Starting phenix.real_space_refine on Sun Mar 24 18:37:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fml_4277/03_2024/6fml_4277_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fml_4277/03_2024/6fml_4277.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fml_4277/03_2024/6fml_4277.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fml_4277/03_2024/6fml_4277.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fml_4277/03_2024/6fml_4277_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fml_4277/03_2024/6fml_4277_updated.pdb" } resolution = 4.34 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 303 5.49 5 S 160 5.16 5 C 26392 2.51 5 N 7810 2.21 5 O 8795 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 334": "NH1" <-> "NH2" Residue "D ARG 71": "NH1" <-> "NH2" Residue "D ARG 329": "NH1" <-> "NH2" Residue "D ARG 373": "NH1" <-> "NH2" Residue "D ARG 416": "NH1" <-> "NH2" Residue "E ARG 329": "NH1" <-> "NH2" Residue "E ARG 373": "NH1" <-> "NH2" Residue "E ARG 416": "NH1" <-> "NH2" Residue "F PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 329": "NH1" <-> "NH2" Residue "F ARG 373": "NH1" <-> "NH2" Residue "F ARG 416": "NH1" <-> "NH2" Residue "G ARG 1685": "NH1" <-> "NH2" Residue "G ARG 1687": "NH1" <-> "NH2" Residue "G ARG 1698": "NH1" <-> "NH2" Residue "I TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 69": "NH1" <-> "NH2" Residue "J ARG 221": "NH1" <-> "NH2" Residue "J ARG 279": "NH1" <-> "NH2" Residue "J ARG 293": "NH1" <-> "NH2" Residue "J ARG 295": "NH1" <-> "NH2" Residue "J ARG 703": "NH1" <-> "NH2" Residue "J ARG 717": "NH1" <-> "NH2" Residue "J ARG 719": "NH1" <-> "NH2" Residue "J ARG 720": "NH1" <-> "NH2" Residue "J ARG 730": "NH1" <-> "NH2" Residue "J ARG 748": "NH1" <-> "NH2" Residue "Q ARG 49": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 43460 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 3432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3432 Classifications: {'peptide': 449} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 429} Chain: "B" Number of atoms: 3352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3352 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 419} Chain breaks: 1 Chain: "C" Number of atoms: 3511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3511 Classifications: {'peptide': 459} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 439} Chain: "D" Number of atoms: 3383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3383 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 14, 'TRANS': 424} Chain: "E" Number of atoms: 3396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3396 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 14, 'TRANS': 426} Chain breaks: 1 Chain: "F" Number of atoms: 3376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3376 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 14, 'TRANS': 422} Chain breaks: 1 Chain: "G" Number of atoms: 5964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 731, 5964 Classifications: {'peptide': 731} Link IDs: {'PTRANS': 33, 'TRANS': 697} Chain breaks: 1 Chain: "H" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 413 Classifications: {'peptide': 66} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 4, 'TRANS': 61} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'UNK:plan-1': 30} Unresolved non-hydrogen planarities: 30 Chain: "I" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 875 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 8, 'TRANS': 100} Chain breaks: 1 Chain: "J" Number of atoms: 3843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 3843 Classifications: {'peptide': 503} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 28, 'TRANS': 474} Chain breaks: 6 Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 174 Unresolved non-hydrogen dihedrals: 58 Planarities with less than four sites: {'UNK:plan-1': 58} Unresolved non-hydrogen planarities: 58 Chain: "K" Number of atoms: 2969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2969 Classifications: {'DNA': 144} Link IDs: {'rna3p': 143} Chain: "L" Number of atoms: 2935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2935 Classifications: {'DNA': 144} Link IDs: {'rna3p': 143} Chain: "M" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 766 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "N" Number of atoms: 623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 623 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "O" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 764 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 98} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "P" Number of atoms: 728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 