deviations from ideal: 99.38 - 106.31: 550 106.31 - 113.25: 11066 113.25 - 120.18: 6638 120.18 - 127.11: 8554 127.11 - 134.04: 202 Bond angle restraints: 27010 Sorted by residual: angle pdb=" N PRO I 136 " pdb=" CA PRO I 136 " pdb=" CB PRO I 136 " ideal model delta sigma weight residual 103.00 110.36 -7.36 1.10e+00 8.26e-01 4.48e+01 angle pdb=" CA VAL A 312 " pdb=" C VAL A 312 " pdb=" N PRO A 313 " ideal model delta sigma weight residual 116.57 120.70 -4.13 9.80e-01 1.04e+00 1.78e+01 angle pdb=" C TYR E 51 " pdb=" N ASN E 52 " pdb=" CA ASN E 52 " ideal model delta sigma weight residual 121.54 129.24 -7.70 1.91e+00 2.74e-01 1.62e+01 angle pdb=" C SER D 156 " pdb=" N SER D 157 " pdb=" CA SER D 157 " ideal model delta sigma weight residual 122.74 113.27 9.47 2.44e+00 1.68e-01 1.51e+01 angle pdb=" N GLU C 136 " pdb=" CA GLU C 136 " pdb=" CB GLU C 136 " ideal model delta sigma weight residual 110.22 116.14 -5.92 1.54e+00 4.22e-01 1.48e+01 ... (remaining 27005 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 11342 17.82 - 35.64: 597 35.64 - 53.45: 116 53.45 - 71.27: 45 71.27 - 89.09: 22 Dihedral angle restraints: 12122 sinusoidal: 4699 harmonic: 7423 Sorted by residual: dihedral pdb=" CB CYS C 394 " pdb=" SG CYS C 394 " pdb=" SG CYS C 417 " pdb=" CB CYS C 417 " ideal model delta sinusoidal sigma weight residual 93.00 146.43 -53.43 1 1.00e+01 1.00e-02 3.88e+01 dihedral pdb=" CB CYS A 71 " pdb=" SG CYS A 71 " pdb=" SG CYS A 192 " pdb=" CB CYS A 192 " ideal model delta sinusoidal sigma weight residual -86.00 -139.24 53.24 1 1.00e+01 1.00e-02 3.85e+01 dihedral pdb=" CB CYS B 71 " pdb=" SG CYS B 71 " pdb=" SG CYS B 192 " pdb=" CB CYS B 192 " ideal model delta sinusoidal sigma weight residual -86.00 -134.98 48.98 1 1.00e+01 1.00e-02 3.30e+01 ... (remaining 12119 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.760: 3209 0.760 - 1.521: 0 1.521 - 2.281: 0 2.281 - 3.041: 0 3.041 - 3.801: 1 Chirality restraints: 3210 Sorted by residual: chirality pdb=" C1 NAG C 602 " pdb=" ND2 ASN C 414 " pdb=" C2 NAG C 602 " pdb=" O5 NAG C 602 " both_signs ideal model delta sigma weight residual False -2.40 1.40 -3.80 2.00e-01 2.50e+01 3.61e+02 chirality pdb=" C1 NAG A 601 " pdb=" ND2 ASN A 99 " pdb=" C2 NAG A 601 " pdb=" O5 NAG A 601 " both_signs ideal model delta sigma weight residual False -2.40 -1.66 -0.74 2.00e-01 2.50e+01 1.38e+01 chirality pdb=" C1 NAG B 601 " pdb=" ND2 ASN B 99 " pdb=" C2 NAG B 601 " pdb=" O5 NAG B 601 " both_signs ideal model delta sigma weight residual False -2.40 -1.68 -0.72 2.00e-01 2.50e+01 1.30e+01 ... (remaining 3207 not shown) Planarity restraints: 3414 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 602 " 0.192 2.00e-02 2.50e+03 1.60e-01 3.19e+02 pdb=" C7 NAG B 602 " -0.049 2.00e-02 2.50e+03 pdb=" C8 NAG B 602 " 0.137 2.00e-02 2.50e+03 pdb=" N2 NAG B 602 " -0.263 2.00e-02 2.50e+03 pdb=" O7 NAG B 602 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 602 " -0.176 2.00e-02 2.50e+03 1.53e-01 2.93e+02 pdb=" C7 NAG C 602 " 0.038 2.00e-02 2.50e+03 pdb=" C8 NAG C 602 " -0.119 2.00e-02 2.50e+03 pdb=" N2 NAG C 602 " 0.265 2.00e-02 2.50e+03 pdb=" O7 NAG C 602 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 601 " 0.169 2.00e-02 2.50e+03 1.42e-01 2.50e+02 pdb=" C7 NAG A 601 " -0.039 2.00e-02 2.50e+03 pdb=" C8 NAG A 601 " 0.120 2.00e-02 2.50e+03 pdb=" N2 NAG A 601 " -0.236 2.00e-02 2.50e+03 pdb=" O7 NAG A 601 " -0.013 2.00e-02 2.50e+03 ... (remaining 3411 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2013 2.76 - 3.29: 18146 3.29 - 3.83: 30877 3.83 - 4.36: 37381 4.36 - 4.90: 64437 Nonbonded interactions: 152854 Sorted by model distance: nonbonded pdb=" OD1 ASP B 304 " pdb=" N ASN B 305 " model vdw 2.220 3.120 nonbonded pdb=" OD2 ASP I 73 " pdb=" NZ LYS I 76 " model vdw 2.223 3.120 nonbonded pdb=" OD2 ASP G 73 " pdb=" NZ LYS G 76 " model vdw 2.237 3.120 nonbonded pdb=" OD2 ASP H 73 " pdb=" OG SER H 75 " model vdw 2.244 3.040 nonbonded pdb=" OD1 ASN C 414 " pdb=" O LEU C 429 " model vdw 2.246 3.040 ... (remaining 152849 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and resid 2 through 210) selection = chain 'E' selection = (chain 'F' and resid 2 through 210) } ncs_group { reference = (chain 'G' and (resid 1 through 134 or resid 153 through 222)) selection = (chain 'H' and (resid 1 through 196 or resid 208 through 222)) selection = (chain 