Starting phenix.real_space_refine on Tue Jul 23 17:36:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tl0_41358/07_2024/8tl0_41358.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tl0_41358/07_2024/8tl0_41358.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tl0_41358/07_2024/8tl0_41358.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tl0_41358/07_2024/8tl0_41358.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tl0_41358/07_2024/8tl0_41358.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tl0_41358/07_2024/8tl0_41358.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 14 5.49 5 S 129 5.16 5 C 14421 2.51 5 N 4281 2.21 5 O 4274 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 52": "OE1" <-> "OE2" Residue "A GLU 61": "OE1" <-> "OE2" Residue "A GLU 95": "OE1" <-> "OE2" Residue "A PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 161": "OE1" <-> "OE2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A ARG 185": "NH1" <-> "NH2" Residue "A GLU 237": "OE1" <-> "OE2" Residue "A ARG 276": "NH1" <-> "NH2" Residue "A GLU 290": "OE1" <-> "OE2" Residue "A GLU 326": "OE1" <-> "OE2" Residue "A GLU 346": "OE1" <-> "OE2" Residue "A GLU 397": "OE1" <-> "OE2" Residue "A ASP 411": "OD1" <-> "OD2" Residue "A GLU 444": "OE1" <-> "OE2" Residue "A GLU 510": "OE1" <-> "OE2" Residue "B GLU 61": "OE1" <-> "OE2" Residue "B ASP 166": "OD1" <-> "OD2" Residue "B ARG 193": "NH1" <-> "NH2" Residue "B ASP 203": "OD1" <-> "OD2" Residue "B PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 290": "OE1" <-> "OE2" Residue "B GLU 326": "OE1" <-> "OE2" Residue "B GLU 397": "OE1" <-> "OE2" Residue "B GLU 413": "OE1" <-> "OE2" Residue "B GLU 444": "OE1" <-> "OE2" Residue "C GLU 161": "OE1" <-> "OE2" Residue "C GLU 173": "OE1" <-> "OE2" Residue "C TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 292": "OE1" <-> "OE2" Residue "C GLU 326": "OE1" <-> "OE2" Residue "C GLU 346": "OE1" <-> "OE2" Residue "C ASP 357": "OD1" <-> "OD2" Residue "C GLU 397": "OE1" <-> "OE2" Residue "C GLU 444": "OE1" <-> "OE2" Residue "D ARG 75": "NH1" <-> "NH2" Residue "D GLU 173": "OE1" <-> "OE2" Residue "D GLU 237": "OE1" <-> "OE2" Residue "D GLU 317": "OE1" <-> "OE2" Residue "D GLU 346": "OE1" <-> "OE2" Residue "D GLU 397": "OE1" <-> "OE2" Residue "D GLU 444": "OE1" <-> "OE2" Residue "I PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 72": "NH1" <-> "NH2" Residue "I GLU 95": "OE1" <-> "OE2" Residue "I ARG 106": "NH1" <-> "NH2" Residue "I GLU 237": "OE1" <-> "OE2" Residue "I GLU 292": "OE1" <-> "OE2" Residue "I GLU 319": "OE1" <-> "OE2" Residue "I GLU 326": "OE1" <-> "OE2" Residue "I GLU 346": "OE1" <-> "OE2" Residue "I ASP 357": "OD1" <-> "OD2" Residue "I GLU 397": "OE1" <-> "OE2" Residue "I ASP 411": "OD1" <-> "OD2" Residue "I GLU 426": "OE1" <-> "OE2" Residue "I GLU 444": "OE1" <-> "OE2" Residue "I PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 477": "OE1" <-> "OE2" Residue "I GLU 487": "OE1" <-> "OE2" Residue "K PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 95": "OE1" <-> "OE2" Residue "K ARG 143": "NH1" <-> "NH2" Residue "K ARG 163": "NH1" <-> "NH2" Residue "K ARG 185": "NH1" <-> "NH2" Residue "K GLU 227": "OE1" <-> "OE2" Residue "K ARG 276": "NH1" <-> "NH2" Residue "K GLU 292": "OE1" <-> "OE2" Residue "L GLU 95": "OE1" <-> "OE2" Residue "L ARG 143": "NH1" <-> "NH2" Residue "L ARG 163": "NH1" <-> "NH2" Residue "L ARG 185": "NH1" <-> "NH2" Residue "L GLU 227": "OE1" <-> "OE2" Residue "L ARG 276": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 23119 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3708 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 28, 'TRANS': 449} Chain breaks: 3 Chain: "B" Number of atoms: 3700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3700 Classifications: {'peptide': 477} Link IDs: {'PTRANS': 27, 'TRANS': 449} Chain breaks: 3 Chain: "C" Number of atoms: 3678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3678 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 26, 'TRANS': 446} Chain breaks: 3 Chain: "D" Number of atoms: 3708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3708 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 27, 'TRANS': 450} Chain breaks: 3 Chain: "E" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Classifications: {'RNA': 3} Modifications used: {'5*END': 1, 'rna2p_pur': 2, 'rna3p_pur': 1} Link IDs: {'rna2p': 1, 'rna3p': 1} Chain: "F" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Classifications: {'RNA': 3} Modifications used: {'5*END': 1, 'rna2p_pur': 2, 'rna3p_pur': 1} Link IDs: {'rna2p': 1, 'rna3p': 1} Chain: "G" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Classifications: {'RNA': 3} Modifications used: {'5*END': 1, 'rna2p_pur': 2, 'rna3p_pur': 1} Link IDs: {'rna2p': 1, 'rna3p': 1} Chain: "H" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Classifications: {'RNA': 3} Modifications used: {'5*END': 1, 'rna2p_pur': 2, 'rna3p_pur': 1} Link IDs: {'rna2p': 1, 'rna3p': 1} Chain: "I" Number of atoms: 3711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3711 Classifications: {'peptide': 479} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 450} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Classifications: {'RNA': 3} Modifications used: {'5*END': 1, 'rna2p_pur': 2, 'rna3p_pur': 1} Link IDs: {'rna2p': 1, 'rna3p': 1} Chain: "K" Number of atoms: 2084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2084 Classifications: {'peptide': 267} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 250} Chain breaks: 1 Chain: "L" Number of atoms: 2089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2089 Classifications: {'peptide': 268} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 251} Chain breaks: 1 Chain: "M" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Classifications: {'RNA': 3} Modifications used: {'5*END': 1, 'rna2p_pur': 2, 'rna3p_pur': 1} Link IDs: {'rna2p': 1, 'rna3p': 1} Chain: "N" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Classifications: {'RNA': 3} Modifications used: {'5*END': 1, 'rna2p_pur': 2, 'rna3p_pur': 1} Link IDs: {'rna2p': 1, 'rna3p': 1} Time building chain proxies: 13.74, per 1000 atoms: 0.59 Number of scatterers: 23119 At special positions: 0 Unit cell: (108.1, 121.26, 157.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 129 16.00 P 14 15.00 O 4274 8.00 N 4281 7.00 C 14421 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.38 Conformation dependent library (CDL) restraints added in 4.1 seconds 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5418 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 27 sheets defined 40.1% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.80 Creating SS restraints... Processing helix chain 'A' and resid 36 through 40 removed outlier: 3.526A pdb=" N VAL A 40 " --> pdb=" O ALA A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 59 removed outlier: 3.870A pdb=" N GLY A 59 " --> pdb=" O ASN A 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 56 through 59' Processing helix chain 'A' and resid 63 through 67 removed outlier: 3.525A pdb=" N GLY A 66 " --> pdb=" O ALA A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 93 Processing helix chain 'A' and resid 94 through 98 removed outlier: 3.711A pdb=" N GLU A 97 " --> pdb=" O ALA A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 119 removed outlier: 3.629A pdb=" N PHE A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 199 Processing helix chain 'A' and resid 230 through 249 Proline residue: A 246 - end of helix Processing helix chain 'A' and resid 262 through 273 Processing helix chain 'A' and resid 274 through 279 removed outlier: 3.667A pdb=" N HIS A 278 " --> pdb=" O ASN A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 336 removed outlier: 3.769A pdb=" N GLU A 328 " --> pdb=" O ASP A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 365 Processing helix chain 'A' and resid 396 through 407 removed outlier: 3.612A pdb=" N SER A 406 " --> pdb=" O MET A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 432 Processing helix chain 'A' and resid 447 through 463 removed outlier: 3.726A pdb=" N ILE A 451 " --> pdb=" O ASP A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 480 Processing helix chain 'B' and resid 36 through 41 removed outlier: 3.746A pdb=" N VAL B 40 " --> pdb=" O THR B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 44 No H-bonds generated for 'chain 'B' and resid 42 through 44' Processing helix chain 'B' and resid 56 through 59 removed outlier: 3.723A pdb=" N GLY B 59 " --> pdb=" O ASN B 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 56 through 59' Processing helix chain 'B' and resid 63 through 67 Processing helix chain 'B' and resid 70 through 93 Processing helix chain 'B' and resid 94 through 98 removed outlier: 3.969A pdb=" N GLU B 97 " --> pdb=" O ALA B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 120 removed