728 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Q" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 787 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 93} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "R" Number of atoms: 635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 635 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "S" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 791 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "T" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 724 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 22.60, per 1000 atoms: 0.52 Number of scatterers: 43460 At special positions: 0 Unit cell: (149.46, 177.02, 219.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 160 16.00 P 303 15.00 O 8795 8.00 N 7810 7.00 C 26392 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 17.63 Conformation dependent library (CDL) restraints added in 6.9 seconds 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8952 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 198 helices and 38 sheets defined 42.8% alpha, 10.0% beta 102 base pairs and 215 stacking pairs defined. Time for finding SS restraints: 20.49 Creating SS restraints... Processing helix chain 'A' and resid 44 through 59 removed outlier: 3.825A pdb=" N ALA A 49 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA A 59 " --> pdb=" O ASP A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 88 Processing helix chain 'A' and resid 109 through 119 Processing helix chain 'A' and resid 175 through 184 removed outlier: 3.719A pdb=" N GLU A 184 " --> pdb=" O ALA A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 241 through 249 Processing helix chain 'A' and resid 258 through 261 No H-bonds generated for 'chain 'A' and resid 258 through 261' Processing helix chain 'A' and resid 274 through 290 removed outlier: 3.845A pdb=" N ASN A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 307 No H-bonds generated for 'chain 'A' and resid 305 through 307' Processing helix chain 'A' and resid 310 through 320 removed outlier: 3.907A pdb=" N TYR A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASN A 317 " --> pdb=" O PHE A 313 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LYS A 318 " --> pdb=" O THR A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 350 No H-bonds generated for 'chain 'A' and resid 348 through 350' Processing helix chain 'A' and resid 355 through 358 Processing helix chain 'A' and resid 371 through 383 Processing helix chain 'A' and resid 389 through 401 Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.603A pdb=" N LEU A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N GLN A 409 " --> pdb=" O ARG A 405 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A 410 " --> pdb=" O TYR A 406 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 410' Processing helix chain 'A' and resid 412 through 420 removed outlier: 3.681A pdb=" N ILE A 416 " --> pdb=" O ALA A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 437 removed outlier: 4.103A pdb=" N GLU A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 451 Processing helix chain 'B' and resid 44 through 59 Processing helix chain 'B' and resid 77 through 88 Processing helix chain 'B' and resid 99 through 102 Processing helix chain 'B' and resid 112 through 120 Processing helix chain 'B' and resid 178 through 181 No H-bonds generated for 'chain 'B' and resid 178 through 181' Processing helix chain 'B' and resid 208 through 210 No H-bonds generated for 'chain 'B' and resid 208 through 210' Processing helix chain 'B' and resid 241 through 249 Processing helix chain 'B' and resid 257 through 260 Processing helix chain 'B' and resid 274 through 289 removed outlier: 3.744A pdb=" N LYS B 282 " --> pdb=" O MET B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 321 removed outlier: 4.733A pdb=" N TYR B 315 " --> pdb=" O GLU B 311 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN B 317 " --> pdb=" O PHE B 313 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS B 318 " --> pdb=" O THR B 314 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N GLU B 321 " --> pdb=" O ASN B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 350 No H-bonds generated for 'chain 'B' and resid 348 through 350' Processing helix chain 'B' and resid 353 through 356 No H-bonds generated for 'chain 'B' and resid 353 through 356' Processing helix chain 'B' and resid 369 through 371 No H-bonds generated for 'chain 'B' and resid 369 through 371' Processing helix chain 'B' and resid 373 through 382 Processing helix chain 'B' and resid 389 through 401 removed outlier: 3.721A pdb=" N ASP B 393 " --> pdb=" O ASP B 389 