'I' and (resid 1 through 134 or resid 153 through 196 or resid 208 throug \ h 222)) } 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: 4.900 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: 0.760 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 53.730 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 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 0.087 19846 Z= 0.281 Angle : 0.760 9.468 27010 Z= 0.430 Chirality : 0.088 3.801 3210 Planarity : 0.009 0.185 3408 Dihedral : 12.682 89.089 7271 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.26 % 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: 0.40 (0.16), residues: 2516 helix: 1.07 (0.23), residues: 488 sheet: 1.13 (0.18), residues: 800 loop : -0.66 (0.17), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP I 116 HIS 0.009 0.002 HIS H 111 PHE 0.015 0.002 PHE B 301 TYR 0.026 0.002 TYR I 189 ARG 0.009 0.001 ARG I 101 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 2.247 Fit side-chains revert: symmetry clash REVERT: F 170 LYS cc_start: 0.7819 (ttmt) cc_final: 0.7586 (ttmt) REVERT: I 133 SER cc_start: 0.7639 (p) cc_final: 0.7413 (p) outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 1.5854 time to fit residues: 421.0229 Evaluate side-chains 211 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 2.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 211 optimal weight: 9.9990 chunk 190 optimal weight: 10.0000 chunk 105 optimal weight: 6.9990 chunk 64 optimal weight: 7.9990 chunk 128 optimal weight: 8.9990 chunk 101 optimal weight: 5.9990 chunk 196 optimal weight: 8.9990 chunk 76 optimal weight: 8.9990 chunk 119 optimal weight: 7.9990 chunk 146 optimal weight: 9.9990 chunk 227 optimal weight: 0.6980 overall best weight: 5.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 GLN B 342 GLN B 395 GLN C 102 HIS C 305 ASN ** C 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 GLN H 111 HIS F 54 GLN I 3 GLN I 111 HIS I 184 GLN I 212 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.104 19846 Z= 0.556 Angle : 0.986 13.044 27010 Z= 0.541 Chirality : 0.065 0.725 3210 Planarity : 0.007 0.057 3408 Dihedral : 6.400 59.630 2830 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.22 % Allowed : 5.54 % Favored : 93.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.03 (0.16), residues: 2516 helix: 0.84 (0.22), residues: 486 sheet: 0.76 (0.18), residues: 806 loop : -0.81 (0.16), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.004 TRP I 116 HIS 0.011 0.003 HIS G 111 PHE 0.023 0.004 PHE C 376 TYR 0.032 0.004 TYR I 189 ARG 0.014 0.002 ARG H 101 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 218 time to evaluate : 2.248 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7653 (mp0) REVERT: A 406 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.7134 (mm-30) REVERT: E 86 ASP cc_start: 0.8181 (OUTLIER) cc_final: 0.7727 (m-30) REVERT: F 12 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7167 (tm-30) REVERT: F 170 LYS cc_start: 0.7765 (ttmt) cc_final: 0.7492 (ttmt) outliers start: 27 outliers final: 16 residues processed: 231 average time/residue: 1.5434 time to fit residues: 395.3138 Evaluate side-chains 227 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 207 time to evaluate : 2.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 219 GLN Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 327 GLU Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain F residue 2 PRO Chi-restraints excluded: chain F residue 12 GLU Chi-restraints excluded: chain I residue 163 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 126 optimal weight: 0.4980 chunk 70 optimal weight: 0.0020 chunk 189 optimal weight: 2.9990 chunk 155 optimal weight: 8.9990 chunk 62 optimal weight: 0.9990 chunk 228 optimal weight: 9.9990 chunk 246 optimal weight: 4.9990 chunk 203 optimal weight: 0.9990 chunk 226 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 183 optimal weight: 0.4980 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 GLN B 342 GLN ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 HIS C 305 ASN D 54 GLN F 54 GLN I 3 GLN I 184 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 19846 Z= 0.155 Angle : 0.559 9.418 27010 Z= 0.300 Chirality : 0.047 0.600 3210 Planarity : 0.004 0.040 3408 Dihedral : 5.154 51.750 2830 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.95 % Allowed : 6.85 % Favored : 92.