outlier: 3.580A pdb=" N PHE B 112 " --> pdb=" O ALA B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 170 removed outlier: 3.516A pdb=" N GLU B 169 " --> pdb=" O ASP B 166 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG B 170 " --> pdb=" O THR B 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 166 through 170' Processing helix chain 'B' and resid 188 through 199 Processing helix chain 'B' and resid 230 through 249 Proline residue: B 246 - end of helix Processing helix chain 'B' and resid 262 through 272 Processing helix chain 'B' and resid 274 through 279 Processing helix chain 'B' and resid 324 through 336 removed outlier: 3.757A pdb=" N GLU B 328 " --> pdb=" O ASP B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 345 removed outlier: 3.613A pdb=" N CYS B 345 " --> pdb=" O ARG B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 365 Processing helix chain 'B' and resid 396 through 407 removed outlier: 3.684A pdb=" N SER B 406 " --> pdb=" O MET B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 432 Processing helix chain 'B' and resid 447 through 463 Processing helix chain 'B' and resid 466 through 481 removed outlier: 3.667A pdb=" N ALA B 480 " --> pdb=" O ASP B 476 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N HIS B 481 " --> pdb=" O GLU B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 511 removed outlier: 3.866A pdb=" N LEU B 511 " --> pdb=" O ALA B 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 44 removed outlier: 4.559A pdb=" N THR C 41 " --> pdb=" O CYS C 38 " (cutoff:3.500A) Proline residue: C 42 - end of helix Processing helix chain 'C' and resid 56 through 59 removed outlier: 3.789A pdb=" N GLY C 59 " --> pdb=" O ASN C 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 56 through 59' Processing helix chain 'C' and resid 63 through 67 Processing helix chain 'C' and resid 70 through 93 Processing helix chain 'C' and resid 94 through 98 removed outlier: 4.443A pdb=" N GLU C 97 " --> pdb=" O ALA C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 120 removed outlier: 3.577A pdb=" N PHE C 112 " --> pdb=" O ALA C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 199 removed outlier: 3.614A pdb=" N LEU C 192 " --> pdb=" O ASP C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 249 Proline residue: C 246 - end of helix Processing helix chain 'C' and resid 262 through 273 removed outlier: 3.690A pdb=" N ALA C 272 " --> pdb=" O MET C 268 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE C 273 " --> pdb=" O VAL C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 279 removed outlier: 3.699A pdb=" N GLY C 279 " --> pdb=" O PRO C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 334 removed outlier: 3.642A pdb=" N GLU C 328 " --> pdb=" O ASP C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 365 Processing helix chain 'C' and resid 396 through 407 removed outlier: 3.546A pdb=" N SER C 406 " --> pdb=" O MET C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 432 Processing helix chain 'C' and resid 447 through 463 removed outlier: 3.527A pdb=" N ILE C 451 " --> pdb=" O ASP C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 480 Processing helix chain 'D' and resid 36 through 41 removed outlier: 3.723A pdb=" N VAL D 40 " --> pdb=" O THR D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 44 No H-bonds generated for 'chain 'D' and resid 42 through 44' Processing helix chain 'D' and resid 56 through 59 removed outlier: 3.720A pdb=" N GLY D 59 " --> pdb=" O ASN D 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 56 through 59' Processing helix chain 'D' and resid 63 through 67 Processing helix chain 'D' and resid 70 through 93 Processing helix chain 'D' and resid 95 through 99 Processing helix chain 'D' and resid 108 through 120 removed outlier: 3.656A pdb=" N PHE D 112 " --> pdb=" O ALA D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 170 removed outlier: 3.704A pdb=" N ARG D 170 " --> pdb=" O THR D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 199 Processing helix chain 'D' and resid 230 through 249 Proline residue: D 246 - end of helix Processing helix chain 'D' and resid 262 through 273 removed outlier: 3.551A pdb=" N ILE D 273 " --> pdb=" O VAL D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 279 Processing helix chain 'D' and resid 324 through 336 removed outlier: 3.736A pdb=" N GLU D 328 " --> pdb=" O ASP D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 365 Processing helix chain 'D' and resid 396 through 407 removed outlier: 3.599A pdb=" N SER D 406 " --> pdb=" O MET D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 432 Processing helix chain 'D' and resid 447 through 462 removed outlier: 3.502A pdb=" N ILE D 451 " --> pdb=" O ASP D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 481 removed outlier: 3.727A pdb=" N HIS D 481 " --> pdb=" O GLU D 477 " (cutoff:3.500A) Processing helix chain 'I' and resid 36 through 41 Processing helix chain 'I' and resid 42 through 44 No H-bonds generated for 'chain 'I' and resid 42 through 44' Processing helix chain 'I' and resid 56 through 59 Processing helix chain 'I' and resid 63 through 67 Processing helix chain 'I' and resid 70 through 93 Processing helix chain 'I' and resid 94 through 97 removed outlier: 3.810A pdb=" N GLU I 97 " --> pdb=" O ALA I 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 94 through 97' Processing helix chain 'I' and resid 108 through 120 removed outlier: 3.593A pdb=" N PHE I 112 " --> pdb=" O ALA I 108 " (cutoff:3.500A) Processing helix chain 'I' and resid 188 through 200 removed outlier: 3.589A pdb=" N LEU I 192 " --> pdb=" O ASP I 188 " (cutoff:3.500A) Processing helix chain 'I' and resid 230 through 249 Proline residue: I 246 - end of helix Processing helix chain 'I' and resid 262 through 273 Processing helix chain 'I' and resid 274 through 279 Processing helix chain 'I' and resid 324 through 335 Processing helix chain 'I' and resid 338 through 345 Processing helix chain 'I' and resid 354 through 365 Processing helix chain 'I' and resid 395 through 407 Processing helix chain 'I' and resid 425 through 431 Processing helix chain 'I' and resid 450 through 462 removed outlier: 3.909A pdb=" N ALA I 454 " --> pdb=" O SER I 450 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA I 455 " --> pdb=" O ILE I 451 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG I 456 " --> pdb=" O HIS I 452 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR I 458 " --> pdb=" O ALA I 454 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP I 459 " --> pdb=" O ALA I 455 " (cutoff:3.500A) Processing helix chain 'I' and resid 466 through 481 Processing helix chain 'K' and resid 36 through 44 removed outlier: 3.972A pdb=" N THR K 41 " --> pdb=" O CYS K 38 " (cutoff:3.500A) Proline residue: K 42 - end of helix Processing helix chain 'K' and resid 56 through 59 removed outlier: 4.131A pdb=" N GLY K 59 " --> pdb=" O ASN K 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 56 through 59' Processing helix chain 'K' and resid 63 through 67 removed outlier: 3.556A pdb=" N GLY K 66 " --> pdb=" O ALA K 63 " (cutoff:3.500A) Processing helix chain 'K' and resid 70 through 93 Processing helix chain 'K' and resid 94 through 98 removed outlier: 4.416A pdb=" N GLU K 97 " --> pdb=" O ALA K 94 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 120 removed outlier: 3.565A pdb=" N PHE K 112 " --> pdb=" O ALA K 108 " (cutoff:3.500A) Processing helix chain 'K' and resid 188 through 199 removed outlier: 3.917A pdb=" N LEU K 192 " --> pdb=" O ASP K 188 " (cutoff:3.500A) Processing helix chain 'K' and resid 230 through 243 removed outlier: 3.504A pdb=" N ARG K 243 " --> pdb=" O VAL K 239 " (cutoff:3.500A) Processing helix chain 'K' and resid 244 through 249 Processing helix chain 'K' and resid 262 through 273 Processing helix chain 'K' and resid 274 through 279 Processing helix chain 'L' and resid 36 through 44 removed outlier: 3.975A pdb=" N THR L 41 " --> pdb=" O CYS L 38 " (cutoff:3.500A) Proline residue: L 42 - end of helix Processing helix chain 'L' and resid 55 through 59 removed outlier: 3.683A pdb=" N GLY L 59 " --> pdb=" O ASN L 56 " (cutoff:3.500A) Processing helix chain 'L' and resid 63 through 67 removed outlier: 3.559A pdb=" N GLY L 66 " --> pdb=" O ALA L 63 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 93 Processing helix chain 'L' and resid 108 through 120 removed outlier: 3.648A pdb=" N PHE L 112 " --> pdb=" O ALA L 108 " (cutoff:3.500A) Processing helix chain 'L' and resid 188 through 199 removed outlier: 3.877A pdb=" N LEU L 192 " --> pdb=" O ASP L 188 " (cutoff:3.500A) Processing helix chain 'L' and resid 230 through 243 removed outlier: 3.531A pdb=" N ALA L 234 " --> pdb=" O ASP L 230 " (cutoff:3.500A) Processing helix chain 'L' and resid 244 through 249 Processing helix chain 'L' and resid 262 through 273 removed outlier: 3.556A pdb=" N