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ARG B 394 " --> pdb=" O ALA B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 409 removed outlier: 3.690A pdb=" N GLN B 409 " --> pdb=" O ARG B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 419 removed outlier: 3.581A pdb=" N SER B 415 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE B 416 " --> pdb=" O ALA B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 437 removed outlier: 4.027A pdb=" N GLU B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 449 Processing helix chain 'C' and resid 44 through 58 Processing helix chain 'C' and resid 77 through 88 Processing helix chain 'C' and resid 99 through 101 No H-bonds generated for 'chain 'C' and resid 99 through 101' Processing helix chain 'C' and resid 109 through 120 removed outlier: 4.322A pdb=" N LEU C 113 " --> pdb=" O LYS C 109 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N MET C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 184 Processing helix chain 'C' and resid 241 through 249 Processing helix chain 'C' and resid 259 through 262 No H-bonds generated for 'chain 'C' and resid 259 through 262' Processing helix chain 'C' and resid 274 through 290 removed outlier: 3.557A pdb=" N LYS C 286 " --> pdb=" O LYS C 282 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN C 289 " --> pdb=" O GLN C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 320 removed outlier: 3.731A pdb=" N THR C 314 " --> pdb=" O ILE C 310 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N TYR C 315 " --> pdb=" O GLU C 311 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS C 318 " --> pdb=" O THR C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 350 No H-bonds generated for 'chain 'C' and resid 348 through 350' Processing helix chain 'C' and resid 353 through 358 removed outlier: 4.021A pdb=" N GLN C 357 " --> pdb=" O PRO C 353 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ARG C 358 " --> pdb=" O ASP C 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 353 through 358' Processing helix chain 'C' and resid 372 through 383 Processing helix chain 'C' and resid 389 through 401 Processing helix chain 'C' and resid 404 through 407 No H-bonds generated for 'chain 'C' and resid 404 through 407' Processing helix chain 'C' and resid 412 through 421 Processing helix chain 'C' and resid 428 through 434 Processing helix chain 'C' and resid 441 through 450 Processing helix chain 'D' and resid 51 through 65 Processing helix chain 'D' and resid 83 through 94 Processing helix chain 'D' and resid 115 through 126 removed outlier: 3.698A pdb=" N LEU D 119 " --> pdb=" O LYS D 115 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N SER D 126 " --> pdb=" O ALA D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 184 removed outlier: 3.538A pdb=" N LYS D 183 " --> pdb=" O ASP D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 251 Processing helix chain 'D' and resid 269 through 284 removed outlier: 3.595A pdb=" N GLN D 274 " --> pdb=" O GLU D 270 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N THR D 277 " --> pdb=" O ASP D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 302 No H-bonds generated for 'chain 'D' and resid 300 through 302' Processing helix chain 'D' and resid 305 through 314 removed outlier: 4.059A pdb=" N TYR D 310 " --> pdb=" O GLU D 306 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ARG D 313 " --> pdb=" O SER D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 344 No H-bonds generated for 'chain 'D' and resid 342 through 344' Processing helix chain 'D' and resid 363 through 376 removed outlier: 4.104A pdb=" N GLN D 368 " --> pdb=" O ASP D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 414 removed outlier: 3.835A pdb=" N GLU D 395 " --> pdb=" O LYS D 391 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N LEU D 398 " --> pdb=" O GLN D 394 " (cutoff:3.500A) removed outlier: 9.452A pdb=" N ARG D 399 " --> pdb=" O GLU D 395 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N TYR D 400 " --> pdb=" O ALA D 396 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA D 401 " --> pdb=" O GLY D 397 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ASN D 403 " --> pdb=" O ARG D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 431 Processing helix chain 'D' and resid 435 through 444 removed outlier: 4.028A pdb=" N ARG D 440 " --> pdb=" O ALA D 436 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 63 Processing helix chain 'E' and resid 84 through 92 Processing helix chain 'E' and resid 116 through 126 removed outlier: 3.504A pdb=" N ALA E 122 " --> pdb=" O ALA E 118 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N SER E 126 " --> pdb=" O ALA