Starting phenix.real_space_refine on Fri Mar 22 10:38:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ffe_31566/03_2024/7ffe_31566.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ffe_31566/03_2024/7ffe_31566.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ffe_31566/03_2024/7ffe_31566.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ffe_31566/03_2024/7ffe_31566.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ffe_31566/03_2024/7ffe_31566.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ffe_31566/03_2024/7ffe_31566.pdb" } resolution = 3.5 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 ------------------------------------------------------------------------------- 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 240 5.16 5 C 20973 2.51 5 N 5656 2.21 5 O 6194 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 115": "NH1" <-> "NH2" Residue "B ARG 21": "NH1" <-> "NH2" Residue "B TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 175": "NH1" <-> "NH2" Residue "B PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 289": "NH1" <-> "NH2" Residue "C ARG 21": "NH1" <-> "NH2" Residue "C TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 289": "NH1" <-> "NH2" Residue "C PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 115": "NH1" <-> "NH2" Residue "G ARG 21": "NH1" <-> "NH2" Residue "G TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 289": "NH1" <-> "NH2" Residue "J ARG 18": "NH1" <-> "NH2" Residue "J ARG 21": "NH1" <-> "NH2" Residue "J TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 88": "NH1" <-> "NH2" Residue "J ARG 103": "NH1" <-> "NH2" Residue "J ARG 120": "NH1" <-> "NH2" Residue "J TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 161": "NH1" <-> "NH2" Residue "J ARG 281": "NH1" <-> "NH2" Residue "J ARG 419": "NH1" <-> "NH2" Residue "N ARG 13": "NH1" <-> "NH2" Residue "N TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 18": "NH1" <-> "NH2" Residue "N ARG 21": "NH1" <-> "NH2" Residue "N ARG 103": "NH1" <-> "NH2" Residue "N ARG 120": "NH1" <-> "NH2" Residue "N ARG 281": "NH1" <-> "NH2" Residue "N ARG 362": "NH1" <-> "NH2" Residue "O ARG 21": "NH1" <-> "NH2" Residue "O TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 18": "NH1" <-> "NH2" Residue "Q TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 88": "NH1" <-> "NH2" Residue "Q ARG 103": "NH1" <-> "NH2" Residue "Q ARG 120": "NH1" <-> "NH2" Residue "Q ARG 281": "NH1" <-> "NH2" Residue "Q ARG 419": "NH1" <-> "NH2" Residue "R ARG 18": "NH1" <-> "NH2" Residue "R ARG 88": "NH1" <-> "NH2" Residue "R ARG 103": "NH1" <-> "NH2" Residue "R ARG 120": "NH1" <-> "NH2" Residue "R TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 281": "NH1" <-> "NH2" Residue "R ARG 419": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 33063 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1281 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 155} Chain: "B" Number of atoms: 3370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3370 Classifications: {'peptide': 442} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 413} Chain: "C" Number of atoms: 3370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3370 Classifications: {'peptide': 442} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 413} Chain: "F" Number of atoms: 1281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1281 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 155} Chain: "G" Number of atoms: 3351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3351 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 28, 'TRANS': 411} Chain: "I" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 375 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 5, 'TRANS': 44} Chain: "J" Number of atoms: 3257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3257 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 30, 'TRANS': 385} Chain breaks: 1 Chain: "K" Number of atoms: 1281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1281 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 155} Chain: "L" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 375 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 5, 'TRANS': 44} Chain: "N" Number of atoms: 3229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3229 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 30, 'TRANS': 381} Chain breaks: 1 Chain: "O" Number of atoms: 3370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3370 Classifications: {'peptide': 442} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 413} Chain: "P" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 375 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 5, 'TRANS': 44} Chain: "Q" Number of atoms: 3243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3243 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 30, 'TRANS': 383} Chain breaks: 1 Chain: "R" Number of atoms: 3249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3249 Classifications: {'peptide': 415} Link IDs: {'PTRANS': 30, 'TRANS': 384} Chain breaks: 1 Chain: "S" Number of atoms: 1281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1281 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 155} Chain: "T" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 375 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 5, 'TRANS': 44} Time building chain proxies: 16.36, per 1000 atoms: 0.49 Number of scatterers: 33063 At special positions: 0 Unit cell: (153.12, 209.88, 217.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 240 16.00 O 6194 8.00 N 5656 7.00 C 20973 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=53, symmetry=0 Simple disulfide: pdb=" SG CYS B 49 " - pdb=" SG CYS B 114 " distance=2.04 Simple disulfide: pdb=" SG CYS B 62 " - pdb=" SG CYS B 94 " distance=2.03 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 271 " distance=2.03 Simple disulfide: pdb=" SG CYS B 301 " - pdb=" SG CYS B 376 " distance=2.03 Simple disulfide: pdb=" SG CYS B 306 " - pdb=" SG CYS B 380 " distance=2.03 Simple disulfide: pdb=" SG CYS B 328 " - pdb=" SG CYS B 370 " distance=2.02 Simple disulfide: pdb=" SG CYS C 62 " - pdb=" SG CYS C 94 " distance=2.03 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 259 " - pdb=" SG CYS C 271 " distance=2.03 Simple disulfide: pdb=" SG CYS C 301 " - pdb=" SG CYS C 376 " distance=2.03 Simple disulfide: pdb=" SG CYS C 306 " - pdb=" SG CYS C 380 " distance=2.03 Simple disulfide: pdb=" SG CYS C 328 " - pdb=" SG CYS C 370 " distance=2.03 Simple disulfide: pdb=" SG CYS G 62 " - pdb=" SG CYS G 94 " distance=2.03 Simple disulfide: pdb=" SG CYS G 63 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 259 " - pdb=" SG CYS G 271 " distance=2.03 Simple disulfide: pdb=" SG CYS G 301 " - pdb=" SG CYS G 376 " distance=2.03 Simple disulfide: pdb=" SG CYS G 306 " - pdb=" SG CYS G 380 " distance=2.03 Simple disulfide: pdb=" SG CYS G 328 " - pdb=" SG CYS G 370 " distance=2.03 Simple disulfide: pdb=" SG CYS I 7 " - pdb=" SG CYS I 16 " distance=2.03 Simple disulfide: pdb=" SG CYS J 19 " - pdb=" SG CYS J 123 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 27 " distance=2.03 Simple disulfide: pdb=" SG CYS J 90 " - pdb=" SG CYS J 104 " distance=2.02 Simple disulfide: pdb=" SG CYS J 151 " - pdb=" SG CYS J 266 " distance=2.03 Simple disulfide: pdb=" SG CYS J 200 " - pdb=" SG CYS J 226 " distance=2.03 Simple disulfide: pdb=" SG CYS J 202 " - pdb=" SG CYS J 220 " distance=2.03 Simple disulfide: pdb=" SG CYS L 7 " - pdb=" SG CYS L 16 " distance=2.03 Simple disulfide: pdb=" SG CYS N 19 " - pdb=" SG CYS N 123 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 27 " distance=2.03 Simple disulfide: pdb=" SG CYS N 90 " - pdb=" SG CYS N 104 " distance=2.02 Simple disulfide: pdb=" SG CYS N 151 " - pdb=" SG CYS N 266 " distance=2.03 Simple disulfide: pdb=" SG CYS N 200 " - pdb=" SG CYS N 226 " distance=2.02 Simple disulfide: pdb=" SG CYS N 202 " - pdb=" SG CYS N 220 " distance=2.02 Simple disulfide: pdb=" SG CYS O 62 " - pdb=" SG CYS O 94 " distance=2.04 Simple disulfide: pdb=" SG CYS O 63 " - pdb=" SG CYS O 96 " distance=2.03 Simple disulfide: pdb=" SG CYS O 259 " - pdb=" SG CYS O 271 " distance=2.03 Simple disulfide: pdb=" SG CYS O 301 " - pdb=" SG CYS O 376 " distance=2.03 Simple disulfide: pdb=" SG CYS O 306 " - pdb=" SG CYS O 380 " distance=2.03 Simple disulfide: pdb=" SG CYS O 328 " - pdb=" SG CYS O 370 " distance=2.03 Simple disulfide: pdb=" SG CYS P 7 " - pdb=" SG CYS P 16 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 19 " - pdb=" SG CYS Q 123 " distance=2.02 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 27 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 90 " - pdb=" SG CYS Q 104 " distance=2.02 Simple disulfide: pdb=" SG CYS Q 151 " - pdb=" SG CYS Q 266 " distance=1.56 Simple disulfide: pdb=" SG CYS Q 200 " - pdb=" SG CYS Q 226 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 202 " - pdb=" SG CYS Q 220 " distance=2.03 Simple disulfide: pdb=" SG CYS R 19 " - pdb=" SG CYS R 123 " distance=2.03 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 27 " distance=2.03 Simple disulfide: pdb=" SG CYS R 90 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 151 " - pdb=" SG CYS R 266 " distance=2.03 Simple disulfide: pdb=" SG CYS R 200 " - pdb=" SG CYS R 226 " distance=2.03 Simple disulfide: pdb=" SG CYS R 202 " - pdb=" SG CYS R 220 " distance=2.03 Simple disulfide: pdb=" SG CYS T 7 " - pdb=" SG CYS T 16 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.52 Conformation dependent library (CDL) restraints added in 6.4 seconds 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7958 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 92 sheets defined 16.6% alpha, 25.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.86 Creating SS restraints... Processing helix chain 'A' and resid 114 through 127 removed outlier: 4.093A pdb=" N MET A 118 " --> pdb=" O LYS A 114 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL A 119 " --> pdb=" O ARG A 115 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASP A 125 " --> pdb=" O LYS A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 164 removed outlier: 3.858A pdb=" N ALA A 164 " --> pdb=" O ASP A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 186 removed outlier: 4.238A pdb=" N ALA A 186 " --> pdb=" O ASN A 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 247 Processing helix chain 'B' and resid 250 through 255 Processing helix chain 'B' and resid 256 through 259 removed outlier: 3.542A pdb=" N CYS B 259 " --> pdb=" O PRO B 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 256 through 259' Processing helix chain 'B' and resid 404 through 438 removed outlier: 4.834A pdb=" N SER B 417 " --> pdb=" O LEU B 413 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ALA B 418 " --> pdb=" O LEU B 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 247 Processing helix chain 'C' and resid 250 through 255 Processing helix chain 'C' and resid 256 through 259 removed outlier: 3.729A pdb=" N CYS C 259 " --> pdb=" O PRO C 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 256 through 259' Processing helix chain 'C' and resid 283 through 287 removed outlier: 3.662A pdb=" N LEU C 286 " --> pdb=" O PRO C 283 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE C 287 " --> pdb=" O ASP C 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 283 through 287' Processing helix chain 'C' and resid 404 through 439 removed outlier: 3.665A pdb=" N LEU C 414 " --> pdb=" O LEU C 410 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N SER C 417 " --> pdb=" O LEU C 413 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA C 418 " --> pdb=" O LEU C 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 126 removed outlier: 4.743A pdb=" N ASP F 125 " --> pdb=" O LYS F 121 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS F 126 " --> pdb=" O LEU F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 164 removed outlier: 3.648A pdb=" N ALA F 164 " --> pdb=" O ASP F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 185 removed outlier: 3.567A pdb=" N ARG F 185 " --> pdb=" O GLN F 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 247 Processing helix chain 'G' and resid 250 through 255 Processing helix chain 'G' and resid 289 through 293 removed outlier: 3.588A pdb=" N GLU G 292 " --> pdb=" O ARG G 289 " (cutoff:3.500A) Processing helix chain 'G' and resid 404 through 439 removed outlier: 4.758A pdb=" N SER G 417 " --> pdb=" O LEU G 413 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA G 418 " --> pdb=" O LEU G 414 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 37 removed outlier: 3.968A pdb=" N VAL I 36 " --> pdb=" O