ILE L 273 " --> pdb=" O VAL L 269 " (cutoff:3.500A) Processing helix chain 'L' and resid 274 through 279 Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 54 removed outlier: 6.222A pdb=" N TYR A 101 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N VAL A 128 " --> pdb=" O TYR A 101 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LEU A 103 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N ARG A 130 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG A 131 " --> pdb=" O CYS A 135 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N CYS A 135 " --> pdb=" O ARG A 131 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 161 through 163 removed outlier: 7.365A pdb=" N MET A 176 " --> pdb=" O ALA A 205 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE A 207 " --> pdb=" O MET A 176 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ALA A 178 " --> pdb=" O ILE A 207 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N SER A 209 " --> pdb=" O ALA A 178 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N TRP A 180 " --> pdb=" O SER A 209 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ARG A 211 " --> pdb=" O TRP A 180 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N SER A 182 " --> pdb=" O ARG A 211 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N GLY A 175 " --> pdb=" O SER A 253 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU A 255 " --> pdb=" O GLY A 175 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL A 177 " --> pdb=" O LEU A 255 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N VAL A 257 " --> pdb=" O VAL A 177 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL A 179 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N VAL A 259 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL A 181 " --> pdb=" O VAL A 259 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 285 through 287 Processing sheet with id=AA4, first strand: chain 'A' and resid 346 through 350 removed outlier: 12.803A pdb=" N ILE A 373 " --> pdb=" O ARG A 384 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N ARG A 384 " --> pdb=" O ILE A 373 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N HIS A 375 " --> pdb=" O TYR A 382 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 346 through 350 removed outlier: 6.581A pdb=" N LEU A 370 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ASN A 420 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N PHE A 372 " --> pdb=" O ASN A 420 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR A 441 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ALA A 421 " --> pdb=" O THR A 441 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 50 through 54 removed outlier: 6.255A pdb=" N TYR B 101 " --> pdb=" O THR B 126 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N VAL B 128 " --> pdb=" O TYR B 101 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU B 103 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N ARG B 130 " --> pdb=" O LEU B 103 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 161 through 163 removed outlier: 7.688A pdb=" N GLY B 175 " --> pdb=" O GLY B 254 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N MET B 256 " --> pdb=" O GLY B 175 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL B 177 " --> pdb=" O MET B 256 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N PHE B 258 " --> pdb=" O VAL B 177 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL B 179 " --> pdb=" O PHE B 258 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N SER B 260 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL B 181 " --> pdb=" O SER B 260 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 285 through 287 Processing sheet with id=AA9, first strand: chain 'B' and resid 346 through 350 removed outlier: 3.507A pdb=" N THR B 312 " --> pdb=" O CYS B 350 " (cutoff:3.500A) removed outlier: 12.788A pdb=" N ILE B 373 " --> pdb=" O ARG B 384 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N ARG B 384 " --> pdb=" O ILE B 373 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N HIS B 375 " --> pdb=" O TYR B 382 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 346 through 350 removed outlier: 3.507A pdb=" N THR B 312 " --> pdb=" O CYS B 350 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU B 370 " --> pdb=" O VAL B 418 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ASN B 420 " --> pdb=" O LEU B 370 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N PHE B 372 " --> pdb=" O ASN B 420 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR B 441 " --> pdb=" O LEU B 419 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ALA B 421 " --> pdb=" O THR B 441 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR B 438 " --> pdb=" O HIS B 492 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 50 through 54 Processing sheet with id=AB3, first strand: chain 'C' and resid 161 through 163 removed outlier: 7.381A pdb=" N MET C 176 " --> pdb=" O ALA C 205 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE C 207 " --> pdb=" O MET C 176 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ALA C 178 " --> pdb=" O ILE C 207 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N SER C 209 " --> pdb=" O ALA C 178 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N TRP C 180 " --> pdb=" O SER C 209 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ARG C 211 " --> pdb=" O TRP C 180 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N SER C 182 " --> pdb=" O ARG C 211 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N VAL C 177 " --> pdb=" O MET C 256 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N PHE C 258 " --> pdb=" O VAL C 177 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL C 179 " --> pdb=" O PHE C 258 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N SER C 260 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL C 181 " --> pdb=" O SER C 260 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N VAL C 259 " --> pdb=" O PRO C 284 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N PHE C 286 " --> pdb=" O VAL C 259 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL C 281 " --> pdb=" O GLU C 296 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLU C 296 " --> pdb=" O VAL C 281 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N TRP C 283 " --> pdb=" O ALA C 294 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA C 294 " --> pdb=" O TRP C 283 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 346 through 350 removed outlier: 3.877A pdb=" N THR C 441 " --> pdb=" O LEU C 419 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ALA C 421 " --> pdb=" O THR C 441 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 380 through 384 Processing sheet with id=AB6, first strand: chain 'D' and resid 50 through 54 removed outlier: 6.472A pdb=" N CYS D 23 " --> pdb=" O TYR D 102 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ALA D 104 " --> pdb=" O CYS D 23 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU D 25 " --> pdb=" O ALA D 104 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N GLY D 105 " --> pdb=" O VAL D 128 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ARG D 130 " --> pdb=" O GLY D 105 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 161 through 163 removed outlier: 7.278A pdb=" N MET D 176 " --> pdb=" O ALA D 205 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE D 207 " --> pdb=" O MET D 176 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA D 178 " --> pdb=" O ILE D 207 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N SER D 209 " --> pdb=" O ALA D 178 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TRP D 180 " --> pdb=" O SER D 209 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ARG D 211 " --> pdb=" O TRP D 180 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N SER D 182 " --> pdb=" O ARG D 211 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 285 through 287 removed outlier: 3.531A pdb=" N GLU D 290 " --> pdb=" O ARG D 287 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 346 through 350 removed outlier: 12.739A pdb=" N ILE D 373 " --> pdb=" O ARG D 384 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N ARG D 384 " --> pdb=" O ILE D 373 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N HIS D 375 " --> pdb=" O TYR D 382 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 346 through 350 removed outlier: 3.990A pdb=" N THR D 441 " --> pdb=" O LEU D 419 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ALA D 421 " --> pdb=" O THR D 441 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 50 through 54 removed outlier: 6.814A pdb=" N GLN I 22 " --> pdb=" O VAL I 51 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N LEU I 53 " --> pdb=" O GLN I 22 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE I 24 " --> pdb=" O LEU I 53 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N