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.26 % 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: 0.64 (0.16), residues: 2516 helix: 1.79 (0.24), residues: 498 sheet: 1.09 (0.18), residues: 802 loop : -0.62 (0.17), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 33 HIS 0.006 0.001 HIS C 102 PHE 0.013 0.001 PHE H 79 TYR 0.011 0.001 TYR B 46 ARG 0.005 0.000 ARG E 106 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 212 time to evaluate : 2.117 Fit side-chains revert: symmetry clash REVERT: A 136 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7523 (mp0) REVERT: B 138 MET cc_start: 0.8258 (mmm) cc_final: 0.7982 (mmm) REVERT: F 170 LYS cc_start: 0.7735 (ttmt) cc_final: 0.7474 (ttmt) outliers start: 21 outliers final: 7 residues processed: 219 average time/residue: 1.4485 time to fit residues: 350.5197 Evaluate side-chains 208 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 200 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 335 LYS Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 163 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 225 optimal weight: 0.8980 chunk 171 optimal weight: 10.0000 chunk 118 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 chunk 153 optimal weight: 8.9990 chunk 229 optimal weight: 0.2980 chunk 242 optimal weight: 5.9990 chunk 119 optimal weight: 0.0470 chunk 217 optimal weight: 8.9990 chunk 65 optimal weight: 8.9990 overall best weight: 1.8482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 342 GLN B 380 ASN B 395 GLN C 102 HIS C 305 ASN D 54 GLN H 184 GLN I 3 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 19846 Z= 0.235 Angle : 0.650 10.775 27010 Z= 0.353 Chirality : 0.050 0.529 3210 Planarity : 0.005 0.038 3408 Dihedral : 5.261 48.505 2830 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.08 % Allowed : 7.88 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.16), residues: 2516 helix: 1.75 (0.23), residues: 489 sheet: 1.09 (0.18), residues: 811 loop : -0.65 (0.17), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP I 116 HIS 0.008 0.001 HIS C 102 PHE 0.013 0.002 PHE B 301 TYR 0.015 0.002 TYR B 274 ARG 0.007 0.001 ARG A 375 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 207 time to evaluate : 2.307 Fit side-chains revert: symmetry clash REVERT: A 136 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7595 (mp0) REVERT: E 86 ASP cc_start: 0.8172 (OUTLIER) cc_final: 0.7761 (m-30) REVERT: F 170 LYS cc_start: 0.7752 (ttmt) cc_final: 0.7459 (ttmt) REVERT: I 65 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.8029 (tmtp) outliers start: 24 outliers final: 12 residues processed: 217 average time/residue: 1.5770 time to fit residues: 378.8080 Evaluate side-chains 217 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 202 time to evaluate : 2.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 335 LYS Chi-restraints excluded: chain C residue 393 GLN Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 163 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 202 optimal weight: 0.8980 chunk 137 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 180 optimal weight: 2.9990 chunk 100 optimal weight: 0.0980 chunk 207 optimal weight: 20.0000 chunk 167 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 123 optimal weight: 6.9990 chunk 217 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 342 GLN B 380 ASN ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 HIS C 219 GLN C 305 ASN D 54 GLN F 54 GLN F 192 HIS I 3 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 19846 Z= 0.233 Angle : 0.645 10.611 27010 Z= 0.351 Chirality : 0.050 0.487 3210 Planarity : 0.005 0.038 3408 Dihedral : 5.239 47.133 2830 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.31 % Allowed : 8.56 % Favored : 90.