ALA I 32 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN I 37 " --> pdb=" O MET I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 52 removed outlier: 4.544A pdb=" N LYS I 52 " --> pdb=" O GLU I 48 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 7 Processing helix chain 'J' and resid 80 through 82 No H-bonds generated for 'chain 'J' and resid 80 through 82' Processing helix chain 'J' and resid 175 through 177 No H-bonds generated for 'chain 'J' and resid 175 through 177' Processing helix chain 'J' and resid 222 through 224 No H-bonds generated for 'chain 'J' and resid 222 through 224' Processing helix chain 'J' and resid 351 through 363 removed outlier: 3.784A pdb=" N VAL J 355 " --> pdb=" O LEU J 351 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE J 356 " --> pdb=" O PRO J 352 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N THR J 357 " --> pdb=" O HIS J 353 " (cutoff:3.500A) Processing helix chain 'J' and resid 363 through 398 removed outlier: 3.863A pdb=" N ILE J 368 " --> pdb=" O PRO J 364 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU J 369 " --> pdb=" O MET J 365 " (cutoff:3.500A) Processing helix chain 'J' and resid 409 through 416 Processing helix chain 'K' and resid 114 through 123 Processing helix chain 'K' and resid 159 through 164 removed outlier: 3.874A pdb=" N ALA K 164 " --> pdb=" O ASP K 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 181 through 185 removed outlier: 3.590A pdb=" N ARG K 185 " --> pdb=" O GLN K 182 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 37 removed outlier: 3.786A pdb=" N THR L 30 " --> pdb=" O LYS L 26 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU L 31 " --> pdb=" O PRO L 27 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ALA L 32 " --> pdb=" O ALA L 28 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N VAL L 36 " --> pdb=" O ALA L 32 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASN L 37 " --> pdb=" O MET L 33 " (cutoff:3.500A) Processing helix chain 'L' and resid 42 through 52 removed outlier: 4.141A pdb=" N LYS L 52 " --> pdb=" O GLU L 48 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 5 removed outlier: 3.729A pdb=" N LEU N 5 " --> pdb=" O THR N 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 2 through 5' Processing helix chain 'N' and resid 6 through 11 Processing helix chain 'N' and resid 80 through 82 No H-bonds generated for 'chain 'N' and resid 80 through 82' Processing helix chain 'N' and resid 351 through 363 removed outlier: 3.803A pdb=" N VAL N 355 " --> pdb=" O LEU N 351 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE N 356 " --> pdb=" O PRO N 352 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N THR N 357 " --> pdb=" O HIS N 353 " (cutoff:3.500A) Processing helix chain 'N' and resid 363 through 402 removed outlier: 3.514A pdb=" N THR N 367 " --> pdb=" O TYR N 363 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE N 368 " --> pdb=" O PRO N 364 " (cutoff:3.500A) Proline residue: N 399 - end of helix removed outlier: 3.617A pdb=" N LEU N 402 " --> pdb=" O THR N 398 " (cutoff:3.500A) Processing helix chain 'N' and resid 409 through 415 removed outlier: 4.118A pdb=" N VAL N 414 " --> pdb=" O PHE N 410 " (cutoff:3.500A) Processing helix chain 'O' and resid 238 through 246 Processing helix chain 'O' and resid 250 through 255 Processing helix chain 'O' and resid 256 through 259 removed outlier: 3.504A pdb=" N CYS O 259 " --> pdb=" O PRO O 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 256 through 259' Processing helix chain 'O' and resid 283 through 287 removed outlier: 3.573A pdb=" N LEU O 286 " --> pdb=" O PRO O 283 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE O 287 " --> pdb=" O ASP O 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 283 through 287' Processing helix chain 'O' and resid 289 through 293 removed outlier: 3.582A pdb=" N GLU O 292 " --> pdb=" O ARG O 289 " (cutoff:3.500A) Processing helix chain 'O' and resid 403 through 415 removed outlier: 3.901A pdb=" N LEU O 413 " --> pdb=" O TRP O 409 " (cutoff:3.500A) Processing helix chain 'O' and resid 415 through 440 removed outlier: 3.538A pdb=" N LYS O 440 " --> pdb=" O LEU O 436 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 37 removed outlier: 3.592A pdb=" N VAL P 36 " --> pdb=" O ALA P 32 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN P 37 " --> pdb=" O MET P 33 " (cutoff:3.500A) Processing helix chain 'P' and resid 42 through 52 removed outlier: 4.207A pdb=" N LYS P 52 " --> pdb=" O GLU P 48 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 7 Processing helix chain 'Q' and resid 8 through 12 removed outlier: 3.530A pdb=" N THR Q 12 " --> pdb=" O TYR Q 9 " (cutoff:3.500A) Processing helix chain 'Q' and resid 222 through 224 No H-bonds generated for 'chain 'Q' and resid 222 through 224' Processing helix chain 'Q' and resid 354 through 363 Processing helix chain 'Q' and resid 363 through 402 removed outlier: 3.772A pdb=" N ILE Q 368 " --> pdb=" O PRO Q 364 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU Q 369 " --> pdb=" O MET Q 365 " (cutoff:3.500A) Proline residue: Q 399 - end of helix Processing helix chain 'Q' and resid 409 through 416 Processing helix chain 'R' and resid 2 through 7 Processing helix chain 'R' and resid 8 through 12 Processing helix chain 'R' and resid 80 through 82 No H-bonds generated for 'chain 'R' and resid 80 through 82' Processing helix chain 'R' and resid 222 through 224 No H-bonds generated for 'chain 'R' and resid 222 through 224' Processing helix chain 'R' and resid 352 through 363 removed outlier: 3.735A pdb=" N ILE R 356 " --> pdb=" O PRO R 352 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR R 357 " --> pdb=" O HIS R 353 " (cutoff:3.500A) Processing helix chain 'R' and resid 363 through 398 removed outlier: 3.862A pdb=" N ILE R 368 " --> pdb=" O PRO R 364 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU R 369 " --> pdb=" O MET R 365 " (cutoff:3.500A) Processing helix chain 'R' and resid 399 through 401 No H-bonds generated for 'chain 'R' and resid 399 through 401' Processing helix chain 'R' and resid 409 through 416 Processing helix chain 'S' and resid 114 through 123 Processing helix chain 'S' and resid 159 through 164 removed outlier: 3.874A pdb=" N ALA S 164 " --> pdb=" O ASP S 160 " (cutoff:3.500A) Processing helix chain 'S' and resid 181 through 185 removed outlier: 3.591A pdb=" N ARG S 185 " --> pdb=" O GLN S 182 " (cutoff:3.500A) Processing helix chain 'T' and resid 28 through 37 removed outlier: 4.100A pdb=" N VAL T 36 " --> pdb=" O ALA T 32 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASN T 37 " --> pdb=" O MET T 33 " (cutoff:3.500A) Processing helix chain 'T' and resid 42 through 52 removed outlier: 3.655A pdb=" N LEU T 46 " --> pdb=" O GLY T 42 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS T 52 " --> pdb=" O GLU T 48 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 128 through 129 removed outlier: 7.734A pdb=" N TYR A 139 " --> pdb=" O PRO A 150 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL A 143 " --> pdb=" O LYS A 146 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 198 through 202 removed outlier: 8.099A pdb=" N ALA A 206 " --> pdb=" O PRO A 217 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 214 through 217 current: chain 'A' and resid 239 through 247 removed outlier: 7.859A pdb=" N ALA A 239 " --> pdb=" O TRP A 258 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N TRP A 258 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N VAL A 241 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL A 256 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY A 243 " --> pdb=" O SER A 254 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG A 250 " --> pdb=" O GLU A 247 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 2 through 3 Processing sheet with id=AA4, first strand: chain 'B' and resid 6 through 8 Processing sheet with id=AA5, first strand: chain 'B' and resid 16 through 19 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 27 through 31 current: chain 'B' and resid 119 through 137 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 141 through 147 current: chain 'B' and resid 183 through 185 Processing sheet with id=AA6, first strand: chain 'B' and resid 51 through 61 removed outlier: 4.752A pdb=" N LYS B 105 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N VAL B 103 " --> pdb=" O PRO B 58 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ILE B 60 " --> pdb=" O THR B 101 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N THR B 101 " --> pdb=" O ILE B 60 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AA8, first strand: chain 'B' and resid 220 through 221 Processing sheet with id=AA9, first strand: chain 'B' and resid 260 through 262 Processing sheet with id=AB1, first strand: chain 'B' and resid 300 through 306 removed outlier: 6.308A pdb=" N ILE B 315 " --> pdb=" O ASN B 304 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 343 through 344 removed outlier: 3.647A pdb=" N CYS B 328 " --> pdb=" O VAL B 344 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 387 through 388 Processing sheet with id=AB4, first strand: chain 'C' and resid 2 through 8 Processing sheet with id=AB5, first strand: chain 'C' and resid 15 through 19 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 27 through 31 current: chain 'C' and resid 119 through 137 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 141 through 147 current: chain 'C' and resid 183 through 185 Processing sheet with id=AB6, first strand: chain 'C' and resid 51 through 55 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 51 through 55 current: chain 'C' and resid 101 through 110 No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 87 through 88 removed outlier: 3.697A pdb=" N GLY C 91 " --> pdb=" O MET C 88 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 203 through 205 Processing sheet with id=AB9, first strand: chain 'C' and resid 220 through 221 Processing sheet with id=AC1, first strand: chain 'C' and resid 300 through 306 removed outlier: 6.406A pdb=" N ILE C 315 " --> pdb=" O ASN C 304 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 327 through 329 Processing sheet with id=AC3, first strand: chain 'C' and resid 364 through 369 Processing sheet with id=AC4, first strand: chain 'C' and resid 387 through 388 Processing sheet with id=AC5, first strand: chain 'F' and resid 146 through 148 removed outlier: 5.342A pdb=" N ILE F 136 " --> pdb=" O LEU F 132 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU F 132 " --> pdb=" O ILE F 136 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY F 138 " --> pdb=" O ILE F 130 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 168 through 170 Processing sheet with id=AC7, first strand: chain 'F' and resid 190 through 191 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 190 through 191 current: chain 'F' and resid 205 through 209 removed outlier: 8.539A pdb=" N ALA F 206 " --> pdb=" O PRO F 217 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 214 through 217 current: chain 'F' and resid 236 through 246 removed outlier: 5.775A pdb=" N VAL F 241 " --> pdb=" O VAL F 256 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL F 256 " --> pdb=" O VAL F 241 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 2 through 8 Processing sheet with id=AC9, first strand: chain 'G' and resid 15 through 19 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 27 through 31 current: chain 'G' and resid 119 through 137 removed outlier: 3.505A pdb=" N THR G 144 " --> pdb=" O LEU G 133 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 141 through 147 current: chain 'G' and resid 183 through 186 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 183 through 186 current: chain 'G' and resid 267 through 269 Processing sheet with id=AD1, first strand: chain 'G' and resid 51 through 55 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 51 through 55 current: chain 'G' and resid 101 through 110 No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'G' and resid 203 through 205 Processing sheet with id=AD3, first strand: chain 'G' and resid 220 through 221 Processing sheet with id=AD4, first strand: chain 'G' and resid 296 through 306 removed outlier: 5.339A pdb=" N ALA G 298 " --> pdb=" O SER G 321 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER G 321 " --> pdb=" O ALA G 298 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE G 315 " --> pdb=" O ASN G 304 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 327 through 329 Processing sheet with id=AD6, first strand: chain 'G' and resid 364 through 367 