GLY I 105 " --> pdb=" O VAL I 128 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ARG I 130 " --> pdb=" O GLY I 105 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 204 through 211 removed outlier: 7.689A pdb=" N MET I 176 " --> pdb=" O ALA I 205 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ILE I 207 " --> pdb=" O MET I 176 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ALA I 178 " --> pdb=" O ILE I 207 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N SER I 209 " --> pdb=" O ALA I 178 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N TRP I 180 " --> pdb=" O SER I 209 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ARG I 211 " --> pdb=" O TRP I 180 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N SER I 182 " --> pdb=" O ARG I 211 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N VAL I 259 " --> pdb=" O PRO I 284 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N PHE I 286 " --> pdb=" O VAL I 259 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL I 281 " --> pdb=" O GLU I 296 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLU I 296 " --> pdb=" O VAL I 281 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N TRP I 283 " --> pdb=" O ALA I 294 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA I 294 " --> pdb=" O TRP I 283 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 346 through 350 removed outlier: 6.161A pdb=" N ILE I 308 " --> pdb=" O GLN I 348 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N CYS I 350 " --> pdb=" O ILE I 308 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE I 310 " --> pdb=" O CYS I 350 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ARG I 307 " --> pdb=" O ILE I 369 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N HIS I 371 " --> pdb=" O ARG I 307 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU I 309 " --> pdb=" O HIS I 371 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ILE I 373 " --> pdb=" O LEU I 309 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ALA I 311 " --> pdb=" O ILE I 373 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU I 370 " --> pdb=" O VAL I 418 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASN I 420 " --> pdb=" O LEU I 370 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N PHE I 372 " --> pdb=" O ASN I 420 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N THR I 441 " --> pdb=" O LEU I 419 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR I 438 " --> pdb=" O HIS I 492 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 382 through 384 Processing sheet with id=AC6, first strand: chain 'K' and resid 50 through 54 removed outlier: 3.514A pdb=" N LEU K 53 " --> pdb=" O ILE K 24 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N CYS K 23 " --> pdb=" O HIS K 100 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR K 102 " --> pdb=" O CYS K 23 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N TYR K 101 " --> pdb=" O THR K 126 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N VAL K 128 " --> pdb=" O TYR K 101 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N LEU K 103 " --> pdb=" O VAL K 128 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N ARG K 130 " --> pdb=" O LEU K 103 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 161 through 163 removed outlier: 5.375A pdb=" N MET K 176 " --> pdb=" O LEU K 204 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLY K 206 " --> pdb=" O MET K 176 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N VAL K 177 " --> pdb=" O MET K 256 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N PHE K 258 " --> pdb=" O VAL K 177 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL K 179 " --> pdb=" O PHE K 258 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N SER K 260 " --> pdb=" O VAL K 179 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL K 181 " --> pdb=" O SER K 260 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LEU K 255 " --> pdb=" O TRP K 282 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N VAL K 257 " --> pdb=" O PRO K 284 " (cutoff:3.500A) removed outlier: 8.913A pdb=" N PHE K 286 " --> pdb=" O VAL K 257 " (cutoff:3.500A) removed outlier: 10.121A pdb=" N VAL K 259 " --> pdb=" O PHE K 286 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL K 281 " --> pdb=" O GLU K 296 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLU K 296 " --> pdb=" O VAL K 281 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N TRP K 283 " --> pdb=" O ALA K 294 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 50 through 51 removed outlier: 6.267A pdb=" N CYS L 23 " --> pdb=" O TYR L 102 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N ALA L 104 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU L 25 " --> pdb=" O ALA L 104 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N TYR L 101 " --> pdb=" O THR L 126 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N VAL L 128 " --> pdb=" O TYR L 101 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU L 103 " --> pdb=" O VAL L 128 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N ARG L 130 " --> pdb=" O LEU L 103 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 161 through 163 removed outlier: 6.676A pdb=" N MET L 176 " --> pdb=" O ALA L 205 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ILE L 207 " --> pdb=" O MET L 176 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA L 178 " --> pdb=" O ILE L 207 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N SER L 209 " --> pdb=" O ALA L 178 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N TRP L 180 " --> pdb=" O SER L 209 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ARG L 211 " --> pdb=" O TRP L 180 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N SER L 182 " --> pdb=" O ARG L 211 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N GLY L 175 " --> pdb=" O SER L 252 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLY L 254 " --> pdb=" O GLY L 175 " (cutoff:3.500A) removed outlier: 8.686A pdb=" N TRP L 282 " --> pdb=" O SER L 253 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU L 255 " --> pdb=" O TRP L 282 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N VAL L 257 " --> pdb=" O PRO L 284 " (cutoff:3.500A) removed outlier: 8.922A pdb=" N PHE L 286 " --> pdb=" O VAL L 257 " (cutoff:3.500A) removed outlier: 10.096A pdb=" N VAL L 259 " --> pdb=" O PHE L 286 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL L 281 " --> pdb=" O GLU L 296 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N GLU L 296 " --> pdb=" O VAL L 281 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N TRP L 283 " --> pdb=" O ALA L 294 " (cutoff:3.500A) 976 hydrogen bonds defined for protein. 2775 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: 8.21 Time building geometry restraints manager: 10.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7927 1.34 - 1.46: 5305 1.46 - 1.58: 10259 1.58 - 1.70: 28 1.70 - 1.82: 181 Bond restraints: 23700 Sorted by residual: bond pdb=" C HIS L 43 " pdb=" N LEU L 44 " ideal model delta sigma weight residual 1.329 1.268 0.061 1.86e-02 2.89e+03 1.07e+01 bond pdb=" CG LYS B 341 " pdb=" CD LYS B 341 " ideal model delta sigma weight residual 1.520 1.440 0.080 3.00e-02 1.11e+03 7.11e+00 bond pdb=" CG LYS C 121 " pdb=" CD LYS C 121 " ideal model delta sigma weight residual 1.520 1.443 0.077 3.00e-02 1.11e+03 6.56e+00 bond pdb=" CG LYS D 341 " pdb=" CD LYS D 341 " ideal model delta sigma weight residual 1.520 1.445 0.075 3.00e-02 1.11e+03 6.19e+00 bond pdb=" CB LYS B 341 " pdb=" CG LYS B 341 " ideal model delta sigma weight residual 1.520 1.449 0.071 3.00e-02 1.11e+03 5.61e+00 ... (remaining 23695 not shown) Histogram of bond angle deviations from ideal: 94.86 - 102.93: 211 102.93 - 111.00: 9174 111.00 - 119.06: 10160 119.06 - 127.13: 12311 127.13 - 135.20: 435 Bond angle restraints: 32291 Sorted by residual: angle pdb=" CG LYS C 121 " pdb=" CD LYS C 121 " pdb=" CE LYS C 121 " ideal model delta sigma weight residual 111.30 99.49 11.81 2.30e+00 1.89e-01 2.63e+01 angle pdb=" N VAL I 381 " pdb=" CA VAL I 381 " pdb=" C VAL I 381 " ideal model delta sigma weight residual 109.30 115.05 -5.75 1.31e+00 5.83e-01 1.93e+01 angle pdb=" C VAL I 40 " pdb=" N THR I 41 " pdb=" CA THR I 41 " ideal model delta sigma weight residual 120.58 126.36 -5.78 1.32e+00 5.74e-01 1.91e+01 angle pdb=" C TYR A 297 " pdb=" N PRO A 298 " pdb=" CA PRO A 298 " ideal model delta sigma weight residual 119.84 114.45 5.39 1.25e+00 6.40e-01 1.86e+01 angle pdb=" CA LYS B 341 " pdb=" CB LYS B 341 " pdb=" CG LYS B 341 " ideal model delta sigma weight residual 114.10 106.43 7.67 2.00e+00 2.50e-01 1.47e+01 ... (remaining 32286 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 12774 17.85 - 35.70: 1104 35.70 - 53.56: 179 53.56 - 71.41: 20 71.41 - 89.26: 16 Dihedral angle restraints: 14093 sinusoidal: 5702 harmonic: 8391 