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.26 % 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: 0.55 (0.16), residues: 2516 helix: 1.69 (0.23), residues: 491 sheet: 1.07 (0.18), residues: 812 loop : -0.70 (0.17), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP I 116 HIS 0.008 0.001 HIS C 102 PHE 0.013 0.002 PHE C 376 TYR 0.015 0.002 TYR B 274 ARG 0.007 0.001 ARG E 106 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 202 time to evaluate : 2.172 Fit side-chains revert: symmetry clash REVERT: A 136 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7590 (mp0) REVERT: E 46 LYS cc_start: 0.8873 (ptmt) cc_final: 0.8566 (ptmt) REVERT: E 86 ASP cc_start: 0.8192 (OUTLIER) cc_final: 0.7774 (m-30) REVERT: F 170 LYS cc_start: 0.7758 (ttmt) cc_final: 0.7462 (ttmt) REVERT: I 65 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.8063 (tmtp) outliers start: 29 outliers final: 16 residues processed: 216 average time/residue: 1.5627 time to fit residues: 373.4348 Evaluate side-chains 219 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 200 time to evaluate : 2.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 335 LYS Chi-restraints excluded: chain C residue 393 GLN Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 93 MET Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 163 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 81 optimal weight: 7.9990 chunk 218 optimal weight: 10.0000 chunk 47 optimal weight: 7.9990 chunk 142 optimal weight: 6.9990 chunk 59 optimal weight: 0.7980 chunk 242 optimal weight: 5.9990 chunk 201 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 342 GLN B 380 ASN B 395 GLN C 102 HIS C 219 GLN C 305 ASN D 54 GLN F 54 GLN F 80 GLN I 3 GLN I 184 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 19846 Z= 0.387 Angle : 0.800 12.436 27010 Z= 0.439 Chirality : 0.056 0.544 3210 Planarity : 0.005 0.049 3408 Dihedral : 5.731 49.285 2830 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.53 % Allowed : 8.78 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.26 % 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: 0.30 (0.16), residues: 2516 helix: 1.27 (0.23), residues: 488 sheet: 0.93 (0.18), residues: 810 loop : -0.75 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP I 116 HIS 0.011 0.002 HIS C 102 PHE 0.019 0.003 PHE C 376 TYR 0.022 0.003 TYR B 274 ARG 0.008 0.001 ARG E 106 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 205 time to evaluate : 2.227 Fit side-chains revert: symmetry clash REVERT: A 136 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7627 (mp0) REVERT: E 46 LYS cc_start: 0.8910 (ptmt) cc_final: 0.8595 (ptmt) REVERT: E 86 ASP cc_start: 0.8184 (OUTLIER) cc_final: 0.7740 (m-30) REVERT: G 3 GLN cc_start: 0.7939 (OUTLIER) cc_final: 0.7589 (tp40) REVERT: F 12 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7222 (tm-30) REVERT: I 65 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.8088 (tmtp) outliers start: 34 outliers final: 18 residues processed: 220 average time/residue: 1.5740 time to fit residues: 383.6177 Evaluate side-chains 226 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 203 time to evaluate : 2.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain B residue 219 GLN Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 335 LYS Chi-restraints excluded: chain C residue 393 GLN Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 3 GLN Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain F residue 12 GLU Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 163 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 234 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 138 optimal weight: 10.0000 chunk 177 optimal weight: 7.9990 chunk 137 optimal weight: 5.9990 chunk 204 optimal weight: 6.9990 chunk 135 optimal weight: 0.9990 chunk 241 optimal weight: 4.9990 chunk 151 optimal weight: 6.9990 chunk 147 optimal weight: 5.9990 chunk 111 optimal weight: 0.9980 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 342 GLN B 380 ASN B 395 GLN C 102 HIS C 219 GLN C 305 ASN D 54 GLN I 3 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.104 19846 Z= 0.387 Angle : 0.806 13.456 27010 Z= 0.443 Chirality : 0.057 0.537 3210 Planarity : 0.006 0.055 3408 Dihedral : 5.794 50.524 2830 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.34 % Favored : 96.62 % Rotamer: Outliers : 1.49 % Allowed : 9.41 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.26 % 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: 0.20 (0.16), residues: 2516 helix: 1.13 (0.22), residues: 488 sheet: 0.96 (0.18), residues: 795 loop : -0.85 (0.16), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP I 116 HIS 0.010 0.002 HIS C 102 PHE 0.021 0.003 PHE B 212 TYR 0.023 0.003 TYR B 274 ARG 0.008 0.001 ARG E 106 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 208 time to evaluate : 2.268 Fit