Processing sheet with id=AD7, first strand: chain 'G' and resid 387 through 388 Processing sheet with id=AD8, first strand: chain 'I' and resid 6 through 8 removed outlier: 3.616A pdb=" N PHE I 14 " --> pdb=" O CYS I 7 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 17 through 19 Processing sheet with id=AE1, first strand: chain 'J' and resid 33 through 37 removed outlier: 6.588A pdb=" N GLN J 48 " --> pdb=" O GLU J 34 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N VAL J 36 " --> pdb=" O ARG J 46 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ARG J 46 " --> pdb=" O VAL J 36 " (cutoff:3.500A) removed outlier: 9.614A pdb=" N SER J 50 " --> pdb=" O ASP J 69 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ASP J 69 " --> pdb=" O SER J 50 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 83 through 85 removed outlier: 3.504A pdb=" N ILE J 110 " --> pdb=" O VAL J 125 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 147 through 149 Processing sheet with id=AE4, first strand: chain 'J' and resid 152 through 154 Processing sheet with id=AE5, first strand: chain 'J' and resid 237 through 238 removed outlier: 3.533A pdb=" N VAL J 237 " --> pdb=" O HIS J 168 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLY J 253 " --> pdb=" O MET J 167 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 179 through 181 Processing sheet with id=AE7, first strand: chain 'J' and resid 196 through 200 removed outlier: 3.983A pdb=" N LEU J 197 " --> pdb=" O TYR J 229 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 275 through 279 Processing sheet with id=AE9, first strand: chain 'K' and resid 135 through 139 removed outlier: 5.657A pdb=" N ILE K 136 " --> pdb=" O LEU K 132 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N LEU K 132 " --> pdb=" O ILE K 136 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLY K 138 " --> pdb=" O ILE K 130 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 141 through 143 Processing sheet with id=AF2, first strand: chain 'K' and resid 168 through 170 Processing sheet with id=AF3, first strand: chain 'K' and resid 190 through 191 removed outlier: 6.706A pdb=" N LYS K 190 " --> pdb=" O VAL K 237 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'K' and resid 198 through 202 removed outlier: 8.493A pdb=" N ALA K 206 " --> pdb=" O PRO K 217 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 213 through 217 current: chain 'K' and resid 239 through 245 removed outlier: 6.158A pdb=" N VAL K 241 " --> pdb=" O VAL K 256 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N VAL K 256 " --> pdb=" O VAL K 241 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 6 through 8 Processing sheet with id=AF6, first strand: chain 'N' and resid 17 through 19 removed outlier: 3.928A pdb=" N CYS N 27 " --> pdb=" O CYS N 19 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'N' and resid 33 through 37 removed outlier: 6.554A pdb=" N GLN N 48 " --> pdb=" O GLU N 34 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N VAL N 36 " --> pdb=" O ARG N 46 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ARG N 46 " --> pdb=" O VAL N 36 " (cutoff:3.500A) removed outlier: 9.536A pdb=" N SER N 50 " --> pdb=" O ASP N 69 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ASP N 69 " --> pdb=" O SER N 50 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'N' and resid 83 through 85 Processing sheet with id=AF9, first strand: chain 'N' and resid 147 through 154 Processing sheet with id=AG1, first strand: chain 'N' and resid 237 through 238 Processing sheet with id=AG2, first strand: chain 'N' and resid 173 through 174 removed outlier: 3.715A pdb=" N GLU N 173 " --> pdb=" O ARG N 230 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU N 197 " --> pdb=" O TYR N 229 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'N' and resid 179 through 181 removed outlier: 3.683A pdb=" N VAL N 186 " --> pdb=" O PHE N 217 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'N' and resid 275 through 279 Processing sheet with id=AG5, first strand: chain 'N' and resid 307 through 311 Processing sheet with id=AG6, first strand: chain 'O' and resid 2 through 8 Processing sheet with id=AG7, first strand: chain 'O' and resid 15 through 19 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 27 through 42 current: chain 'O' and resid 119 through 137 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 141 through 147 current: chain 'O' and resid 183 through 185 Processing sheet with id=AG8, first strand: chain 'O' and resid 51 through 55 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 51 through 55 current: chain 'O' and resid 101 through 110 No H-bonds generated for sheet with id=AG8 Processing sheet with id=AG9, first strand: chain 'O' and resid 87 through 88 removed outlier: 3.890A pdb=" N GLY O 91 " --> pdb=" O MET O 88 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'O' and resid 203 through 205 Processing sheet with id=AH2, first strand: chain 'O' and resid 220 through 221 Processing sheet with id=AH3, first strand: chain 'O' and resid 260 through 262 Processing sheet with id=AH4, first strand: chain 'O' and resid 296 through 306 removed outlier: 5.013A pdb=" N ALA O 298 " --> pdb=" O SER O 321 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER O 321 " --> pdb=" O ALA O 298 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE O 315 " --> pdb=" O ASN O 304 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLY O 350 " --> pdb=" O TYR O 320 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'O' and resid 326 through 328 Processing sheet with id=AH6, first strand: chain 'O' and resid 364 through 369 Processing sheet with id=AH7, first strand: chain 'P' and resid 6 through 7 Processing sheet with id=AH8, first strand: chain 'Q' and resid 17 through 19 Processing sheet with id=AH9, first strand: chain 'Q' and resid 33 through 37 removed outlier: 6.624A pdb=" N GLN Q 48 " --> pdb=" O GLU Q 34 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL Q 36 " --> pdb=" O ARG Q 46 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ARG Q 46 " --> pdb=" O VAL Q 36 " (cutoff:3.500A) removed outlier: 9.384A pdb=" N SER Q 50 " --> pdb=" O ASP Q 69 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ASP Q 69 " --> pdb=" O SER Q 50 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'Q' and resid 82 through 85 Processing sheet with id=AI2, first strand: chain 'Q' and resid 148 through 151 Processing sheet with id=AI3, first strand: chain 'Q' and resid 237 through 238 removed outlier: 3.785A pdb=" N GLY Q 253 " --> pdb=" O MET Q 167 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'Q' and resid 179 through 181 removed outlier: 4.120A pdb=" N VAL Q 186 " --> pdb=" O PHE Q 217 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'Q' and resid 206 through 208 Processing sheet with id=AI6, first strand: chain 'Q' and resid 275 through 279 Processing sheet with id=AI7, first strand: chain 'R' and resid 17 through 19 Processing sheet with id=AI8, first strand: chain 'R' and resid 33 through 37 removed outlier: 6.795A pdb=" N GLN R 48 " --> pdb=" O GLU R 34 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N VAL R 36 " --> pdb=" O ARG R 46 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ARG R 46 " --> pdb=" O VAL R 36 " (cutoff:3.500A) removed outlier: 9.903A pdb=" N SER R 50 " --> pdb=" O ASP R 69 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N ASP R 69 " --> pdb=" O SER R 50 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'R' and resid 83 through 85 Processing sheet with id=AJ1, first strand: chain 'R' and resid 147 through 154 Processing sheet with id=AJ2, first strand: chain 'R' and resid 237 through 238 removed outlier: 3.630A pdb=" N GLY R 253 " --> pdb=" O MET R 167 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'R' and resid 179 through 181 removed outlier: 3.878A pdb=" N VAL R 186 " --> pdb=" O PHE R 217 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'R' and resid 206 through 211 removed outlier: 3.563A pdb=" N LYS R 206 " --> pdb=" O CYS R 200 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU R 197 " --> pdb=" O TYR R 229 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'R' and resid 275 through 279 Processing sheet with id=AJ6, first strand: chain 'S' and resid 135 through 139 removed outlier: 5.656A pdb=" N ILE S 136 " --> pdb=" O LEU S 132 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N LEU S 132 " --> pdb=" O ILE S 136 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLY S 138 " --> pdb=" O ILE S 130 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'S' and resid 141 through 143 Processing sheet with id=AJ8, first strand: chain 'S' and resid 168 through 170 Processing sheet with id=AJ9, first strand: chain 'S' and resid 190 through 191 removed outlier: 6.706A pdb=" N LYS S 190 " --> pdb=" O VAL S 237 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ9 Processing sheet with id=AK1, first strand: chain 'S' and resid 198 through 202 removed outlier: 8.494A pdb=" N ALA S 206 " --> pdb=" O PRO S 217 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 213 through 217 current: chain 'S' and resid 239 through 245 removed outlier: 6.157A pdb=" N VAL S 241 " --> pdb=" O VAL S 256 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N VAL S 256 " --> pdb=" O VAL S 241 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'T' and resid 6 through 8 removed outlier: 3.517A pdb=" N PHE T 14 " --> pdb=" O CYS T 7 " (cutoff:3.500A) 1004 hydrogen bonds defined for protein. 2604 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: 10.73 Time building geometry restraints manager: 13.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 10549 1.34 - 1.47: 8346 1.47 - 1.59: 14710 1.59 - 1.72: 1 1.72 - 1.84: 320 Bond restraints: 33926 Sorted by residual: bond pdb=" CA ASP N 175 " pdb=" C ASP N 175 " ideal model delta sigma weight residual 1.526 1.614 -0.088 1.08e-02 8.57e+03 6.64e+01 bond pdb=" C ASP N 175 " pdb=" O ASP N 175 " ideal model delta sigma weight residual 1.235 1.311 -0.076 1.21e-02 6.83e+03 3.99e+01 bond pdb=" N VAL N 179 " pdb=" CA VAL N 179 " ideal model delta sigma weight residual 1.457 1.528 -0.071 1.32e-02 5.74e+03 2.88e+01 bond pdb=" CA VAL N 179 " pdb=" C VAL N 179 " ideal model delta sigma weight residual 1.525 1.589 -0.064 1.22e-02 6.72e+03 2.74e+01 bond pdb=" N ASP N 175 " pdb=" CA ASP N 175 " ideal model delta sigma weight residual 1.464 1.507 -0.043 1.25e-02 6.40e+03 1.18e+01 ... (remaining 33921 not shown) Histogram of bond angle deviations from ideal: 96.94 - 104.41: 776 104.41 - 111.88: 16231 111.88 - 119.34: 11383 119.34 - 126.81: 17213 126.81 - 134.28: 585 Bond angle restraints: 46188 Sorted by residual: angle pdb=" N ASP N 175 " pdb=" CA ASP N 175 " pdb=" C ASP N 175 " ideal model delta sigma weight residual 107.44 123.30 -15.86 1.93e+00 2.68e-01 6.75e+01 angle pdb=" N GLU R 148 " pdb=" CA GLU R 148 " pdb=" C GLU R 148 " ideal model delta sigma weight residual 107.69 119.41 -11.72 2.01e+00 2.48e-01 3.40e+01 angle pdb=" CA VAL N 179 " pdb=" C VAL N 179 " pdb=" N SER N 180 " ideal model delta sigma weight residual 115.77 123.03 -7.26 1.25e+00 6.40e-01 3.37e+01 angle pdb=" N VAL N 179 " pdb=" CA VAL N 179 " pdb=" C VAL N 179 " ideal model delta sigma weight residual 109.80 117.18 -7.38 1.33e+00 5.65e-01 3.08e+01 angle pdb=" N THR R 140 " pdb=" CA THR R 140 " pdb=" C THR R 140 " ideal model delta sigma weight residual 114.56 108.31 6.25 1.27e+00 6.20e-01 2.42e+01 ... (remaining 46183 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 19653 17.61 - 35.22: 604 35.22 - 52.83: 122 52.83 - 70.44: 26 70.44 - 88.05: 7 Dihedral angle restraints: 20412 sinusoidal: 7991 harmonic: 12421 Sorted by residual: dihedral pdb=" CA ILE G 369 " pdb=" C ILE G 369 " pdb=" N CYS G 370 " pdb=" CA CYS G 370 " ideal model delta harmonic sigma weight residual -180.00 -129.96 -50.04 0 5.00e+00 4.00e-02 1.00e+02 dihedral pdb=" CA ASN B 264 " pdb=" C ASN B 264 " pdb=" N PRO B 265 " pdb=" CA PRO B 265 " ideal model delta harmonic sigma weight residual 180.00 131.47 48.53 0 5.00e+00 4.00e-02 9.42e+01 dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 27 " pdb=" CB CYS N 27 " ideal model delta sinusoidal sigma weight residual 93.00 173.62 -80.62 1 1.00e+01 1.00e-02 8.03e+01 ... (remaining 20409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 4546 0.091 - 0.182: 573 0.182 - 0.273: 25 0.273 - 0.364: 3 0.364 - 0.455: 2 Chirality restraints: 5149 Sorted by residual: chirality pdb=" CB ILE B 369 " pdb=" CA ILE B 369 " pdb=" CG1 ILE B 369 " pdb=" CG2 ILE B 369 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.46 2.00e-01 2.50e+01 5.18e+00 chirality