Sorted by residual: dihedral pdb=" CA LYS C 121 " pdb=" C LYS C 121 " pdb=" N GLN C 122 " pdb=" CA GLN C 122 " ideal model delta harmonic sigma weight residual 180.00 130.05 49.95 0 5.00e+00 4.00e-02 9.98e+01 dihedral pdb=" CA ASN I 320 " pdb=" C ASN I 320 " pdb=" N PRO I 321 " pdb=" CA PRO I 321 " ideal model delta harmonic sigma weight residual -180.00 -137.81 -42.19 0 5.00e+00 4.00e-02 7.12e+01 dihedral pdb=" CA LEU I 379 " pdb=" C LEU I 379 " pdb=" N GLY I 380 " pdb=" CA GLY I 380 " ideal model delta harmonic sigma weight residual -180.00 -148.19 -31.81 0 5.00e+00 4.00e-02 4.05e+01 ... (remaining 14090 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2563 0.048 - 0.096: 716 0.096 - 0.144: 234 0.144 - 0.193: 21 0.193 - 0.241: 3 Chirality restraints: 3537 Sorted by residual: chirality pdb=" CB ILE I 373 " pdb=" CA ILE I 373 " pdb=" CG1 ILE I 373 " pdb=" CG2 ILE I 373 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CG LEU A 44 " pdb=" CB LEU A 44 " pdb=" CD1 LEU A 44 " pdb=" CD2 LEU A 44 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA THR L 41 " pdb=" N THR L 41 " pdb=" C THR L 41 " pdb=" CB THR L 41 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.20 2.00e-01 2.50e+01 1.00e+00 ... (remaining 3534 not shown) Planarity restraints: 4208 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 41 " -0.039 5.00e-02 4.00e+02 5.79e-02 5.36e+00 pdb=" N PRO C 42 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO C 42 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 42 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 121 " -0.011 2.00e-02 2.50e+03 2.25e-02 5.07e+00 pdb=" C LYS C 121 " 0.039 2.00e-02 2.50e+03 pdb=" O LYS C 121 " -0.015 2.00e-02 2.50e+03 pdb=" N GLN C 122 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP A 283 " -0.035 5.00e-02 4.00e+02 5.34e-02 4.56e+00 pdb=" N PRO A 284 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 284 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 284 " -0.030 5.00e-02 4.00e+02 ... (remaining 4205 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3614 2.76 - 3.29: 21497 3.29 - 3.83: 39353 3.83 - 4.36: 44882 4.36 - 4.90: 78402 Nonbonded interactions: 187748 Sorted by model distance: nonbonded pdb=" O ALA A 335 " pdb=" NZ LYS A 341 " model vdw 2.221 2.520 nonbonded pdb=" NH2 ARG B 243 " pdb=" O2' A H 3 " model vdw 2.227 2.520 nonbonded pdb=" NH2 ARG D 243 " pdb=" O2' A E 3 " model vdw 2.242 2.520 nonbonded pdb=" OG SER I 30 " pdb=" OD1 ASP I 32 " model vdw 2.248 2.440 nonbonded pdb=" OG1 THR I 377 " pdb=" O LEU I 379 " model vdw 2.259 2.440 ... (remaining 187743 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 21 through 144 or resid 156 through 446 or (resid 447 and \ (name N or name CA or name C or name O or name CB )) or resid 448 through 493 or \ resid 505 through 521)) selection = (chain 'B' and (resid 21 through 144 or resid 156 through 446 or (resid 447 and \ (name N or name CA or name C or name O or name CB )) or resid 448 through 493 or \ resid 505 through 521)) selection = (chain 'C' and (resid 21 through 446 or (resid 447 and (name N or name CA or nam \ e C or name O or name CB )) or resid 448 through 521)) selection = (chain 'D' and (resid 21 through 144 or resid 156 through 446 or (resid 447 and \ (name N or name CA or name C or name O or name CB )) or resid 448 through 493 or \ resid 505 through 521)) selection = (chain 'I' and (resid 21 through 144 or resid 156 through 493 or resid 505 throu \ gh 515)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'K' selection = (chain 'L' and (resid 21 through 144 or resid 157 through 299)) } 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=0.00 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: 8.450 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: 0.030 Extract box with map and model: 0.820 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 63.780 Find NCS groups from input model: 1.350 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 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 : 0.007 0.080 23700 Z= 0.472 Angle : 0.836 11.806 32291 Z= 0.473 Chirality : 0.049 0.241 3537 Planarity : 0.005 0.058 4208 Dihedral : 13.377 89.260 8675 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.07 % Favored : 94.89 % Rotamer: Outliers : 0.04 % Allowed : 0.26 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.11 % 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: -1.22 (0.15), residues: 2878 helix: 0.35 (0.16), residues: 928 sheet: -0.58 (0.20), residues: 690 loop : -1.81 (0.16), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 282 HIS 0.013 0.001 HIS L 54 PHE 0.016 0.002 PHE D 453 TYR 0.034 0.002 TYR D 446 ARG 0.020 0.001 ARG C 243 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 204 time to evaluate : 2.417 Fit side-chains revert: symmetry clash REVERT: A 188 ASP cc_start: 0.8109 (t70) cc_final: 0.7731 (t0) REVERT: A 251 ARG cc_start: 0.8919 (tpp80) cc_final: 0.8706 (ttm-80) REVERT: B 35 ILE cc_start: 0.9152 (mm) cc_final: 0.8938 (mt) REVERT: B 357 ASP cc_start: 0.8805 (m-30) cc_final: 0.8331 (m-30) REVERT: C 176 MET cc_start: 0.8676 (mtp) cc_final: 0.7834 (mtp) REVERT: D 357 ASP cc_start: 0.9025 (m-30) cc_final: 0.8699 (m-30) REVERT: I 340 ARG cc_start: 0.7719 (mpp-170) cc_final: 0.7503 (mpt180) REVERT: K 87 ASP cc_start: 0.8882 (t70) cc_final: 0.8537 (t0) REVERT: K 142 GLN cc_start: 0.6750 (pm20) cc_final: 0.6085 (pm20) REVERT: K 240 ASN cc_start: 0.7569 (m110) cc_final: 0.7291 (m110) REVERT: K 251 ARG cc_start: 0.7206 (tpm170) cc_final: 0.6695 (tpp-160) REVERT: L 220 THR cc_start: 0.8800 (p) cc_final: 0.8487 (p) outliers start: 1 outliers final: 0 residues processed: 205 average time/residue: 0.3705 time to fit residues: 115.5970 Evaluate side-chains 163 residues out of total 2342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 2.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 242 optimal weight: 10.0000 chunk 217 optimal weight: 8.9990 chunk 120 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 146 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 224 optimal weight: 4.9990 chunk 87 optimal weight: 0.6980 chunk 136 optimal weight: 4.9990 chunk 167 optimal weight: 0.3980 chunk 260 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 425 HIS C 56 ASN ** C 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 ASN I 33 ASN I 240 ASN K 247 ASN L 56 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.0940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23700 Z= 0.202 Angle : 0.542 7.197 32291 Z= 0.280 Chirality : 0.041 0.150 3537 Planarity : 0.004 0.056 4208 Dihedral : 5.450 43.053 3474 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.60 % Allowed : 5.98 % Favored : 93.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.07 % 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: -0.52 (0.16), residues: 2878 helix: 1.32 (0.17), residues: 953 sheet: -0.48 (0.19), residues: 709 loop : -1.62 (0.17), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 283 HIS 0.004 0.001 HIS L 54 PHE 0.014 0.001 PHE K 98 TYR 0.027 0.001 TYR L 114 ARG 0.007 0.000 ARG D 199 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 185 time to evaluate : 2.551 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 328 GLU cc_start: 0.8394 (mp0) cc_final: 0.8014 (mp0) REVERT: B 357 ASP cc_start: 0.8798 (m-30) cc_final: 0.8306 (m-30) REVERT: C 219 ASP cc_start: 0.8609 (p0) cc_final: 0.8286 (p0) REVERT: I 176 MET cc_start: 0.8630 (mmt) cc_final: 0.7998 (mmt) REVERT: I 381 VAL cc_start: 0.9217 (t) cc_final: 0.8966 (p) REVERT: K 38 CYS cc_start: 0.9084 (m) cc_final: 0.8795 (m) REVERT: K 87 ASP cc_start: 0.8884 (t70) cc_final: 0.8568 (t0) REVERT: K 142 GLN cc_start: 0.6771 (pm20) cc_final: 0.6163 (pm20) REVERT: K 176 MET cc_start: 0.6511 (OUTLIER) cc_final: 0.6221 (mtp) REVERT: K 182 SER cc_start: 0.6840 (t) cc_final: 0.5979 (m) REVERT: K 251 ARG cc_start: 0.7123 (tpm170) cc_final: 0.6597 (tpp-160) REVERT: L 176 MET cc_start: 0.8536 (mtp) cc_final: 0.7920 (mtp) REVERT: L 220 THR cc_start: 0.8808 (p) cc_final: 0.8496 (p) outliers start: 14 outliers final: 11 residues processed: 194 average time/residue: 0.3834 time to fit residues: 114.6622 Evaluate side-chains 174 residues out of total 2342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 162 time to evaluate : 2.