side-chains revert: symmetry clash REVERT: A 136 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7629 (mp0) REVERT: E 46 LYS cc_start: 0.8889 (ptmt) cc_final: 0.8673 (ptmt) REVERT: E 86 ASP cc_start: 0.8202 (OUTLIER) cc_final: 0.7752 (m-30) REVERT: G 3 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.7589 (tp40) REVERT: F 12 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7228 (tm-30) REVERT: I 65 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.8096 (tmtp) REVERT: I 219 LYS cc_start: 0.6884 (mtpp) cc_final: 0.6591 (tptp) outliers start: 33 outliers final: 22 residues processed: 223 average time/residue: 1.4707 time to fit residues: 364.4558 Evaluate side-chains 230 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 203 time to evaluate : 2.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain B residue 219 GLN Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 335 LYS Chi-restraints excluded: chain C residue 393 GLN Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 3 GLN Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain F residue 12 GLU Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 176 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 149 optimal weight: 7.9990 chunk 96 optimal weight: 0.5980 chunk 144 optimal weight: 0.0870 chunk 72 optimal weight: 0.9990 chunk 47 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 153 optimal weight: 5.9990 chunk 164 optimal weight: 0.8980 chunk 119 optimal weight: 0.9990 chunk 22 optimal weight: 0.4980 chunk 190 optimal weight: 4.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 342 GLN B 380 ASN B 395 GLN C 102 HIS C 219 GLN C 305 ASN C 395 GLN D 54 GLN E 171 GLN G 184 GLN I 3 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 19846 Z= 0.158 Angle : 0.561 11.108 27010 Z= 0.302 Chirality : 0.047 0.437 3210 Planarity : 0.004 0.042 3408 Dihedral : 5.041 48.764 2830 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.08 % Allowed : 9.95 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.26 % 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: 0.59 (0.16), residues: 2516 helix: 1.79 (0.23), residues: 500 sheet: 1.15 (0.18), residues: 793 loop : -0.74 (0.17), residues: 1223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 33 HIS 0.005 0.001 HIS C 102 PHE 0.013 0.001 PHE B 301 TYR 0.011 0.001 TYR B 46 ARG 0.010 0.000 ARG E 106 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 202 time to evaluate : 2.326 Fit side-chains revert: symmetry clash REVERT: A 136 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7561 (mp0) REVERT: B 138 MET cc_start: 0.8209 (mmm) cc_final: 0.7899 (mmm) REVERT: E 46 LYS cc_start: 0.8828 (ptmt) cc_final: 0.8625 (ptmt) REVERT: E 86 ASP cc_start: 0.8178 (OUTLIER) cc_final: 0.7766 (m-30) REVERT: H 76 LYS cc_start: 0.6519 (mtmm) cc_final: 0.6313 (pttm) REVERT: I 130 LYS cc_start: 0.7589 (tttm) cc_final: 0.7367 (tttm) outliers start: 24 outliers final: 11 residues processed: 212 average time/residue: 1.6570 time to fit residues: 387.7550 Evaluate side-chains 211 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 198 time to evaluate : 2.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 335 LYS Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 176 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 220 optimal weight: 3.9990 chunk 231 optimal weight: 20.0000 chunk 211 optimal weight: 8.9990 chunk 225 optimal weight: 5.9990 chunk 135 optimal weight: 8.9990 chunk 98 optimal weight: 0.9980 chunk 177 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 203 optimal weight: 5.9990 chunk 213 optimal weight: 0.2980 chunk 224 optimal weight: 6.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 342 GLN B 395 GLN C 102 HIS C 219 GLN C 305 ASN D 54 GLN I 3 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 19846 Z= 0.250 Angle : 0.666 11.660 27010 Z= 0.362 Chirality : 0.051 0.478 3210 Planarity : 0.005 0.054 3408 Dihedral : 5.313 50.367 2830 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.13 % Allowed : 10.23 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.26 % 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: 0.48 (0.16), residues: 2516 helix: 1.65 (0.23), residues: 491 sheet: 1.00 (0.18), residues: 810 loop : -0.71 (0.17), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP I 116 HIS 0.008 0.001 HIS C 102 PHE 