pdb=" CG LEU I 31 " pdb=" CB LEU I 31 " pdb=" CD1 LEU I 31 " pdb=" CD2 LEU I 31 " both_signs ideal model delta sigma weight residual False -2.59 -2.18 -0.41 2.00e-01 2.50e+01 4.18e+00 chirality pdb=" CA ASP N 175 " pdb=" N ASP N 175 " pdb=" C ASP N 175 " pdb=" CB ASP N 175 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.27e+00 ... (remaining 5146 not shown) Planarity restraints: 5938 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 264 " -0.068 5.00e-02 4.00e+02 1.02e-01 1.68e+01 pdb=" N PRO C 265 " 0.177 5.00e-02 4.00e+02 pdb=" CA PRO C 265 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO C 265 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN O 264 " -0.066 5.00e-02 4.00e+02 9.91e-02 1.57e+01 pdb=" N PRO O 265 " 0.171 5.00e-02 4.00e+02 pdb=" CA PRO O 265 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO O 265 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP J 236 " 0.039 2.00e-02 2.50e+03 2.22e-02 1.23e+01 pdb=" CG TRP J 236 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP J 236 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP J 236 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP J 236 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP J 236 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP J 236 " -0.026 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 236 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 236 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP J 236 " 0.019 2.00e-02 2.50e+03 ... (remaining 5935 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3632 2.75 - 3.29: 28457 3.29 - 3.82: 52554 3.82 - 4.36: 60171 4.36 - 4.90: 108010 Nonbonded interactions: 252824 Sorted by model distance: nonbonded pdb=" NZ LYS K 146 " pdb=" O ARG N 401 " model vdw 2.211 2.520 nonbonded pdb=" OH TYR N 359 " pdb=" O ALA O 401 " model vdw 2.257 2.440 nonbonded pdb=" O ALA C 401 " pdb=" OH TYR R 359 " model vdw 2.267 2.440 nonbonded pdb=" OE1 GLU B 120 " pdb=" OH TYR B 122 " model vdw 2.267 2.440 nonbonded pdb=" O ALA B 401 " pdb=" OH TYR Q 359 " model vdw 2.274 2.440 ... (remaining 252819 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' selection = chain 'K' selection = chain 'S' } ncs_group { reference = (chain 'B' and resid 1 through 440) selection = (chain 'C' and resid 1 through 440) selection = chain 'G' selection = (chain 'O' and resid 1 through 440) } ncs_group { reference = chain 'I' selection = chain 'L' selection = chain 'P' selection = chain 'T' } ncs_group { reference = (chain 'J' and (resid 2 through 55 or resid 62 through 419)) selection = chain 'N' selection = (chain 'Q' and (resid 2 through 55 or resid 62 through 419)) selection = (chain 'R' and (resid 2 through 55 or resid 62 through 419)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 11.280 Check model and map are aligned: 0.380 Set scattering table: 0.250 Process input model: 81.430 Find NCS groups from input model: 2.310 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 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 0.102 33926 Z= 0.495 Angle : 0.932 15.856 46188 Z= 0.509 Chirality : 0.058 0.455 5149 Planarity : 0.008 0.102 5938 Dihedral : 9.400 88.052 12295 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.59 % Favored : 93.32 % Rotamer: Outliers : 0.28 % Allowed : 2.21 % Favored : 97.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.13 % 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: -3.34 (0.11), residues: 4235 helix: -2.31 (0.16), residues: 574 sheet: -1.64 (0.13), residues: 1237 loop : -2.58 (0.10), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.004 TRP J 236 HIS 0.010 0.002 HIS N 28 PHE 0.031 0.004 PHE Q 328 TYR 0.040 0.003 TYR C 308 ARG 0.015 0.001 ARG Q 21 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1014 residues out of total 3615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 1004 time to evaluate : 3.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 TYR cc_start: 0.7934 (t80) cc_final: 0.6926 (t80) REVERT: B 75 ASP cc_start: 0.8485 (t0) cc_final: 0.8136 (t0) REVERT: B 191 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7447 (mm-30) REVERT: B 409 TRP cc_start: 0.8110 (m100) cc_final: 0.7529 (m100) REVERT: F 130 ILE cc_start: 0.7231 (mm) cc_final: 0.6914 (mt) REVERT: F 151 MET cc_start: 0.6360 (mmt) cc_final: 0.5894 (mmt) REVERT: F 199 TYR cc_start: 0.7194 (m-80) cc_final: 0.6451 (m-80) REVERT: G 95 PHE cc_start: 0.7608 (p90) cc_final: 0.7407 (p90) REVERT: I 15 PRO cc_start: 0.7205 (Cg_exo) cc_final: 0.6949 (Cg_endo) REVERT: J 239 ASN cc_start: 0.8120 (t0) cc_final: 0.7848 (t0) REVERT: J 389 PHE cc_start: 0.8133 (t80) cc_final: 0.7894 (t80) REVERT: J 392 SER cc_start: 0.8162 (m) cc_final: 0.7756 (t) REVERT: K 122 LEU cc_start: 0.6433 (mt) cc_final: 0.5962 (mt) REVERT: K 126 LYS cc_start: 0.6054 (mppt) cc_final: 0.5517 (mttp) REVERT: K 132 LEU cc_start: 0.7751 (tp) cc_final: 0.7544 (tt) REVERT: K 159 ASN cc_start: 0.6216 (t0) cc_final: 0.5787 (t0) REVERT: K 162 LEU cc_start: 0.8725 (mt) cc_final: 0.8455 (mt) REVERT: K 187 ASP cc_start: 0.8400 (m-30) cc_final: 0.8151 (t0) REVERT: K 192 THR cc_start: 0.7789 (t) cc_final: 0.7422 (t) REVERT: K 193 HIS cc_start: 0.7421 (p-80) cc_final: 0.7007 (p-80) REVERT: K 231 LEU cc_start: 0.6770 (mt) cc_final: 0.5977 (mm) REVERT: K 236 ARG cc_start: 0.5252 (mtm180) cc_final: 0.5026 (mtm180) REVERT: K 267 TYR cc_start: 0.3122 (t80) cc_final: 0.2847 (t80) REVERT: O 162 THR cc_start: 0.9146 (m) cc_final: 0.8869 (p) REVERT: O 284 ASP cc_start: 0.8277 (m-30) cc_final: 0.7655 (m-30) REVERT: Q 207 ILE cc_start: 0.7794 (tt) cc_final: 0.7530 (tt) REVERT: S 122 LEU cc_start: 0.7959 (mt) cc_final: 0.7485 (mt) REVERT: S 126 LYS cc_start: 0.4861 (mppt) cc_final: 0.4658 (mtmt) REVERT: S 151 MET cc_start: 0.4300 (mmt) cc_final: 0.3453 (mmp) REVERT: S 159 ASN cc_start: 0.5810 (t0) cc_final: 0.5328 (t0) REVERT: S 180 VAL cc_start: 0.6121 (t) cc_final: 0.5435 (t) REVERT: S 211 ASN cc_start: 0.7662 (m-40) cc_final: 0.7403 (m-40) REVERT: S 214 PHE cc_start: 0.5787 (m-80) cc_final: 0.5250 (m-10) REVERT: S 231 LEU cc_start: 0.6916 (mt) cc_final: 0.6319 (mm) REVERT: S 241 VAL cc_start: 0.6758 (t) cc_final: 0.6505 (p) REVERT: S 242 LEU cc_start: 0.5238 (mt) cc_final: 0.4329 (mm) outliers start: 10 outliers final: 3 residues processed: 1009 average time/residue: 0.4902 time to fit residues: 762.9423 Evaluate side-chains 535 residues out of total 3615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 532 time to evaluate : 3.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain K residue 257 MET Chi-restraints excluded: chain S residue 257 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 358 optimal weight: 5.9990 chunk 321 optimal weight: 0.9980 chunk 178 optimal weight: 0.9980 chunk 109 optimal weight: 10.0000 chunk 216 optimal weight: 2.9990 chunk 171 optimal weight: 5.9990 chunk 332 optimal weight: 0.0970 chunk 128 optimal weight: 3.9990 chunk 202 optimal weight: 0.9980 chunk 247 optimal weight: 9.9990 chunk 385 optimal weight: 0.8980 overall best weight: 0.7978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 GLN A 159 ASN A 197 GLN A 204 HIS A 246 ASN ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 ASN B 125 HIS ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 304 ASN B 362 HIS ** B 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 GLN B 442 ASN C 43 ASN C 130 GLN C 140 HIS C 304 ASN C 360 ASN ** C 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 442 ASN ** F 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 43 ASN G 130 GLN G 264 ASN G 304 ASN G 360 ASN G 390 HIS ** G 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 28 HIS ** J 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 216 GLN ** J 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 353 HIS K 197 GLN K 203 HIS K 271 ASN N 7 ASN N 121 HIS N 156 HIS ** N 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 358 HIS O 43 ASN O 304 ASN O 360 ASN O 394 HIS O 396 GLN ** Q 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 156 HIS Q 159 GLN ** Q 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 225 GLN Q 232 GLN Q 305 HIS R 160 ASN ** R 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 225 GLN R 332 ASN ** S 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 33926 Z= 0.182 Angle : 0.633 11.886 46188 Z= 0.328 Chirality : 0.044 0.165 5149 Planarity : 0.006 0.087 5938 Dihedral : 5.967 75.677 4637 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.36 % Favored : 94.57 % Rotamer: Outliers : 2.05 % Allowed : 9.99 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.07 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.12), residues: 4235 helix: -0.15 (0.21), residues: 566 sheet: -1.03 (0.14), residues: 1243 loop : -1.96 (0.11), residues: 2426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 202 HIS 0.011 0.001 HIS F 204 PHE 0.036 0.002 PHE F 189 TYR 0.023 0.001 TYR S 177 ARG 0.008 0.001 ARG A 250 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 3615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 582 time to evaluate : 3.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 TYR cc_start: 0.7608 (p90) cc_final: 0.7198 (p90) REVERT: A 197 GLN cc_start: 0.6352 (OUTLIER) cc_final: 0.6105 (tt0) REVERT: A 223 LYS cc_start: 0.7598 (tmtt) cc_final: 0.7348 (tmtt) REVERT: B 233 TYR cc_start: 0.8626 (p90) cc_final: 0.8381 (p90) REVERT: B 409 TRP cc_start: 0.8150 (m100) cc_final: 0.7450 (m100) REVERT: C 51 TYR cc_start: 0.8240 (p90) cc_final: 0.8031 (p90) REVERT: C 407 TRP cc_start: 0.8283 (m100) cc_final: 0.8080 (m100) REVERT: F 199 TYR cc_start: 0.7148 (m-80) cc_final: 0.6348 (m-80) REVERT: F 202 TRP cc_start: 0.8305 (t60) cc_final: 0.7894 (t60) REVERT: G 6 THR cc_start: 0.8657 (m) cc_final: 0.8437 (p) REVERT: I 33 MET cc_start: 0.7862 (ptp) cc_final: 0.7649 (ptm) REVERT: J 293 THR cc_start: 0.8730 (m) cc_final: 0.8424 (m) REVERT: J 389 PHE cc_start: 0.8181 (t80) cc_final: 0.7950 (t80) REVERT: J 392 SER cc_start: 0.8262 (m) cc_final: 0.7688 (t) REVERT: K 118 MET cc_start: 0.7820 (ttp) cc_final: 0.7393 (tmm) REVERT: K 122 LEU cc_start: 0.6319 (mt) cc_final: 0.6071 (mt) REVERT: K 126 LYS cc_start: 0.6064 (mppt) cc_final: 0.5323 (mtmm) REVERT: K 159 ASN cc_start: 0.6035 (t0) cc_final: 0.5761 (t0) REVERT: K 187 ASP cc_start: 0.8461 (m-30) cc_final: 0.8114 (t0) REVERT: K 192 THR cc_start: 0.8014 (t) cc_final: 0.7553 (p) REVERT: K 202 TRP cc_start: 0.4707 (t60) cc_final: 0.4387 (t60) REVERT: K 231 LEU cc_start: 0.6461 (mt) cc_final: 0.6016 (mm) REVERT: K 260 GLU cc_start: 0.8575 (tt0) cc_final: 0.8203 (pt0) REVERT: L 6 MET cc_start: 0.5380 (mmp) cc_final: 0.4942 (mmm) REVERT: O 144 THR cc_start: 0.8972 (m) cc_final: 0.8570 (p) REVERT: O 162 THR cc_start: 0.9057 (m) cc_final: 0.8830 (p) REVERT: O 377 LYS cc_start: 0.8369 (mtpt) cc_final: 0.8127 (ttmm) REVERT: P 14 PHE cc_start: 0.6657 (p90) cc_final: 0.6358 (p90) REVERT: Q 201 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7876 (tm-30) outliers start: 74 outliers final: 48 residues processed: 627 average time/residue: 0.4397 time to fit residues: 444.0071 Evaluate side-chains 543 residues out of total 3615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 494 time to evaluate : 3.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 156 LYS Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain G residue 63 CYS Chi-restraints excluded: chain G residue 174 ASP Chi-restraints excluded: chain G residue 238 SER Chi-restraints excluded: chain G residue 334 SER Chi-restraints excluded: chain G residue 336 THR Chi-restraints excluded: chain I residue 6 MET Chi-restraints excluded: chain J residue 130 LYS Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 233 ASN Chi-restraints excluded: chain J residue 386 THR Chi-restraints excluded: chain K residue 137 ASN Chi-restraints excluded: chain K residue 172 LYS Chi-restraints excluded: chain K residue 238 VAL Chi-restraints excluded: chain K residue 257 MET Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain N residue 108 ASP Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain O residue 129 VAL Chi-restraints excluded: chain O residue 137 VAL Chi-restraints excluded: chain O residue 295 THR Chi-restraints excluded: chain O residue 397 THR Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain Q residue 221 THR Chi-restraints excluded: chain Q residue 233 ASN Chi-restraints excluded: chain Q residue 282 SER Chi-restraints excluded: chain Q residue 322 THR Chi-restraints excluded: chain Q residue 355 VAL Chi-restraints excluded: chain Q residue 386 THR Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 282 SER Chi-restraints excluded: chain R residue 329 VAL Chi-restraints excluded: chain S residue 201 SER Chi-restraints excluded: chain S residue 257 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 213 optimal weight: 10.0000 chunk 119 optimal weight: 20.0000 chunk 320 optimal weight: 0.6980 chunk 262 optimal weight: 0.9990 chunk 106 optimal weight: 30.0000 chunk 385 optimal weight: 0.3980 chunk 416 optimal weight: 8.9990 chunk 343 optimal weight: 5.9990 chunk 382 optimal weight: 6.9990 chunk 131 optimal weight: 8.9990 chunk 309 optimal weight: 6.