E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 184 removed outlier: 4.397A pdb=" N ALA E 180 " --> pdb=" O LYS E 176 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS E 183 " --> pdb=" O ASP E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 213 removed outlier: 5.361A pdb=" N ARG E 212 " --> pdb=" O ALA E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 251 removed outlier: 3.788A pdb=" N SER E 251 " --> pdb=" O ASP E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 261 Processing helix chain 'E' and resid 269 through 284 removed outlier: 3.719A pdb=" N ALA E 280 " --> pdb=" O ASN E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 302 No H-bonds generated for 'chain 'E' and resid 300 through 302' Processing helix chain 'E' and resid 305 through 314 removed outlier: 3.886A pdb=" N TYR E 310 " --> pdb=" O GLU E 306 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N ARG E 313 " --> pdb=" O SER E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 344 No H-bonds generated for 'chain 'E' and resid 342 through 344' Processing helix chain 'E' and resid 347 through 350 No H-bonds generated for 'chain 'E' and resid 347 through 350' Processing helix chain 'E' and resid 363 through 377 removed outlier: 3.585A pdb=" N GLU E 377 " --> pdb=" O ARG E 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 414 removed outlier: 3.794A pdb=" N GLU E 395 " --> pdb=" O LYS E 391 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N LEU E 398 " --> pdb=" O GLN E 394 " (cutoff:3.500A) removed outlier: 9.886A pdb=" N ARG E 399 " --> pdb=" O GLU E 395 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N TYR E 400 " --> pdb=" O ALA E 396 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA E 401 " --> pdb=" O GLY E 397 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N THR E 406 " --> pdb=" O SER E 402 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU E 410 " --> pdb=" O THR E 406 " (cutoff:3.500A) Processing helix chain 'E' and resid 422 through 431 removed outlier: 4.310A pdb=" N ARG E 427 " --> pdb=" O GLU E 423 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS E 430 " --> pdb=" O GLN E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 443 Processing helix chain 'F' and resid 50 through 65 removed outlier: 3.658A pdb=" N GLN F 65 " --> pdb=" O GLU F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 94 removed outlier: 3.597A pdb=" N ALA F 87 " --> pdb=" O LYS F 83 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU F 94 " --> pdb=" O MET F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 107 No H-bonds generated for 'chain 'F' and resid 105 through 107' Processing helix chain 'F' and resid 115 through 125 removed outlier: 3.954A pdb=" N ALA F 122 " --> pdb=" O ALA F 118 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE F 123 " --> pdb=" O LEU F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 184 Processing helix chain 'F' and resid 208 through 210 No H-bonds generated for 'chain 'F' and resid 208 through 210' Processing helix chain 'F' and resid 243 through 249 Processing helix chain 'F' and resid 255 through 261 removed outlier: 3.716A pdb=" N LEU F 259 " --> pdb=" O PHE F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 284 Processing helix chain 'F' and resid 300 through 302 No H-bonds generated for 'chain 'F' and resid 300 through 302' Processing helix chain 'F' and resid 305 through 314 removed outlier: 4.393A pdb=" N TYR F 310 " --> pdb=" O GLU F 306 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ARG F 313 " --> pdb=" O SER F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 344 No H-bonds generated for 'chain 'F' and resid 342 through 344' Processing helix chain 'F' and resid 347 through 350 No H-bonds generated for 'chain 'F' and resid 347 through 350' Processing helix chain 'F' and resid 363 through 376 removed outlier: 3.872A pdb=" N GLN F 368 " --> pdb=" O ASP F 364 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 396 Processing helix chain 'F' and resid 398 through 414 removed outlier: 3.635A pdb=" N ASN F 403 " --> pdb=" O ARG F 399 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE F 405 " --> pdb=" O ALA F 401 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N THR F 406 " --> pdb=" O SER F 402 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N THR F 407 " --> pdb=" O ASN F 403 " (cutoff:3.500A) Processing helix chain 'F' and resid 422 through 431 Processing helix chain 'F' and resid 435 through 444 removed outlier: 3.854A pdb=" N VAL F 439 " --> pdb=" O PRO F 435 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ARG F 440 " --> pdb=" O ALA F 436 " (cutoff:3.500A) Processing helix chain 'G' and resid 974 through 988 