0.014 0.002 PHE B 301 TYR 0.018 0.002 TYR I 189 ARG 0.011 0.001 ARG E 106 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 199 time to evaluate : 2.299 Fit side-chains revert: symmetry clash REVERT: A 136 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7596 (mp0) REVERT: E 46 LYS cc_start: 0.8857 (ptmt) cc_final: 0.8655 (ptmt) REVERT: E 86 ASP cc_start: 0.8218 (OUTLIER) cc_final: 0.7773 (m-30) REVERT: I 219 LYS cc_start: 0.6787 (mtpp) cc_final: 0.6511 (tptp) outliers start: 25 outliers final: 15 residues processed: 208 average time/residue: 1.5964 time to fit residues: 366.9328 Evaluate side-chains 214 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 197 time to evaluate : 2.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 335 LYS Chi-restraints excluded: chain C residue 393 GLN Chi-restraints excluded: chain C residue 424 ASN Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 176 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 148 optimal weight: 3.9990 chunk 238 optimal weight: 1.9990 chunk 145 optimal weight: 20.0000 chunk 113 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 250 optimal weight: 10.0000 chunk 230 optimal weight: 20.0000 chunk 199 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 153 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 342 GLN B 395 GLN C 102 HIS C 219 GLN C 305 ASN D 54 GLN D 192 HIS F 171 GLN I 3 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.113 19846 Z= 0.390 Angle : 0.812 13.252 27010 Z= 0.443 Chirality : 0.056 0.545 3210 Planarity : 0.006 0.067 3408 Dihedral : 5.769 51.888 2830 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.04 % Allowed : 10.41 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.26 % 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 (0.16), residues: 2516 helix: 1.23 (0.23), residues: 488 sheet: 0.89 (0.18), residues: 812 loop : -0.84 (0.17), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP I 116 HIS 0.011 0.002 HIS C 102 PHE 0.018 0.003 PHE C 376 TYR 0.022 0.003 TYR B 274 ARG 0.012 0.001 ARG E 106 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 196 time to evaluate : 2.205 Fit side-chains revert: symmetry clash REVERT: A 136 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7634 (mp0) REVERT: E 46 LYS cc_start: 0.8894 (ptmt) cc_final: 0.8685 (ptmt) REVERT: E 86 ASP cc_start: 0.8203 (OUTLIER) cc_final: 0.7756 (m-30) REVERT: I 219 LYS cc_start: 0.6810 (mtpp) cc_final: 0.6514 (mmtm) outliers start: 23 outliers final: 16 residues processed: 206 average time/residue: 1.5803 time to fit residues: 360.2701 Evaluate side-chains 212 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 194 time to evaluate : 2.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 335 LYS Chi-restraints excluded: chain C residue 393 GLN Chi-restraints excluded: chain C residue 424 ASN Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 195 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 158 optimal weight: 0.6980 chunk 212 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 55 optimal weight: 0.0970 chunk 199 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 204 optimal weight: 2.9990 chunk 25 optimal weight: 0.3980 chunk 36 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 342 GLN B 395 GLN C 102 HIS C 219 GLN C 305 ASN D 54 GLN I 3 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.192688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.138524 restraints weight = 16544.255| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 1.65 r_work: 0.3445 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 19846 Z= 0.160 Angle : 0.571 11.914 27010 Z= 0.305 Chirality : 0.047 0.435 3210 Planarity : 0.004 0.050 3408 Dihedral : 5.051 49.455 2830 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.81 % Allowed : 10.45 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.26 % 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: 0.57 (0.16), residues: 2516 helix: 1.77 (0.23), residues: 500 sheet: 1.16 (0.18), residues: 797 loop : -0.77 (0.17), residues: 1219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 33 HIS 0.008 0.001 HIS C 102 PHE 0.013 0.001 PHE B 301 TYR 0.018 0.001 TYR I 189 ARG 0.012 0.000 ARG E 106 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8450.11 seconds wall clock time: 160 minutes 36.48 seconds (9636.48 seconds total)