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 GLN A 197 GLN A 203 HIS A 246 ASN A 271 ASN B 3 HIS ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 HIS ** B 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 GLN B 441 HIS C 130 GLN C 235 GLN G 130 GLN G 386 HIS G 394 HIS G 396 GLN J 96 HIS ** K 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 271 ASN ** N 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 212 ASN N 216 GLN O 396 GLN O 438 ASN ** Q 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 216 GLN ** Q 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 353 HIS ** R 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 203 HIS S 233 ASN S 271 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 33926 Z= 0.318 Angle : 0.633 8.942 46188 Z= 0.327 Chirality : 0.045 0.162 5149 Planarity : 0.005 0.084 5938 Dihedral : 5.629 78.124 4636 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.88 % Favored : 94.05 % Rotamer: Outliers : 3.40 % Allowed : 10.90 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.07 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.12), residues: 4235 helix: 0.60 (0.23), residues: 577 sheet: -0.70 (0.14), residues: 1230 loop : -1.67 (0.12), residues: 2428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 202 HIS 0.010 0.001 HIS A 152 PHE 0.028 0.002 PHE F 189 TYR 0.023 0.002 TYR O 308 ARG 0.005 0.001 ARG S 115 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 3615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 527 time to evaluate : 3.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 TYR cc_start: 0.7694 (p90) cc_final: 0.7270 (p90) REVERT: B 377 LYS cc_start: 0.7357 (mttm) cc_final: 0.7127 (mttm) REVERT: B 409 TRP cc_start: 0.8196 (m100) cc_final: 0.7941 (m100) REVERT: C 51 TYR cc_start: 0.8391 (p90) cc_final: 0.8109 (p90) REVERT: C 327 LYS cc_start: 0.8702 (ptmt) cc_final: 0.8370 (pttt) REVERT: C 439 GLN cc_start: 0.7811 (tm-30) cc_final: 0.7518 (tm-30) REVERT: F 199 TYR cc_start: 0.7201 (m-80) cc_final: 0.6477 (m-80) REVERT: F 202 TRP cc_start: 0.8308 (t60) cc_final: 0.7681 (t60) REVERT: F 250 ARG cc_start: 0.7939 (tpp80) cc_final: 0.7700 (tpp80) REVERT: F 270 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7385 (mt-10) REVERT: G 115 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8113 (mt) REVERT: I 33 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.7934 (ptp) REVERT: J 392 SER cc_start: 0.8408 (m) cc_final: 0.7741 (t) REVERT: K 159 ASN cc_start: 0.6280 (t0) cc_final: 0.5937 (t0) REVERT: K 192 THR cc_start: 0.7384 (t) cc_final: 0.7183 (p) REVERT: K 260 GLU cc_start: 0.8662 (tt0) cc_final: 0.8336 (pt0) REVERT: L 6 MET cc_start: 0.5422 (mmp) cc_final: 0.4819 (mmm) REVERT: O 144 THR cc_start: 0.8967 (m) cc_final: 0.8589 (p) REVERT: O 377 LYS cc_start: 0.8521 (mtpt) cc_final: 0.8299 (ttmm) REVERT: P 14 PHE cc_start: 0.6947 (p90) cc_final: 0.6583 (p90) REVERT: Q 201 GLU cc_start: 0.8048 (tm-30) cc_final: 0.7685 (tm-30) REVERT: R 88 ARG cc_start: 0.6057 (mmt180) cc_final: 0.5734 (mmt180) REVERT: S 122 LEU cc_start: 0.7909 (mt) cc_final: 0.7645 (mp) outliers start: 123 outliers final: 88 residues processed: 602 average time/residue: 0.4294 time to fit residues: 419.6318 Evaluate side-chains 561 residues out of total 3615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 471 time to evaluate : 3.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain B residue 68 CYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 109 MET Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 396 GLN Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain G residue 63 CYS Chi-restraints excluded: chain G residue 88 MET Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 125 HIS Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 238 SER Chi-restraints excluded: chain G residue 334 SER Chi-restraints excluded: chain G residue 336 THR Chi-restraints excluded: chain I residue 6 MET Chi-restraints excluded: chain I residue 33 MET Chi-restraints excluded: chain J residue 6 PHE Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 130 LYS Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 211 ILE Chi-restraints excluded: chain J residue 218 SER Chi-restraints excluded: chain J residue 233 ASN Chi-restraints excluded: chain J residue 250 THR Chi-restraints excluded: chain J residue 251 LEU Chi-restraints excluded: chain J residue 291 ASN Chi-restraints excluded: chain J residue 368 ILE Chi-restraints excluded: chain J residue 386 THR Chi-restraints excluded: chain J residue 412 LEU Chi-restraints excluded: chain K residue 137 ASN Chi-restraints excluded: chain K residue 238 VAL Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 249 SER Chi-restraints excluded: chain K residue 257 MET Chi-restraints excluded: chain K residue 265 VAL Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 24 ASP Chi-restraints excluded: chain N residue 29 SER Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain N residue 108 ASP Chi-restraints excluded: chain N residue 130 LYS Chi-restraints excluded: chain N residue 221 THR Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 129 VAL Chi-restraints excluded: chain O residue 137 VAL Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 295 THR Chi-restraints excluded: chain O residue 346 LEU Chi-restraints excluded: chain O residue 379 ASP Chi-restraints excluded: chain O residue 397 THR Chi-restraints excluded: chain O residue 438 ASN Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain Q residue 189 THR Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 218 SER Chi-restraints excluded: chain Q residue 221 THR Chi-restraints excluded: chain Q residue 233 ASN Chi-restraints excluded: chain Q residue 282 SER Chi-restraints excluded: chain Q residue 286 LYS Chi-restraints excluded: chain Q residue 302 ASP Chi-restraints excluded: chain Q residue 322 THR Chi-restraints excluded: chain Q residue 355 VAL Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 282 SER Chi-restraints excluded: chain R residue 329 VAL Chi-restraints excluded: chain R residue 397 LEU Chi-restraints excluded: chain S residue 201 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 381 optimal weight: 5.9990 chunk 290 optimal weight: 0.7980 chunk 200 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 184 optimal weight: 9.9990 chunk 259 optimal weight: 2.9990 chunk 387 optimal weight: 7.9990 chunk 409 optimal weight: 1.9990 chunk 202 optimal weight: 5.9990 chunk 366 optimal weight: 0.0980 chunk 110 optimal weight: 6.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 HIS ** B 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 GLN F 137 ASN K 271 ASN ** N 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 216 GLN ** Q 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 353 HIS ** R 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 271 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 33926 Z= 0.181 Angle : 0.575 8.674 46188 Z= 0.295 Chirality : 0.043 0.157 5149 Planarity : 0.004 0.078 5938 Dihedral : 5.329 78.626 4633 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.29 % Favored : 94.64 % Rotamer: Outliers : 3.21 % Allowed : 12.45 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.07 % Twisted General : 0.03 % 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: -1.23 (0.13), residues: 4235 helix: 0.99 (0.23), residues: 577 sheet: -0.46 (0.15), residues: 1235 loop : -1.50 (0.12), residues: 2423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 409 HIS 0.007 0.001 HIS K 193 PHE 0.019 0.001 PHE B 398 TYR 0.020 0.001 TYR S 177 ARG 0.005 0.000 ARG J 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 3615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 501 time to evaluate : 3.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 TYR cc_start: 0.7657 (p90) cc_final: 0.7254 (p90) REVERT: B 15 TYR cc_start: 0.7885 (t80) cc_final: 0.7189 (t80) REVERT: B 346 LEU cc_start: 0.5835 (OUTLIER) cc_final: 0.5502 (mp) REVERT: B 377 LYS cc_start: 0.7365 (mttm) cc_final: 0.7121 (mttm) REVERT: C 51 TYR cc_start: 0.8223 (p90) cc_final: 0.7954 (p90) REVERT: C 327 LYS cc_start: 0.8741 (ptmt) cc_final: 0.8413 (pttt) REVERT: C 439 GLN cc_start: 0.7896 (tm-30) cc_final: 0.7631 (tm-30) REVERT: F 199 TYR cc_start: 0.7293 (m-80) cc_final: 0.6399 (m-80) REVERT: F 202 TRP cc_start: 0.8237 (t60) cc_final: 0.7805 (t60) REVERT: G 115 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8097 (mt) REVERT: G 125 HIS cc_start: 0.8062 (OUTLIER) cc_final: 0.7740 (p90) REVERT: I 48 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7757 (mt-10) REVERT: J 389 PHE cc_start: 0.8422 (t80) cc_final: 0.8203 (t80) REVERT: J 392 SER cc_start: 0.8031 (m) cc_final: 0.7351 (t) REVERT: K 159 ASN cc_start: 0.6108 (t0) cc_final: 0.5891 (t0) REVERT: K 260 GLU cc_start: 0.8664 (tt0) cc_final: 0.8349 (pt0) REVERT: L 6 MET cc_start: 0.5450 (mmp) cc_final: 0.5048 (mmm) REVERT: N 324 LYS cc_start: 0.8703 (mtmt) cc_final: 0.8204 (mtpp) REVERT: N 351 LEU cc_start: 0.8273 (mm) cc_final: 0.7975 (mt) REVERT: O 144 THR cc_start: 0.8932 (m) cc_final: 0.8578 (p) REVERT: P 29 GLU cc_start: 0.8245 (mp0) cc_final: 0.7682 (mp0) REVERT: Q 201 GLU cc_start: 0.7988 (tm-30) cc_final: 0.7734 (tm-30) REVERT: R 369 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7509 (tp) REVERT: S 116 GLN cc_start: 0.7008 (mm-40) cc_final: 0.6548 (mt0) outliers start: 116 outliers final: 80 residues processed: 577 average time/residue: 0.4377 time to fit residues: 412.7963 Evaluate side-chains 557 residues out of total 3615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 473 time to evaluate : 3.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain B residue 68 CYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 109 MET Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 396 GLN Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 125 HIS Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain G residue 238 SER Chi-restraints excluded: chain G residue 334 SER Chi-restraints excluded: chain G residue 336 THR Chi-restraints excluded: chain G residue 413 LEU Chi-restraints excluded: chain G residue 421 ILE Chi-restraints excluded: chain I residue 6 MET Chi-restraints excluded: chain J residue 130 LYS Chi-restraints excluded: chain J residue 168 HIS Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain J residue 218 SER Chi-restraints excluded: chain J residue 250 THR Chi-restraints excluded: chain J residue 251 LEU Chi-restraints excluded: chain K residue 137 ASN Chi-restraints excluded: chain K residue 161 VAL Chi-restraints excluded: chain K residue 172 LYS Chi-restraints excluded: chain K residue 238 VAL Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 249 SER Chi-restraints excluded: chain K residue 265 VAL Chi-restraints excluded: chain L residue 24 ASP Chi-restraints excluded: chain N residue 29 SER Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain N residue 130 LYS Chi-restraints excluded: chain N residue 221 THR Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 129 VAL Chi-restraints excluded: chain O residue 137 VAL Chi-restraints excluded: chain O residue 168 THR Chi-restraints excluded: chain O residue 213 LEU Chi-restraints excluded: chain O residue 379 ASP Chi-restraints excluded: chain O residue 397 THR Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain Q residue 117 ASP Chi-restraints excluded: chain Q residue 189 THR Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 207 ILE Chi-restraints excluded: chain Q residue 221 THR Chi-restraints excluded: chain Q residue 233 ASN Chi-restraints excluded: chain Q residue 250 THR Chi-restraints excluded: chain Q residue 282 SER Chi-restraints excluded: chain Q residue 286 LYS Chi-restraints excluded: chain Q residue 302 ASP Chi-restraints excluded: chain Q residue 322 THR Chi-restraints excluded: chain Q residue 386 THR Chi-restraints excluded: chain R residue 8 GLU Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 250 THR Chi-restraints excluded: chain R residue 291 ASN Chi-restraints excluded: chain R residue 329 VAL Chi-restraints excluded: chain R residue 369 LEU Chi-restraints excluded: chain S residue 257 MET Chi-restraints excluded: chain S residue 261 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 341 optimal weight: 20.0000 chunk 232 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 305 optimal weight: 3.9990 chunk 169 optimal weight: 8.9990 chunk 349 optimal weight: 3.9990 chunk 283 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 209 optimal weight: 10.0000 chunk 367 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 HIS ** B 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 GLN C 179 GLN C 394 HIS K 271 ASN ** K 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 141 HIS ** N 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 216 GLN ** Q 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 353 HIS R 96 HIS ** R 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.4435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 33926 Z= 0.374 Angle : 0.640 12.220 46188 Z= 0.331 Chirality : 0.046 0.227 5149 Planarity : 0.005 0.084 5938 Dihedral : 5.444 80.584 4630 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.21 % Favored : 93.72 % Rotamer: Outliers : 3.76 % Allowed : 13.14 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % 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: -1.15 (0.13), residues: 4235 helix: 1.04 (0.23), residues: 590 sheet: -0.43 (0.15), residues: 1248 loop : -1.44 (0.12), residues: 2397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 409 HIS 0.008 0.001 HIS K 193 PHE 0.021 0.002 PHE B 398 TYR 0.027 0.002 TYR O 308 ARG 0.012 0.001 ARG C 366 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 3615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 471 time to evaluate : 3.