Processing helix chain 'G' and resid 1003 through 1016 Processing helix chain 'G' and resid 1033 through 1043 Processing helix chain 'G' and resid 1056 through 1064 removed outlier: 3.696A pdb=" N LYS G1064 " --> pdb=" O LYS G1060 " (cutoff:3.500A) Processing helix chain 'G' and resid 1086 through 1091 Processing helix chain 'G' and resid 1093 through 1096 No H-bonds generated for 'chain 'G' and resid 1093 through 1096' Processing helix chain 'G' and resid 1118 through 1124 Processing helix chain 'G' and resid 1144 through 1153 removed outlier: 4.085A pdb=" N PHE G1152 " --> pdb=" O ALA G1148 " (cutoff:3.500A) Processing helix chain 'G' and resid 1166 through 1179 removed outlier: 3.660A pdb=" N HIS G1175 " --> pdb=" O ASP G1171 " (cutoff:3.500A) Processing helix chain 'G' and resid 1187 through 1195 Processing helix chain 'G' and resid 1203 through 1207 Processing helix chain 'G' and resid 1224 through 1240 Processing helix chain 'G' and resid 1257 through 1269 Processing helix chain 'G' and resid 1335 through 1344 removed outlier: 3.699A pdb=" N SER G1340 " --> pdb=" O ALA G1336 " (cutoff:3.500A) Processing helix chain 'G' and resid 1352 through 1356 Processing helix chain 'G' and resid 1366 through 1369 removed outlier: 3.850A pdb=" N ARG G1369 " --> pdb=" O THR G1366 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 1366 through 1369' Processing helix chain 'G' and resid 1375 through 1381 Processing helix chain 'G' and resid 1386 through 1395 removed outlier: 3.865A pdb=" N SER G1395 " --> pdb=" O VAL G1391 " (cutoff:3.500A) Processing helix chain 'G' and resid 1400 through 1406 removed outlier: 4.137A pdb=" N GLN G1404 " --> pdb=" O LEU G1400 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE G1405 " --> pdb=" O GLY G1401 " (cutoff:3.500A) Processing helix chain 'G' and resid 1418 through 1420 No H-bonds generated for 'chain 'G' and resid 1418 through 1420' Processing helix chain 'G' and resid 1430 through 1436 removed outlier: 4.306A pdb=" N ILE G1436 " --> pdb=" O ALA G1432 " (cutoff:3.500A) Processing helix chain 'G' and resid 1443 through 1446 No H-bonds generated for 'chain 'G' and resid 1443 through 1446' Processing helix chain 'G' and resid 1448 through 1455 Processing helix chain 'G' and resid 1481 through 1490 Processing helix chain 'G' and resid 1494 through 1501 Processing helix chain 'G' and resid 1505 through 1512 Processing helix chain 'G' and resid 1553 through 1568 Processing helix chain 'G' and resid 1579 through 1591 Processing helix chain 'G' and resid 1605 through 1617 Processing helix chain 'G' and resid 1629 through 1631 No H-bonds generated for 'chain 'G' and resid 1629 through 1631' Processing helix chain 'G' and resid 1652 through 1662 Processing helix chain 'G' and resid 1682 through 1703 Processing helix chain 'H' and resid 385 through 412 Processing helix chain 'H' and resid 463 through 465 No H-bonds generated for 'chain 'H' and resid 463 through 465' Processing helix chain 'H' and resid 469 through 474 removed outlier: 3.525A pdb=" N VAL H 472 " --> pdb=" O HIS H 469 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N VAL H 473 " --> pdb=" O ALA H 470 " (cutoff:3.500A) Processing helix chain 'I' and resid 11 through 19 Processing helix chain 'I' and resid 44 through 50 Processing helix chain 'I' and resid 191 through 198 Processing helix chain 'I' and resid 205 through 212 removed outlier: 4.189A pdb=" N LEU I 209 " --> pdb=" O GLY I 205 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 19 No H-bonds generated for 'chain 'J' and resid 17 through 19' Processing helix chain 'J' and resid 44 through 49 removed outlier: 3.887A pdb=" N ARG J 48 " --> pdb=" O ASP J 44 " (cutoff:3.500A) Processing helix chain 'J' and resid 102 through 104 No H-bonds generated for 'chain 'J' and resid 102 through 104' Processing helix chain 'J' and resid 129 through 143 removed outlier: 3.948A pdb=" N HIS J 134 " --> pdb=" O ASP J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 166 through 178 Processing helix chain 'J' and resid 190 through 197 Processing helix chain 'J' and resid 235 through 249 Processing helix chain 'J' and resid 260 through 270 removed outlier: 3.625A pdb=" N ASP J 269 " --> pdb=" O HIS J 265 " (cutoff:3.500A) Processing helix chain 'J' and resid 277 through 282 removed outlier: 3.991A pdb=" N ALA J 282 " --> pdb=" O ASP J 278 " (cutoff:3.500A) Processing helix chain 'J' and resid 290 through 293 No H-bonds generated for 'chain 'J' and resid 290 through 293' Processing helix chain 'J' and resid 472 through 497 Processing helix chain 'J' and resid 505 through 518 Processing helix chain 'J' and resid 572 through 583 Processing helix chain 'J' and resid 608 through 613 