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain D residue 341 LYS Chi-restraints excluded: chain I residue 461 LEU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain K residue 127 THR Chi-restraints excluded: chain K residue 176 MET Chi-restraints excluded: chain L residue 56 ASN Chi-restraints excluded: chain L residue 132 ASP Chi-restraints excluded: chain L residue 186 ASP Chi-restraints excluded: chain L residue 241 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 144 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 216 optimal weight: 10.0000 chunk 177 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 261 optimal weight: 7.9990 chunk 282 optimal weight: 4.9990 chunk 232 optimal weight: 2.9990 chunk 258 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 209 optimal weight: 0.9980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 425 HIS C 375 HIS ** C 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 ASN I 240 ASN ** K 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 247 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 23700 Z= 0.321 Angle : 0.548 6.637 32291 Z= 0.282 Chirality : 0.042 0.162 3537 Planarity : 0.004 0.064 4208 Dihedral : 5.278 44.448 3474 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.58 % Allowed : 7.77 % Favored : 90.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.61 % 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: -0.13 (0.16), residues: 2878 helix: 1.93 (0.17), residues: 949 sheet: -0.48 (0.20), residues: 703 loop : -1.48 (0.17), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 283 HIS 0.005 0.001 HIS L 54 PHE 0.016 0.001 PHE B 453 TYR 0.020 0.001 TYR I 446 ARG 0.006 0.000 ARG D 199 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 161 time to evaluate : 2.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 328 GLU cc_start: 0.8498 (mp0) cc_final: 0.8251 (mp0) REVERT: B 171 SER cc_start: 0.9352 (m) cc_final: 0.8784 (p) REVERT: B 357 ASP cc_start: 0.8774 (m-30) cc_final: 0.8301 (m-30) REVERT: I 176 MET cc_start: 0.8580 (mmt) cc_final: 0.7968 (mmt) REVERT: I 381 VAL cc_start: 0.9232 (t) cc_final: 0.8981 (p) REVERT: K 38 CYS cc_start: 0.9039 (m) cc_final: 0.8718 (m) REVERT: K 87 ASP cc_start: 0.8891 (t70) cc_final: 0.8576 (t0) REVERT: K 142 GLN cc_start: 0.6931 (pm20) cc_final: 0.6388 (pm20) REVERT: K 251 ARG cc_start: 0.7191 (tpm170) cc_final: 0.6676 (tpp-160) REVERT: K 282 TRP cc_start: 0.7480 (m-10) cc_final: 0.7198 (m-10) outliers start: 37 outliers final: 27 residues processed: 179 average time/residue: 0.3522 time to fit residues: 98.9060 Evaluate side-chains 183 residues out of total 2342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 156 time to evaluate : 2.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 223 MET Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 142 GLN Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 341 LYS Chi-restraints excluded: chain I residue 125 ILE Chi-restraints excluded: chain I residue 461 LEU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain K residue 127 THR Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 174 SER Chi-restraints excluded: chain K residue 209 SER Chi-restraints excluded: chain K residue 256 MET Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 132 ASP Chi-restraints excluded: chain L residue 186 ASP Chi-restraints excluded: chain L residue 241 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 257 optimal weight: 0.8980 chunk 196 optimal weight: 3.9990 chunk 135 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 175 optimal weight: 1.9990 chunk 262 optimal weight: 0.0070 chunk 277 optimal weight: 6.9990 chunk 136 optimal weight: 0.8980 chunk 248 optimal weight: 8.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 425 HIS ** C 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 ASN I 240 ASN ** K 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 247 ASN L 33 ASN L 56 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23700 Z= 0.171 Angle : 0.480 6.958 32291 Z= 0.246 Chirality : 0.040 0.158 3537 Planarity : 0.004 0.055 4208 Dihedral : 5.015 44.070 3474 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.41 % Allowed : 9.01 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.12 (0.16), residues: 2878 helix: 2.16 (0.17), residues: 952 sheet: -0.42 (0.20), residues: 700 loop : -1.30 (0.17), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 283 HIS 0.003 0.001 HIS I 375 PHE 0.014 0.001 PHE K 98 TYR 0.015 0.001 TYR I 446 ARG 0.005 0.000 ARG B 342 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 169 time to evaluate : 2.771 Fit side-chains revert: symmetry clash REVERT: A 328 GLU cc_start: 0.8497 (mp0) cc_final: 0.8060 (mp0) REVERT: B 357 ASP cc_start: 0.8753 (m-30) cc_final: 0.8279 (m-30) REVERT: C 219 ASP cc_start: 0.8595 (p0) cc_final: 0.8274 (p0) REVERT: I 176 MET cc_start: 0.8598 (mmt) cc_final: 0.8031 (mmt) REVERT: I 381 VAL cc_start: 0.9280 (t) cc_final: 0.9013 (p) REVERT: K 38 CYS cc_start: 0.9054 (m) cc_final: 0.8766 (m) REVERT: K 87 ASP cc_start: 0.8877 (t70) cc_final: 0.8563 (t0) REVERT: K 142 GLN cc_start: 0.6871 (pm20) cc_final: 0.6328 (pm20) REVERT: K 176 MET cc_start: 0.6924 (mtp) cc_final: 0.6554 (mtp) REVERT: K 240 ASN cc_start: 0.7435 (m110) cc_final: 0.7100 (m110) REVERT: K 251 ARG cc_start: 0.7161 (tpm170) cc_final: 0.6888 (tpp-160) REVERT: K 282 TRP cc_start: 0.7548 (m-10) cc_final: 0.7335 (m-10) outliers start: 33 outliers final: 20 residues processed: 189 average time/residue: 0.3711 time to fit residues: 109.8961 Evaluate side-chains 172 residues out of total 2342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 152 time to evaluate : 2.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 341 LYS Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 142 GLN Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain D residue 341 LYS Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain I residue 461 LEU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain K residue 78 MET Chi-restraints excluded: chain K residue 209 SER Chi-restraints excluded: chain L residue 56 ASN Chi-restraints excluded: chain L residue 139 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 231 optimal weight: 6.9990 chunk 157 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 206 optimal weight: 0.0270 chunk 114 optimal weight: 1.9990 chunk 236 optimal weight: 0.9980 chunk 191 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 141 optimal weight: 5.9990 chunk 249 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 ASN ** K 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 56 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23700 Z= 0.178 Angle : 0.474 6.806 32291 Z= 0.241 Chirality : 0.040 0.153 3537 Planarity : 0.004 0.059 4208 Dihedral : 4.891 43.193 3474 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.62 % Allowed : 9.87 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.27 (0.16), residues: 2878 helix: 2.31 (0.17), residues: 954 sheet: -0.35 (0.20), residues: 702 loop : -1.24 (0.18), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 283 HIS 0.003 0.001 HIS D 278 PHE 0.014 0.001 PHE K 98 TYR 0.019 0.001 TYR K 114 ARG 0.006 0.000 ARG A 251 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 155 time to evaluate : 2.742 Fit side-chains revert: symmetry clash REVERT: A 328 GLU cc_start: 0.8474 (mp0) cc_final: 0.8067 (mp0) REVERT: B 357 ASP cc_start: 0.8739 (m-30) cc_final: 0.8276 (m-30) REVERT: C 219 ASP cc_start: 0.8603 (p0) cc_final: 0.8255 (p0) REVERT: I 176 MET cc_start: 0.8603 (mmt) cc_final: 0.8080 (mmt) REVERT: I 346 GLU cc_start: 0.7945 (mp0) cc_final: 0.7714 (mp0) REVERT: I 381 VAL cc_start: 0.9319 (t) cc_final: 0.9048 (p) REVERT: K 27 LEU cc_start: 0.8163 (mt) cc_final: 0.7808 (mt) REVERT: K 38 CYS cc_start: 0.9083 (m) cc_final: 0.8782 (m) REVERT: K 87 ASP cc_start: 0.8880 (t70) cc_final: 0.8567 (t0) REVERT: K 142 GLN cc_start: 0.6905 (pm20) cc_final: 0.6354 (pm20) REVERT: K 240 ASN cc_start: 0.7385 (m110) cc_final: 0.7035 (m110) REVERT: K 251 ARG cc_start: 0.7158 (tpm170) cc_final: 0.6868 (tpp-160) REVERT: L 176 MET cc_start: 0.8461 (mtp) cc_final: 0.7843 (mmm) outliers start: 38 outliers final: 28 residues processed: 180 average time/residue: 0.3615 time to fit residues: 102.8366 Evaluate side-chains 181 residues out of total 2342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 153 time to evaluate : 2.