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 TYR cc_start: 0.7422 (p90) cc_final: 0.7183 (p90) REVERT: B 183 GLU cc_start: 0.6831 (OUTLIER) cc_final: 0.6486 (tt0) REVERT: B 346 LEU cc_start: 0.5916 (OUTLIER) cc_final: 0.5546 (mp) REVERT: B 377 LYS cc_start: 0.7535 (mttm) cc_final: 0.7304 (mttm) REVERT: C 51 TYR cc_start: 0.8417 (p90) cc_final: 0.8121 (p90) REVERT: C 327 LYS cc_start: 0.8776 (ptmt) cc_final: 0.8463 (pttt) REVERT: C 439 GLN cc_start: 0.7955 (tm-30) cc_final: 0.7680 (tm-30) REVERT: F 202 TRP cc_start: 0.8303 (t60) cc_final: 0.7825 (t60) REVERT: G 115 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8228 (mt) REVERT: I 48 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7607 (mt-10) REVERT: J 392 SER cc_start: 0.7877 (m) cc_final: 0.7152 (t) REVERT: N 94 ASP cc_start: 0.7364 (t0) cc_final: 0.7158 (t0) REVERT: O 144 THR cc_start: 0.8964 (m) cc_final: 0.8668 (p) REVERT: P 9 LEU cc_start: 0.6260 (mp) cc_final: 0.5012 (tt) REVERT: P 29 GLU cc_start: 0.8315 (mp0) cc_final: 0.7884 (mp0) REVERT: Q 201 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7753 (tm-30) REVERT: R 88 ARG cc_start: 0.6302 (mmt180) cc_final: 0.6087 (mmt180) REVERT: S 116 GLN cc_start: 0.6968 (mm-40) cc_final: 0.6475 (mt0) REVERT: T 33 MET cc_start: 0.7809 (ptm) cc_final: 0.7423 (ptm) REVERT: T 40 ASN cc_start: 0.8236 (t0) cc_final: 0.7784 (t0) outliers start: 136 outliers final: 105 residues processed: 552 average time/residue: 0.4292 time to fit residues: 385.9641 Evaluate side-chains 557 residues out of total 3615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 449 time to evaluate : 3.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain B residue 68 CYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 109 MET Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain F residue 149 ARG Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain G residue 63 CYS Chi-restraints excluded: chain G residue 88 MET Chi-restraints excluded: chain G residue 109 MET Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 125 HIS Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 238 SER Chi-restraints excluded: chain G residue 334 SER Chi-restraints excluded: chain G residue 336 THR Chi-restraints excluded: chain G residue 413 LEU Chi-restraints excluded: chain I residue 6 MET Chi-restraints excluded: chain J residue 112 MET Chi-restraints excluded: chain J residue 130 LYS Chi-restraints excluded: chain J residue 168 HIS Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain J residue 211 ILE Chi-restraints excluded: chain J residue 218 SER Chi-restraints excluded: chain J residue 250 THR Chi-restraints excluded: chain J residue 291 ASN Chi-restraints excluded: chain K residue 137 ASN Chi-restraints excluded: chain K residue 161 VAL Chi-restraints excluded: chain K residue 187 ASP Chi-restraints excluded: chain K residue 238 VAL Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 249 SER Chi-restraints excluded: chain K residue 265 VAL Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 29 SER Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain N residue 130 LYS Chi-restraints excluded: chain N residue 174 VAL Chi-restraints excluded: chain N residue 221 THR Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain N residue 382 VAL Chi-restraints excluded: chain O residue 7 MET Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 129 VAL Chi-restraints excluded: chain O residue 137 VAL Chi-restraints excluded: chain O residue 168 THR Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 213 LEU Chi-restraints excluded: chain O residue 346 LEU Chi-restraints excluded: chain O residue 379 ASP Chi-restraints excluded: chain O residue 397 THR Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain Q residue 117 ASP Chi-restraints excluded: chain Q residue 189 THR Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 207 ILE Chi-restraints excluded: chain Q residue 221 THR Chi-restraints excluded: chain Q residue 233 ASN Chi-restraints excluded: chain Q residue 250 THR Chi-restraints excluded: chain Q residue 256 HIS Chi-restraints excluded: chain Q residue 282 SER Chi-restraints excluded: chain Q residue 286 LYS Chi-restraints excluded: chain Q residue 322 THR Chi-restraints excluded: chain Q residue 386 THR Chi-restraints excluded: chain R residue 8 GLU Chi-restraints excluded: chain R residue 16 MET Chi-restraints excluded: chain R residue 66 MET Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 250 THR Chi-restraints excluded: chain R residue 291 ASN Chi-restraints excluded: chain R residue 329 VAL Chi-restraints excluded: chain R residue 369 LEU Chi-restraints excluded: chain R residue 397 LEU Chi-restraints excluded: chain S residue 201 SER Chi-restraints excluded: chain S residue 211 ASN Chi-restraints excluded: chain S residue 256 VAL Chi-restraints excluded: chain S residue 257 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 137 optimal weight: 0.7980 chunk 369 optimal weight: 0.8980 chunk 81 optimal weight: 7.9990 chunk 240 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 410 optimal weight: 10.0000 chunk 340 optimal weight: 5.9990 chunk 189 optimal weight: 7.9990 chunk 34 optimal weight: 0.0870 chunk 135 optimal weight: 3.9990 chunk 215 optimal weight: 10.0000 overall best weight: 1.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 HIS ** B 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 182 GLN K 271 ASN ** N 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 125 HIS ** Q 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 33926 Z= 0.220 Angle : 0.592 12.874 46188 Z= 0.303 Chirality : 0.044 0.174 5149 Planarity : 0.004 0.076 5938 Dihedral : 5.256 81.096 4630 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.29 % Favored : 94.64 % Rotamer: Outliers : 3.37 % Allowed : 14.05 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % 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: -1.04 (0.13), residues: 4235 helix: 1.19 (0.23), residues: 589 sheet: -0.38 (0.14), residues: 1288 loop : -1.38 (0.12), residues: 2358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 409 HIS 0.010 0.001 HIS S 203 PHE 0.019 0.001 PHE L 14 TYR 0.028 0.001 TYR S 191 ARG 0.007 0.000 ARG G 73 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 3615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 471 time to evaluate : 3.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 TRP cc_start: 0.7911 (t60) cc_final: 0.7518 (t60) REVERT: B 183 GLU cc_start: 0.6819 (OUTLIER) cc_final: 0.6473 (tt0) REVERT: B 346 LEU cc_start: 0.5845 (OUTLIER) cc_final: 0.5493 (mp) REVERT: B 377 LYS cc_start: 0.7604 (mttm) cc_final: 0.7343 (mttm) REVERT: C 51 TYR cc_start: 0.8257 (p90) cc_final: 0.7977 (p90) REVERT: C 327 LYS cc_start: 0.8774 (ptmt) cc_final: 0.8499 (pttt) REVERT: C 439 GLN cc_start: 0.7950 (tm-30) cc_final: 0.7668 (tm-30) REVERT: F 157 ILE cc_start: 0.8281 (mm) cc_final: 0.7957 (mm) REVERT: G 115 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8235 (mt) REVERT: I 33 MET cc_start: 0.8663 (OUTLIER) cc_final: 0.8340 (ptm) REVERT: I 48 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7584 (mt-10) REVERT: J 392 SER cc_start: 0.7854 (m) cc_final: 0.7154 (t) REVERT: L 6 MET cc_start: 0.5241 (mmp) cc_final: 0.3863 (mmt) REVERT: O 126 THR cc_start: 0.8664 (m) cc_final: 0.8366 (p) REVERT: O 144 THR cc_start: 0.8951 (m) cc_final: 0.8611 (p) REVERT: P 29 GLU cc_start: 0.8202 (mp0) cc_final: 0.7981 (mp0) REVERT: P 43 TYR cc_start: 0.7593 (t80) cc_final: 0.7386 (t80) REVERT: Q 201 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7705 (tm-30) REVERT: R 94 ASP cc_start: 0.6896 (m-30) cc_final: 0.6663 (m-30) REVERT: S 116 GLN cc_start: 0.7029 (mm-40) cc_final: 0.6564 (mt0) REVERT: T 33 MET cc_start: 0.7725 (ptm) cc_final: 0.7405 (ptm) REVERT: T 40 ASN cc_start: 0.8227 (t0) cc_final: 0.7873 (t0) outliers start: 122 outliers final: 95 residues processed: 547 average time/residue: 0.4537 time to fit residues: 403.1989 Evaluate side-chains 547 residues out of total 3615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 448 time to evaluate : 3.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain B residue 68 CYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 109 MET Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 63 CYS Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 88 MET Chi-restraints excluded: chain G residue 109 MET Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain G residue 238 SER Chi-restraints excluded: chain G residue 334 SER Chi-restraints excluded: chain G residue 336 THR Chi-restraints excluded: chain G residue 413 LEU Chi-restraints excluded: chain I residue 6 MET Chi-restraints excluded: chain I residue 33 MET Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 130 LYS Chi-restraints excluded: chain J residue 168 HIS Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain J residue 218 SER Chi-restraints excluded: chain J residue 250 THR Chi-restraints excluded: chain J residue 386 THR Chi-restraints excluded: chain K residue 137 ASN Chi-restraints excluded: chain K residue 187 ASP Chi-restraints excluded: chain K residue 238 VAL Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 249 SER Chi-restraints excluded: chain K residue 265 VAL Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 29 SER Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain N residue 108 ASP Chi-restraints excluded: chain N residue 130 LYS Chi-restraints excluded: chain N residue 174 VAL Chi-restraints excluded: chain N residue 221 THR Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain O residue 7 MET Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain O residue 113 ASP Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 129 VAL Chi-restraints excluded: chain O residue 137 VAL Chi-restraints excluded: chain O residue 213 LEU Chi-restraints excluded: chain O residue 346 LEU Chi-restraints excluded: chain O residue 379 ASP Chi-restraints excluded: chain O residue 397 THR Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain Q residue 117 ASP Chi-restraints excluded: chain Q residue 189 THR Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 207 ILE Chi-restraints excluded: chain Q residue 221 THR Chi-restraints excluded: chain Q residue 233 ASN Chi-restraints excluded: chain Q residue 250 THR Chi-restraints excluded: chain Q residue 282 SER Chi-restraints excluded: chain Q residue 286 LYS Chi-restraints excluded: chain Q residue 322 THR Chi-restraints excluded: chain Q residue 386 THR Chi-restraints excluded: chain R residue 8 GLU Chi-restraints excluded: chain R residue 66 MET Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 195 SER Chi-restraints excluded: chain R residue 250 THR Chi-restraints excluded: chain R residue 291 ASN Chi-restraints excluded: chain R residue 329 VAL Chi-restraints excluded: chain R residue 369 LEU Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 211 ASN Chi-restraints excluded: chain S residue 257 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 395 optimal weight: 0.3980 chunk 46 optimal weight: 6.9990 chunk 233 optimal weight: 7.9990 chunk 299 optimal weight: 1.9990 chunk 232 optimal weight: 2.9990 chunk 345 optimal weight: 6.9990 chunk 229 optimal weight: 0.0870 chunk 408 optimal weight: 9.9990 chunk 255 optimal weight: 0.9990 chunk 249 optimal weight: 8.9990 chunk 188 optimal weight: 5.9990 overall best weight: 1.2964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN A 197 GLN B 10 GLN ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 390 HIS K 271 ASN ** K 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 96 HIS Q 353 HIS ** R 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.4825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 33926 Z= 0.177 Angle : 0.574 11.742 46188 Z= 0.293 Chirality : 0.043 0.174 5149 Planarity : 0.004 0.078 5938 Dihedral : 5.110 81.294 4630 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.57 % Favored : 94.36 % Rotamer: Outliers : 3.26 % Allowed : 14.88 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % 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: -0.88 (0.13), residues: 4235 helix: 1.33 (0.23), residues: 589 sheet: -0.27 (0.15), residues: 1274 loop : -1.28 (0.12), residues: 2372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 202 HIS 0.007 0.001 HIS S 203 PHE 0.020 0.001 PHE G 398 TYR 0.028 0.001 TYR S 191 ARG 0.011 0.000 ARG C 366 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 3615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 477 time to evaluate : 3.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 MET cc_start: 0.6300 (mpp) cc_final: 0.5912 (mmp) REVERT: A 202 TRP cc_start: 0.8108 (t60) cc_final: 0.7740 (t60) REVERT: B 183 GLU cc_start: 0.6793 (OUTLIER) cc_final: 0.6497 (tt0) REVERT: B 233 TYR cc_start: 0.8518 (p90) cc_final: 0.8249 (p90) REVERT: B 346 LEU cc_start: 0.5867 (OUTLIER) cc_final: 0.5647 (mp) REVERT: C 51 TYR cc_start: 0.8253 (p90) cc_final: 0.7969 (p90) REVERT: C 327 LYS cc_start: 0.8787 (ptmt) cc_final: 0.8515 (pttt) REVERT: C 439 GLN cc_start: 0.7923 (tm-30) cc_final: 0.7683 (tm-30) REVERT: F 118 MET cc_start: 0.7799 (tmm) cc_final: 0.7149 (tmm) REVERT: F 151 MET cc_start: 0.7063 (mmt) cc_final: 0.6862 (mmt) REVERT: F 202 TRP cc_start: 0.8213 (t60) cc_final: 0.7527 (t60) REVERT: G 115 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8261 (mt) REVERT: I 26 LYS cc_start: 0.7573 (mmtm) cc_final: 0.7371 (mmtm) REVERT: I 33 MET cc_start: 0.8705 (OUTLIER) cc_final: 0.8179 (ptm) REVERT: I 48 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7551 (mt-10) REVERT: J 392 SER cc_start: 0.8112 (m) cc_final: 0.7448 (t) REVERT: N 10 LYS cc_start: 0.7415 (ttmt) cc_final: 0.7212 (tptt) REVERT: O 126 THR cc_start: 0.8645 (m) cc_final: 0.8343 (p) REVERT: O 144 THR cc_start: 0.8955 (m) cc_final: 0.8663 (p) REVERT: P 8 LEU cc_start: 0.8130 (mt) cc_final: 0.7766 (tt) REVERT: P 29 GLU cc_start: 0.8501 (mp0) cc_final: 0.8047 (mp0) REVERT: P 31 LEU cc_start: 0.8551 (mt) cc_final: 0.8217 (mt) REVERT: Q 201 GLU cc_start: 0.8026 (tm-30) cc_final: 0.7646 (tm-30) REVERT: R 369 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7700 (tp) REVERT: S 116 GLN cc_start: 0.7011 (mm-40) cc_final: 0.6090 (pp30) REVERT: S 121 LYS cc_start: 0.8369 (ptmm) cc_final: 0.8022 (pttt) REVERT: T 33 MET cc_start: 0.7704 (ptm) cc_final: 0.7434 (ptm) REVERT: T 40 ASN cc_start: 0.8294 (t0) cc_final: 0.8033 (t0) outliers start: 118 outliers final: 92 residues processed: 553 average time/residue: 0.4409 time to fit residues: 394.5963 Evaluate side-chains 553 residues out of total 3615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 456 time to evaluate : 3.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain B residue 68 CYS Chi-restraints excluded: chain B residue 109 MET Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 63 CYS Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain G residue 238 SER Chi-restraints excluded: chain G residue 334 SER Chi-restraints excluded: chain G residue 336 THR Chi-restraints excluded: chain G residue 413 LEU Chi-restraints excluded: chain I residue 33 MET Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 130 LYS Chi-restraints excluded: chain J residue 168 HIS Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain J residue 250 THR Chi-restraints excluded: chain J residue 386 THR Chi-restraints excluded: chain K residue 137 ASN Chi-restraints excluded: chain K residue 161 VAL Chi-restraints excluded: chain K residue 187 ASP Chi-restraints excluded: chain K residue 226 SER Chi-restraints excluded: chain K residue 238 VAL Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 249 SER Chi-restraints excluded: chain K residue 265 VAL Chi-restraints excluded: chain K residue 272 CYS Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 29 SER Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain N residue 221 THR Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain O residue 112 ASP Chi-restraints excluded: chain O residue 113 ASP Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 129 VAL Chi-restraints excluded: chain O residue 137 VAL Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 213 LEU Chi-restraints excluded: chain O residue 346 LEU Chi-restraints excluded: chain O residue 379 ASP Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain Q residue 117 ASP Chi-restraints excluded: chain Q residue 189 THR Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 207 ILE Chi-restraints excluded: chain Q residue 221 THR Chi-restraints excluded: chain Q residue 233 ASN Chi-restraints excluded: chain Q residue 250 THR Chi-restraints excluded: chain Q residue 256 HIS Chi-restraints excluded: chain Q residue 282 SER Chi-restraints excluded: chain Q residue 286 LYS Chi-restraints excluded: chain Q residue 386 THR Chi-restraints excluded: chain R residue 8 GLU Chi-restraints excluded: chain R residue 16 MET Chi-restraints excluded: chain R residue 66 MET Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 250 THR Chi-restraints excluded: chain R residue 291 ASN Chi-restraints excluded: chain R residue 329 VAL Chi-restraints excluded: chain R residue 369 LEU Chi-restraints excluded: chain R residue 397 LEU Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 192 THR Chi-restraints excluded: chain S residue 201 SER Chi-restraints excluded: chain S residue 257 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 252 optimal weight: 0.7980 chunk 163 optimal weight: 10.0000 chunk 244 optimal weight: 0.3980 chunk 123 optimal weight: 5.9990 chunk 80 optimal weight: 0.0010 chunk 79 optimal weight: 0.0370 chunk 259 optimal weight: 1.9990 chunk 278 optimal weight: 20.0000 chunk 202 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 321 optimal weight: 4.9990 overall best weight: 0.6466 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 10 GLN B 235 GLN B 362 HIS B 394 HIS K 271 ASN ** K 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.4955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 33926 Z= 0.144 Angle : 0.565 12.656 46188 Z= 0.288 Chirality : 0.043 0.180 5149 Planarity : 0.004 0.074 5938 Dihedral : 4.980 81.039 4630 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.05 % Favored : 94.88 % Rotamer: Outliers : 2.66 % Allowed : 16.10 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % 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: -0.76 (0.13), residues: 4235 helix: 1.35 (0.23), residues: 591 sheet: -0.17 (0.15), residues: 1286 loop : -1.20 (0.13), residues: 2358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP K 202 HIS 0.007 0.001 HIS F 152 PHE 0.028 0.001 PHE G 398 TYR 0.024 0.001 TYR S 191 ARG 0.011 0.000 ARG C 289 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 3615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 481 time to evaluate : 4.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 MET cc_start: 0.6034 (mpp) cc_final: 0.5765 (mmm) REVERT: A 202 TRP cc_start: 0.8076 (t60) cc_final: 0.7717 (t60) REVERT: B 88 MET cc_start: 0.8364 (tpp) cc_final: 0.8089 (mmm) REVERT: B 183 GLU cc_start: 0.6867 (OUTLIER) cc_final: 0.6564 (tt0) REVERT: C 51 TYR cc_start: 0.8248 (p90) cc_final: 0.7960 (p90) REVERT: C 327 LYS cc_start: 0.8796 (ptmt) cc_final: 0.8511 (pttt) REVERT: C 439 GLN cc_start: 0.7908 (tm-30) cc_final: 0.7675 (tm-30) REVERT: F 118 MET cc_start: 0.7793 (tmm) cc_final: 0.7133 (tmm) REVERT: F 202 TRP cc_start: 0.8100 (t60) cc_final: 0.7563 (t60) REVERT: G 115 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8253 (mt) REVERT: I 48 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7528 (mt-10) REVERT: J 392 SER cc_start: 0.8106 (m) cc_final: 0.7457 (t) REVERT: N 324 LYS cc_start: 0.8829 (mtmt) cc_final: 0.8338 (mtpp) REVERT: O 126 THR cc_start: 0.8634 (m) cc_final: 0.8348 (p) REVERT: O 144 THR cc_start: 0.8904 (m) cc_final: 0.8664 (p) REVERT: O 436 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8613 (mt) REVERT: P 26 LYS cc_start: 0.7889 (OUTLIER) cc_final: 0.7111 (ptpp) REVERT: P 29 GLU cc_start: 0.8567 (mp0) cc_final: 0.7638 (mp0) REVERT: Q 70 MET cc_start: 0.8812 (tpp) cc_final: 0.8485 (tpp) REVERT: Q 201 GLU cc_start: 0.7885 (tm-30) cc_final: 0.7602 (tm-30) REVERT: R 44 TYR cc_start: 0.8225 (m-80) cc_final: 0.8003 (m-80) REVERT: R 369 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7419 (tp) REVERT: S 116 GLN cc_start: 0.7127 (mm-40) cc_final: 0.6292 (pp30) REVERT: S 118 MET cc_start: 0.8497 (tpp) cc_final: 0.8169 (mtt) REVERT: S 121 LYS cc_start: 0.8320 (ptmm) cc_final: 0.7985 (pttt) REVERT: T 40 ASN cc_start: 0.8264 (t0) cc_final: 0.7999 (t0) outliers start: 96 outliers final: 77 residues processed: 542 average time/residue: 0.4250 time to fit residues: 376.6494 Evaluate side-chains 534 residues out of total 3615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 452 time to evaluate : 3.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain G residue 63 CYS Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 238 SER Chi-restraints excluded: chain G residue 334 SER Chi-restraints excluded: chain G residue 336 THR Chi-restraints excluded: chain G residue 413 LEU Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 112 MET Chi-restraints excluded: chain J residue 168 HIS Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain J residue 250 THR Chi-restraints excluded: chain J residue 369 LEU Chi-restraints excluded: chain J residue 386 THR Chi-restraints excluded: chain K residue 161 VAL Chi-restraints excluded: chain K residue 238 VAL Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 249 SER Chi-restraints excluded: chain K residue 265 VAL Chi-restraints excluded: chain K residue 272 CYS Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 108 ASP Chi-restraints excluded: chain N residue 130 LYS Chi-restraints excluded: chain N residue 167 MET Chi-restraints excluded: chain N residue 221 THR Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 129 VAL Chi-restraints excluded: chain O residue 137 VAL Chi-restraints excluded: chain O residue 168 THR Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 346 LEU Chi-restraints excluded: chain O residue 379 ASP Chi-restraints excluded: chain O residue 436 LEU Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 26 LYS Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain Q residue 117 ASP Chi-restraints excluded: chain Q residue 189 THR Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 207 ILE Chi-restraints excluded: chain Q residue 221 THR Chi-restraints excluded: chain Q residue 233 ASN Chi-restraints excluded: chain Q residue 250 THR Chi-restraints excluded: chain Q residue 256 HIS Chi-restraints excluded: chain Q residue 286 LYS Chi-restraints excluded: chain R residue 8 GLU Chi-restraints excluded: chain R residue 66 MET Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 250 THR Chi-restraints excluded: chain R residue 291 ASN Chi-restraints excluded: chain R residue 329 VAL Chi-restraints excluded: chain R residue 369 LEU Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 192 THR Chi-restraints excluded: chain S residue 201 SER Chi-restraints excluded: chain S residue 257 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 371 optimal weight: 8.9990 chunk 391 optimal weight: 6.9990 chunk 357 optimal weight: 2.9990 chunk 380 optimal weight: 0.0870 chunk 229 optimal weight: 0.0040 chunk 165 optimal weight: 4.9990 chunk 299 optimal weight: 0.8980 chunk 116 optimal weight: 9.9990 chunk 344 optimal weight: 0.8980 chunk 360 optimal weight: 1.9990 chunk 379 optimal weight: 8.9990 overall best weight: 0.7772 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 10 GLN B 362 HIS J 132 ASN ** K 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 353 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.5096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 33926 Z= 0.150 Angle : 0.586 16.053 46188 Z= 0.292 Chirality : 0.044 0.426 5149 Planarity : 0.004 0.075 5938 Dihedral : 4.902 80.813 4630 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.24 % Favored : 94.69 % Rotamer: Outliers : 2.57 % Allowed : 16.74 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % 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: -0.66 (0.13), residues: 4235 helix: 1.39 (0.23), residues: 599 sheet: -0.11 (0.15), residues: 1289 loop : -1.12 (0.13), residues: 2347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 202 HIS 0.010 0.001 HIS F 152 PHE 0.027 0.001 PHE G 398 TYR 0.024 0.001 TYR A 177 ARG 0.008 0.000 ARG G 73 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 3615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 476 time to evaluate : 3.