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 341 LYS Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 142 GLN Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain D residue 341 LYS Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 402 MET Chi-restraints excluded: chain I residue 461 LEU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 78 MET Chi-restraints excluded: chain K residue 127 THR Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 209 SER Chi-restraints excluded: chain L residue 56 ASN Chi-restraints excluded: chain L residue 132 ASP Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain L residue 241 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 93 optimal weight: 3.9990 chunk 249 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 162 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 277 optimal weight: 6.9990 chunk 230 optimal weight: 5.9990 chunk 128 optimal weight: 6.9990 chunk 23 optimal weight: 0.7980 chunk 91 optimal weight: 0.5980 chunk 145 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 452 HIS ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 ASN ** I 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 481 HIS ** K 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 247 ASN L 56 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23700 Z= 0.180 Angle : 0.471 7.919 32291 Z= 0.239 Chirality : 0.040 0.157 3537 Planarity : 0.004 0.056 4208 Dihedral : 4.809 42.647 3474 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.62 % Allowed : 10.34 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.16), residues: 2878 helix: 2.41 (0.17), residues: 954 sheet: -0.29 (0.20), residues: 701 loop : -1.19 (0.18), residues: 1223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 283 HIS 0.003 0.000 HIS D 278 PHE 0.014 0.001 PHE K 98 TYR 0.013 0.001 TYR I 446 ARG 0.005 0.000 ARG A 251 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 161 time to evaluate : 2.469 Fit side-chains revert: symmetry clash REVERT: A 188 ASP cc_start: 0.7948 (t70) cc_final: 0.7139 (t0) REVERT: A 251 ARG cc_start: 0.8765 (ttm-80) cc_final: 0.8549 (ttm-80) REVERT: A 328 GLU cc_start: 0.8481 (mp0) cc_final: 0.8067 (mp0) REVERT: B 357 ASP cc_start: 0.8741 (m-30) cc_final: 0.8258 (m-30) REVERT: C 219 ASP cc_start: 0.8608 (p0) cc_final: 0.8261 (p0) REVERT: C 341 LYS cc_start: 0.7094 (OUTLIER) cc_final: 0.6536 (pttm) REVERT: I 176 MET cc_start: 0.8611 (mmt) cc_final: 0.8093 (mmt) REVERT: I 346 GLU cc_start: 0.7995 (mp0) cc_final: 0.7740 (mp0) REVERT: I 381 VAL cc_start: 0.9305 (t) cc_final: 0.9023 (p) REVERT: K 27 LEU cc_start: 0.8205 (mt) cc_final: 0.7898 (mt) REVERT: K 38 CYS cc_start: 0.9083 (m) cc_final: 0.8795 (m) REVERT: K 87 ASP cc_start: 0.8875 (t70) cc_final: 0.8565 (t0) REVERT: K 142 GLN cc_start: 0.6972 (pm20) cc_final: 0.6384 (pm20) REVERT: K 176 MET cc_start: 0.6956 (mtp) cc_final: 0.5751 (mmm) REVERT: K 240 ASN cc_start: 0.7368 (m110) cc_final: 0.7035 (m110) REVERT: K 251 ARG cc_start: 0.7180 (tpm170) cc_final: 0.6875 (tpp-160) outliers start: 38 outliers final: 29 residues processed: 185 average time/residue: 0.3497 time to fit residues: 101.2525 Evaluate side-chains 183 residues out of total 2342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 153 time to evaluate : 2.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 223 MET Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 341 LYS Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 142 GLN Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain D residue 341 LYS Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 461 LEU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain K residue 78 MET Chi-restraints excluded: chain K residue 122 GLN Chi-restraints excluded: chain K residue 127 THR Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 209 SER Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 132 ASP Chi-restraints excluded: chain L residue 139 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 267 optimal weight: 8.9990 chunk 31 optimal weight: 0.0980 chunk 158 optimal weight: 7.9990 chunk 202 optimal weight: 6.9990 chunk 157 optimal weight: 0.9990 chunk 233 optimal weight: 8.9990 chunk 155 optimal weight: 0.7980 chunk 276 optimal weight: 0.9990 chunk 173 optimal weight: 2.9990 chunk 168 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 56 ASN ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 ASN ** I 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 248 GLN L 56 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23700 Z= 0.203 Angle : 0.479 7.772 32291 Z= 0.243 Chirality : 0.040 0.160 3537 Planarity : 0.004 0.057 4208 Dihedral : 4.770 42.469 3474 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.67 % Allowed : 10.64 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.46 (0.16), residues: 2878 helix: 2.49 (0.17), residues: 953 sheet: -0.28 (0.20), residues: 703 loop : -1.13 (0.18), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 283 HIS 0.003 0.001 HIS D 278 PHE 0.015 0.001 PHE K 98 TYR 0.022 0.001 TYR K 114 ARG 0.006 0.000 ARG A 251 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 161 time to evaluate : 2.551 Fit side-chains revert: symmetry clash REVERT: A 188 ASP cc_start: 0.7971 (t70) cc_final: 0.7127 (t0) REVERT: A 328 GLU cc_start: 0.8471 (mp0) cc_final: 0.8002 (mp0) REVERT: B 357 ASP cc_start: 0.8741 (m-30) cc_final: 0.8267 (m-30) REVERT: C 219 ASP cc_start: 0.8616 (p0) cc_final: 0.8274 (p0) REVERT: C 341 LYS cc_start: 0.7308 (OUTLIER) cc_final: 0.6779 (pttm) REVERT: I 176 MET cc_start: 0.8599 (mmt) cc_final: 0.8113 (mmt) REVERT: I 346 GLU cc_start: 0.7935 (mp0) cc_final: 0.7672 (mp0) REVERT: K 27 LEU cc_start: 0.8247 (mt) cc_final: 0.7960 (mt) REVERT: K 38 CYS cc_start: 0.9101 (m) cc_final: 0.8815 (m) REVERT: K 87 ASP cc_start: 0.8879 (t70) cc_final: 0.8568 (t0) REVERT: K 142 GLN cc_start: 0.7000 (pm20) cc_final: 0.6423 (pm20) REVERT: K 176 MET cc_start: 0.6967 (mtp) cc_final: 0.6561 (mtp) REVERT: K 240 ASN cc_start: 0.7312 (m110) cc_final: 0.6923 (m110) REVERT: K 251 ARG cc_start: 0.7142 (tpm170) cc_final: 0.6644 (tpp-160) outliers start: 39 outliers final: 33 residues processed: 185 average time/residue: 0.3717 time to fit residues: 107.8079 Evaluate side-chains 188 residues out of total 2342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 154 time to evaluate : 2.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 223 MET Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 341 LYS Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 142 GLN Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain D residue 341 LYS Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 402 MET Chi-restraints excluded: chain I residue 461 LEU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain K residue 78 MET Chi-restraints excluded: chain K residue 122 GLN Chi-restraints excluded: chain K residue 127 THR Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 209 SER Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 132 ASP Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain L residue 241 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 171 optimal weight: 0.3980 chunk 110 optimal weight: 3.9990 chunk 165 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 175 optimal weight: 3.9990 chunk 188 optimal weight: 5.9990 chunk 136 optimal weight: 1.9990 chunk 25 optimal weight: 0.3980 chunk 217 optimal weight: 7.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 56 ASN C 184 GLN ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 ASN ** I 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 56 ASN L 247 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23700 Z= 0.200 Angle : 0.481 8.488 32291 Z= 0.243 Chirality : 0.041 0.155 3537 Planarity : 0.004 0.055 4208 Dihedral : 4.739 42.374 3474 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.84 % Allowed : 11.06 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.51 (0.16), residues: 2878 helix: 2.54 (0.17), residues: 952 sheet: -0.26 (0.20), residues: 706 loop : -1.10 (0.18), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 283 HIS 0.003 0.001 HIS D 278 PHE 0.015 0.001 PHE K 98 TYR 0.013 0.001 TYR L 114 ARG 0.006 0.000 ARG D 213 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 158 time to evaluate : 2.591 Fit side-chains revert: symmetry clash REVERT: A 188 ASP cc_start: 0.7949 (t70) cc_final: 0.7141 (t0) REVERT: A 328 GLU cc_start: 0.8462 (mp0) cc_final: 0.8016 (mp0) REVERT: B 357 ASP cc_start: 0.8737 (m-30) cc_final: 0.8266 (m-30) REVERT: C 219 ASP cc_start: 0.8605 (p0) cc_final: 0.8257 (p0) REVERT: C 341 LYS cc_start: 0.7291 (OUTLIER) cc_final: 0.6746 (pttm) REVERT: I 176 MET cc_start: 0.8570 (mmt) cc_final: 0.8096 (mmt) REVERT: I 346 GLU cc_start: 0.7982 (mp0) cc_final: 0.7716 (mp0) REVERT: K 27 LEU cc_start: 0.8245 (mt) cc_final: 0.7970 (mt) REVERT: K 38 CYS cc_start: 0.9092 (m) cc_final: 0.8803 (m) REVERT: K 87 ASP cc_start: 0.8871 (t70) cc_final: 0.8599 (t0) REVERT: K 176 MET cc_start: 0.6966 (mtp) cc_final: 0.6532 (mtp) REVERT: K 240 ASN cc_start: 0.7389 (m110) cc_final: 0.6998 (m110) REVERT: K 251 ARG cc_start: 0.7146 (tpm170) cc_final: 0.6596 (tpp-160) REVERT: L 176 MET cc_start: 0.8309 (mmm) cc_final: 0.7732 (mmm) outliers start: 43 outliers final: 37 residues processed: 182 average time/residue: 0.3452 time to fit residues: 99.6524 Evaluate side-chains 191 residues out of total 2342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 153 time to evaluate : 2.