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.7474 (tmm) cc_final: 0.6897 (ppp) REVERT: A 131 MET cc_start: 0.6034 (mpp) cc_final: 0.5628 (mmm) REVERT: A 202 TRP cc_start: 0.7986 (t60) cc_final: 0.7637 (t60) REVERT: B 183 GLU cc_start: 0.6816 (OUTLIER) cc_final: 0.6575 (tt0) REVERT: B 366 ARG cc_start: 0.8126 (ttp80) cc_final: 0.7396 (ttp80) REVERT: C 51 TYR cc_start: 0.8224 (p90) cc_final: 0.7923 (p90) REVERT: C 241 GLU cc_start: 0.7765 (tp30) cc_final: 0.7392 (tp30) REVERT: C 327 LYS cc_start: 0.8804 (ptmt) cc_final: 0.8519 (pttt) REVERT: C 439 GLN cc_start: 0.7896 (tm-30) cc_final: 0.7679 (tm-30) REVERT: F 118 MET cc_start: 0.7788 (tmm) cc_final: 0.7138 (tmm) REVERT: F 131 MET cc_start: 0.6799 (pmm) cc_final: 0.6459 (pmm) REVERT: F 202 TRP cc_start: 0.8121 (t60) cc_final: 0.7638 (t60) REVERT: I 48 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7550 (mt-10) REVERT: J 389 PHE cc_start: 0.8438 (t80) cc_final: 0.8214 (t80) REVERT: J 392 SER cc_start: 0.8120 (m) cc_final: 0.7477 (t) REVERT: K 193 HIS cc_start: 0.7583 (p-80) cc_final: 0.7184 (p-80) REVERT: N 324 LYS cc_start: 0.8824 (mtmt) cc_final: 0.8332 (mtpp) REVERT: O 126 THR cc_start: 0.8616 (m) cc_final: 0.8315 (p) REVERT: O 436 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8593 (mt) REVERT: P 26 LYS cc_start: 0.7783 (ptpt) cc_final: 0.7308 (ptpt) REVERT: P 29 GLU cc_start: 0.8507 (mp0) cc_final: 0.7793 (mp0) REVERT: Q 70 MET cc_start: 0.8799 (tpp) cc_final: 0.8584 (tpp) REVERT: Q 201 GLU cc_start: 0.7781 (tm-30) cc_final: 0.7579 (tm-30) REVERT: R 44 TYR cc_start: 0.8227 (m-80) cc_final: 0.8009 (m-80) REVERT: R 369 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7389 (tp) REVERT: S 116 GLN cc_start: 0.7009 (mm-40) cc_final: 0.6004 (pp30) REVERT: S 121 LYS cc_start: 0.8352 (ptmm) cc_final: 0.7973 (pttt) REVERT: T 40 ASN cc_start: 0.8208 (t0) cc_final: 0.7963 (t0) outliers start: 93 outliers final: 79 residues processed: 537 average time/residue: 0.4513 time to fit residues: 397.1313 Evaluate side-chains 535 residues out of total 3615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 453 time to evaluate : 3.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain G residue 63 CYS Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 238 SER Chi-restraints excluded: chain G residue 334 SER Chi-restraints excluded: chain G residue 336 THR Chi-restraints excluded: chain G residue 413 LEU Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 112 MET Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain J residue 250 THR Chi-restraints excluded: chain J residue 291 ASN Chi-restraints excluded: chain J residue 369 LEU Chi-restraints excluded: chain J residue 386 THR Chi-restraints excluded: chain K residue 238 VAL Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 249 SER Chi-restraints excluded: chain K residue 265 VAL Chi-restraints excluded: chain K residue 272 CYS Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 108 ASP Chi-restraints excluded: chain N residue 130 LYS Chi-restraints excluded: chain N residue 167 MET Chi-restraints excluded: chain N residue 221 THR Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain O residue 112 ASP Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 129 VAL Chi-restraints excluded: chain O residue 137 VAL Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 346 LEU Chi-restraints excluded: chain O residue 379 ASP Chi-restraints excluded: chain O residue 436 LEU Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain Q residue 117 ASP Chi-restraints excluded: chain Q residue 189 THR Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 207 ILE Chi-restraints excluded: chain Q residue 221 THR Chi-restraints excluded: chain Q residue 233 ASN Chi-restraints excluded: chain Q residue 241 ASP Chi-restraints excluded: chain Q residue 250 THR Chi-restraints excluded: chain Q residue 256 HIS Chi-restraints excluded: chain Q residue 286 LYS Chi-restraints excluded: chain Q residue 386 THR Chi-restraints excluded: chain R residue 8 GLU Chi-restraints excluded: chain R residue 66 MET Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 195 SER Chi-restraints excluded: chain R residue 250 THR Chi-restraints excluded: chain R residue 291 ASN Chi-restraints excluded: chain R residue 329 VAL Chi-restraints excluded: chain R residue 369 LEU Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 192 THR Chi-restraints excluded: chain S residue 201 SER Chi-restraints excluded: chain S residue 257 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 250 optimal weight: 8.9990 chunk 402 optimal weight: 5.9990 chunk 245 optimal weight: 1.9990 chunk 191 optimal weight: 10.0000 chunk 279 optimal weight: 7.9990 chunk 422 optimal weight: 0.5980 chunk 388 optimal weight: 0.7980 chunk 336 optimal weight: 9.9990 chunk 34 optimal weight: 0.7980 chunk 259 optimal weight: 1.9990 chunk 206 optimal weight: 8.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 10 GLN G 20 ASN ** N 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 37 ASN ** S 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.5207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 33926 Z= 0.175 Angle : 0.593 13.547 46188 Z= 0.296 Chirality : 0.044 0.405 5149 Planarity : 0.004 0.074 5938 Dihedral : 4.916 80.862 4630 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.17 % Favored : 94.78 % Rotamer: Outliers : 2.49 % Allowed : 16.85 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.13), residues: 4235 helix: 1.45 (0.23), residues: 594 sheet: -0.07 (0.15), residues: 1279 loop : -1.09 (0.13), residues: 2362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP K 202 HIS 0.009 0.001 HIS F 152 PHE 0.033 0.001 PHE J 217 TYR 0.025 0.001 TYR A 177 ARG 0.005 0.000 ARG B 366 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 3615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 462 time to evaluate : 4.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 MET cc_start: 0.5930 (mpp) cc_final: 0.5607 (mmm) REVERT: A 202 TRP cc_start: 0.7955 (t60) cc_final: 0.7668 (t60) REVERT: A 257 MET cc_start: 0.7275 (mpp) cc_final: 0.6744 (ptt) REVERT: B 183 GLU cc_start: 0.6821 (OUTLIER) cc_final: 0.6581 (tt0) REVERT: B 409 TRP cc_start: 0.8129 (m100) cc_final: 0.7857 (m100) REVERT: C 51 TYR cc_start: 0.8250 (p90) cc_final: 0.7942 (p90) REVERT: C 241 GLU cc_start: 0.7812 (tp30) cc_final: 0.7426 (tp30) REVERT: C 327 LYS cc_start: 0.8788 (ptmt) cc_final: 0.8498 (pttt) REVERT: F 118 MET cc_start: 0.7802 (tmm) cc_final: 0.7144 (tmm) REVERT: F 202 TRP cc_start: 0.8183 (t60) cc_final: 0.7702 (t60) REVERT: G 20 ASN cc_start: 0.8042 (OUTLIER) cc_final: 0.7756 (t0) REVERT: I 48 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7579 (mt-10) REVERT: J 177 SER cc_start: 0.8533 (m) cc_final: 0.8186 (t) REVERT: J 392 SER cc_start: 0.7868 (m) cc_final: 0.7200 (t) REVERT: K 193 HIS cc_start: 0.7485 (p-80) cc_final: 0.7121 (p-80) REVERT: N 324 LYS cc_start: 0.8887 (mtmt) cc_final: 0.8422 (mtpp) REVERT: O 126 THR cc_start: 0.8612 (m) cc_final: 0.8340 (p) REVERT: O 436 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8581 (mt) REVERT: Q 201 GLU cc_start: 0.7806 (tm-30) cc_final: 0.7599 (tm-30) REVERT: R 44 TYR cc_start: 0.8264 (m-80) cc_final: 0.8029 (m-80) REVERT: R 369 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7609 (tp) REVERT: S 116 GLN cc_start: 0.7126 (mm-40) cc_final: 0.6195 (pp30) REVERT: T 40 ASN cc_start: 0.8213 (t0) cc_final: 0.7966 (t0) outliers start: 90 outliers final: 76 residues processed: 523 average time/residue: 0.4549 time to fit residues: 386.4860 Evaluate side-chains 531 residues out of total 3615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 451 time to evaluate : 4.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain G residue 20 ASN Chi-restraints excluded: chain G residue 63 CYS Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 238 SER Chi-restraints excluded: chain G residue 334 SER Chi-restraints excluded: chain G residue 336 THR Chi-restraints excluded: chain G residue 413 LEU Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 112 MET Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain J residue 291 ASN Chi-restraints excluded: chain J residue 369 LEU Chi-restraints excluded: chain J residue 397 LEU Chi-restraints excluded: chain K residue 238 VAL Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 265 VAL Chi-restraints excluded: chain K residue 272 CYS Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 108 ASP Chi-restraints excluded: chain N residue 130 LYS Chi-restraints excluded: chain N residue 167 MET Chi-restraints excluded: chain N residue 221 THR Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain O residue 112 ASP Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 129 VAL Chi-restraints excluded: chain O residue 137 VAL Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 346 LEU Chi-restraints excluded: chain O residue 379 ASP Chi-restraints excluded: chain O residue 436 LEU Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain Q residue 117 ASP Chi-restraints excluded: chain Q residue 189 THR Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 207 ILE Chi-restraints excluded: chain Q residue 221 THR Chi-restraints excluded: chain Q residue 233 ASN Chi-restraints excluded: chain Q residue 241 ASP Chi-restraints excluded: chain Q residue 250 THR Chi-restraints excluded: chain Q residue 256 HIS Chi-restraints excluded: chain Q residue 282 SER Chi-restraints excluded: chain Q residue 286 LYS Chi-restraints excluded: chain R residue 66 MET Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 250 THR Chi-restraints excluded: chain R residue 291 ASN Chi-restraints excluded: chain R residue 329 VAL Chi-restraints excluded: chain R residue 369 LEU Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 192 THR Chi-restraints excluded: chain S residue 201 SER Chi-restraints excluded: chain S residue 257 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 267 optimal weight: 1.9990 chunk 358 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 310 optimal weight: 0.0670 chunk 49 optimal weight: 0.5980 chunk 93 optimal weight: 10.0000 chunk 336 optimal weight: 9.9990 chunk 140 optimal weight: 10.0000 chunk 345 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 overall best weight: 1.5324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 10 GLN G 20 ASN ** N 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 353 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.133618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.098623 restraints weight = 58269.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.097035 restraints weight = 30136.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.098048 restraints weight = 31033.973| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.5303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33926 Z= 0.193 Angle : 0.596 13.012 46188 Z= 0.299 Chirality : 0.044 0.452 5149 Planarity : 0.004 0.085 5938 Dihedral : 4.947 81.034 4630 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.34 % Favored : 94.59 % Rotamer: Outliers : 2.52 % Allowed : 16.85 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % 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: -0.56 (0.13), residues: 4235 helix: 1.45 (0.23), residues: 594 sheet: -0.02 (0.15), residues: 1271 loop : -1.05 (0.13), residues: 2370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 202 HIS 0.009 0.001 HIS F 152 PHE 0.025 0.001 PHE B 365 TYR 0.026 0.001 TYR A 177 ARG 0.011 0.000 ARG N 227 =============================================================================== Job complete usr+sys time: 7830.73 seconds wall clock time: 141 minutes 40.25 seconds (8500.25 seconds total)