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 223 MET Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 341 LYS Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 142 GLN Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain D residue 341 LYS Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 461 LEU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain K residue 78 MET Chi-restraints excluded: chain K residue 122 GLN Chi-restraints excluded: chain K residue 127 THR Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 209 SER Chi-restraints excluded: chain K residue 256 MET Chi-restraints excluded: chain L residue 56 ASN Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 132 ASP Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain L residue 241 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 251 optimal weight: 4.9990 chunk 265 optimal weight: 3.9990 chunk 241 optimal weight: 8.9990 chunk 257 optimal weight: 0.7980 chunk 264 optimal weight: 0.6980 chunk 155 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 202 optimal weight: 6.9990 chunk 79 optimal weight: 0.0770 chunk 232 optimal weight: 3.9990 chunk 243 optimal weight: 4.9990 overall best weight: 1.5142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 56 ASN ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 ASN ** I 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 33 ASN L 56 ASN L 247 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 23700 Z= 0.282 Angle : 0.519 9.446 32291 Z= 0.261 Chirality : 0.041 0.151 3537 Planarity : 0.004 0.057 4208 Dihedral : 4.815 43.891 3474 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.88 % Allowed : 11.11 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.53 (0.16), residues: 2878 helix: 2.60 (0.17), residues: 950 sheet: -0.27 (0.20), residues: 703 loop : -1.09 (0.18), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 77 HIS 0.007 0.001 HIS L 54 PHE 0.015 0.001 PHE B 453 TYR 0.022 0.001 TYR K 114 ARG 0.009 0.000 ARG B 243 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 154 time to evaluate : 2.702 Fit side-chains revert: symmetry clash REVERT: A 188 ASP cc_start: 0.8049 (t70) cc_final: 0.7237 (t0) REVERT: A 328 GLU cc_start: 0.8501 (mp0) cc_final: 0.8065 (mp0) REVERT: B 290 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8268 (mm-30) REVERT: B 357 ASP cc_start: 0.8750 (m-30) cc_final: 0.8285 (m-30) REVERT: C 219 ASP cc_start: 0.8646 (p0) cc_final: 0.8307 (p0) REVERT: C 341 LYS cc_start: 0.7476 (OUTLIER) cc_final: 0.6806 (pttm) REVERT: I 32 ASP cc_start: 0.8473 (OUTLIER) cc_final: 0.8209 (p0) REVERT: I 176 MET cc_start: 0.8534 (mmt) cc_final: 0.8122 (mmt) REVERT: I 346 GLU cc_start: 0.8008 (mp0) cc_final: 0.7734 (mp0) REVERT: K 27 LEU cc_start: 0.8309 (mt) cc_final: 0.8011 (mt) REVERT: K 38 CYS cc_start: 0.9077 (m) cc_final: 0.8787 (m) REVERT: K 87 ASP cc_start: 0.8872 (t70) cc_final: 0.8597 (t0) REVERT: K 142 GLN cc_start: 0.7694 (pm20) cc_final: 0.7145 (pm20) REVERT: K 176 MET cc_start: 0.6823 (mtp) cc_final: 0.6386 (mtp) REVERT: K 240 ASN cc_start: 0.7454 (m110) cc_final: 0.7105 (m110) REVERT: K 251 ARG cc_start: 0.7183 (tpm170) cc_final: 0.6604 (tpp-160) outliers start: 44 outliers final: 35 residues processed: 181 average time/residue: 0.3526 time to fit residues: 101.4646 Evaluate side-chains 188 residues out of total 2342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 151 time to evaluate : 2.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 223 MET Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 341 LYS Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 142 GLN Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain D residue 341 LYS Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 32 ASP Chi-restraints excluded: chain I residue 33 ASN Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 461 LEU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain K residue 78 MET Chi-restraints excluded: chain K residue 122 GLN Chi-restraints excluded: chain K residue 127 THR Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 209 SER Chi-restraints excluded: chain K residue 256 MET Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 132 ASP Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain L residue 241 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 256 optimal weight: 2.9990 chunk 169 optimal weight: 5.9990 chunk 272 optimal weight: 0.7980 chunk 166 optimal weight: 0.0670 chunk 129 optimal weight: 2.9990 chunk 189 optimal weight: 9.9990 chunk 285 optimal weight: 2.9990 chunk 263 optimal weight: 0.9990 chunk 227 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 175 optimal weight: 4.9990 overall best weight: 1.1724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 56 ASN ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 ASN ** I 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 33 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.128 23700 Z= 0.298 Angle : 0.664 59.199 32291 Z= 0.366 Chirality : 0.042 0.559 3537 Planarity : 0.004 0.066 4208 Dihedral : 4.824 43.937 3474 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.38 % Favored : 95.59 % Rotamer: Outliers : 1.75 % Allowed : 11.49 % Favored : 86.76 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.44 % 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: 0.54 (0.16), residues: 2878 helix: 2.61 (0.17), residues: 950 sheet: -0.28 (0.20), residues: 703 loop : -1.09 (0.18), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 77 HIS 0.005 0.001 HIS L 54 PHE 0.015 0.001 PHE K 98 TYR 0.016 0.001 TYR K 114 ARG 0.027 0.000 ARG D 199 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 151 time to evaluate : 2.551 Fit side-chains revert: symmetry clash REVERT: A 188 ASP cc_start: 0.8045 (t70) cc_final: 0.7233 (t0) REVERT: A 328 GLU cc_start: 0.8499 (mp0) cc_final: 0.8062 (mp0) REVERT: B 290 GLU cc_start: 0.8471 (mm-30) cc_final: 0.8266 (mm-30) REVERT: B 357 ASP cc_start: 0.8750 (m-30) cc_final: 0.8284 (m-30) REVERT: C 219 ASP cc_start: 0.8645 (p0) cc_final: 0.8306 (p0) REVERT: C 341 LYS cc_start: 0.7471 (OUTLIER) cc_final: 0.6799 (pttm) REVERT: I 32 ASP cc_start: 0.8512 (OUTLIER) cc_final: 0.8206 (p0) REVERT: I 176 MET cc_start: 0.8551 (mmt) cc_final: 0.8119 (mmt) REVERT: I 346 GLU cc_start: 0.8008 (mp0) cc_final: 0.7731 (mp0) REVERT: K 27 LEU cc_start: 0.8303 (mt) cc_final: 0.8003 (mt) REVERT: K 38 CYS cc_start: 0.9077 (m) cc_final: 0.8787 (m) REVERT: K 87 ASP cc_start: 0.8872 (t70) cc_final: 0.8596 (t0) REVERT: K 142 GLN cc_start: 0.7648 (pm20) cc_final: 0.7101 (pm20) REVERT: K 176 MET cc_start: 0.6824 (mtp) cc_final: 0.6379 (mtp) REVERT: K 240 ASN cc_start: 0.7453 (m110) cc_final: 0.7104 (m110) REVERT: K 251 ARG cc_start: 0.7182 (tpm170) cc_final: 0.6603 (tpp-160) REVERT: L 176 MET cc_start: 0.8268 (mmm) cc_final: 0.7662 (mmm) outliers start: 41 outliers final: 35 residues processed: 174 average time/residue: 0.3398 time to fit residues: 94.4170 Evaluate side-chains 187 residues out of total 2342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 150 time to evaluate : 2.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 223 MET Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 341 LYS Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 142 GLN Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain D residue 341 LYS Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 32 ASP Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 461 LEU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain K residue 78 MET Chi-restraints excluded: chain K residue 122 GLN Chi-restraints excluded: chain K residue 127 THR Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 209 SER Chi-restraints excluded: chain K residue 256 MET Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 132 ASP Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain L residue 241 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 139 optimal weight: 6.9990 chunk 180 optimal weight: 6.9990 chunk 242 optimal weight: 0.0970 chunk 69 optimal weight: 0.9980 chunk 209 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 228 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 chunk 234 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 56 ASN ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 33 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.089009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.066516 restraints weight = 54557.601| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 3.55 r_work: 0.2853 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.128 23700 Z= 0.298 Angle : 0.664 59.199 32291 Z= 0.366 Chirality : 0.042 0.559 3537 Planarity : 0.004 0.066 4208 Dihedral : 4.824 43.937 3474 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.38 % Favored : 95.59 % Rotamer: Outliers : 1.62 % Allowed : 11.58 % Favored : 86.80 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.44 % 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: 0.54 (0.16), residues: 2878 helix: 2.61 (0.17), residues: 950 sheet: -0.28 (0.20), residues: 703 loop : -1.09 (0.18), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 77 HIS 0.005 0.001 HIS L 54 PHE 0.015 0.001 PHE K 98 TYR 0.016 0.001 TYR K 114 ARG 0.027 0.000 ARG D 199 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4206.63 seconds wall clock time: 76 minutes 32.99 seconds (4592.99 seconds total)