Processing helix chain 'J' and resid 624 through 627 No H-bonds generated for 'chain 'J' and resid 624 through 627' Processing helix chain 'J' and resid 634 through 641 removed outlier: 4.056A pdb=" N ARG J 638 " --> pdb=" O GLU J 635 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N VAL J 639 " --> pdb=" O ARG J 636 " (cutoff:3.500A) Proline residue: J 640 - end of helix Processing helix chain 'J' and resid 646 through 649 No H-bonds generated for 'chain 'J' and resid 646 through 649' Processing helix chain 'J' and resid 657 through 667 Processing helix chain 'J' and resid 679 through 682 No H-bonds generated for 'chain 'J' and resid 679 through 682' Processing helix chain 'J' and resid 699 through 709 Processing helix chain 'J' and resid 727 through 735 removed outlier: 3.934A pdb=" N ALA J 732 " --> pdb=" O ALA J 728 " (cutoff:3.500A) Processing helix chain 'J' and resid 739 through 742 No H-bonds generated for 'chain 'J' and resid 739 through 742' Processing helix chain 'J' and resid 748 through 754 Processing helix chain 'M' and resid 45 through 54 Processing helix chain 'M' and resid 64 through 77 removed outlier: 4.495A pdb=" N ASP M 77 " --> pdb=" O GLU M 73 " (cutoff:3.500A) Processing helix chain 'M' and resid 86 through 113 Processing helix chain 'M' and resid 121 through 131 Processing helix chain 'N' and resid 26 through 28 No H-bonds generated for 'chain 'N' and resid 26 through 28' Processing helix chain 'N' and resid 31 through 41 Processing helix chain 'N' and resid 50 through 75 Processing helix chain 'N' and resid 83 through 92 Processing helix chain 'O' and resid 17 through 20 No H-bonds generated for 'chain 'O' and resid 17 through 20' Processing helix chain 'O' and resid 27 through 35 Processing helix chain 'O' and resid 47 through 72 Processing helix chain 'O' and resid 80 through 88 Processing helix chain 'O' and resid 91 through 96 Processing helix chain 'O' and resid 113 through 115 No H-bonds generated for 'chain 'O' and resid 113 through 115' Processing helix chain 'P' and resid 38 through 48 Processing helix chain 'P' and resid 56 through 83 Processing helix chain 'P' and resid 91 through 101 Processing helix chain 'P' and resid 104 through 123 removed outlier: 3.998A pdb=" N HIS P 109 " --> pdb=" O LEU P 106 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS P 116 " --> pdb=" O GLU P 113 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL P 118 " --> pdb=" O THR P 115 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TYR P 121 " --> pdb=" O VAL P 118 " (cutoff:3.500A) Processing helix chain 'Q' and resid 45 through 56 Processing helix chain 'Q' and resid 64 through 77 removed outlier: 3.533A pdb=" N GLN Q 76 " --> pdb=" O ARG Q 72 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ASP Q 77 " --> pdb=" O GLU Q 73 " (cutoff:3.500A) Processing helix chain 'Q' and resid 86 through 113 removed outlier: 3.663A pdb=" N GLU Q 105 " --> pdb=" O VAL Q 101 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP Q 106 " --> pdb=" O GLY Q 102 " (cutoff:3.500A) Processing helix chain 'Q' and resid 121 through 131 Processing helix chain 'R' and resid 26 through 28 No H-bonds generated for 'chain 'R' and resid 26 through 28' Processing helix chain 'R' and resid 31 through 41 Processing helix chain 'R' and resid 50 through 75 removed outlier: 3.707A pdb=" N ASP R 68 " --> pdb=" O ASN R 64 " (cutoff:3.500A) Processing helix chain 'R' and resid 83 through 93 Processing helix chain 'S' and resid 17 through 20 No H-bonds generated for 'chain 'S' and resid 17 through 20' Processing helix chain 'S' and resid 27 through 37 Processing helix chain 'S' and resid 45 through 72 removed outlier: 4.609A pdb=" N VAL S 49 " --> pdb=" O ALA S 45 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU S 65 " --> pdb=" O GLU S 61 " (cutoff:3.500A) Processing helix chain 'S' and resid 80 through 89 removed outlier: 3.507A pdb=" N ASN S 89 " --> pdb=" O LEU S 85 " (cutoff:3.500A) Processing helix chain 'S' and resid 91 through 96 Processing helix chain 'T' and resid 38 through 48 Processing helix chain 'T' and resid 56 through 83 Processing helix chain 'T' and resid 91 through 101 Processing helix chain 'T' and resid 105 through 123 Processing sheet with id= A, first strand: chain 'A' and resid 359 through 362 removed outlier: 7.005A pdb=" N GLY A 66 " --> pdb=" O LEU A 360 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ILE A 362 " --> pdb=" O GLY A 66 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LEU A 68 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL A 328 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N LEU A 69 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LEU A 330 " --> pdb=" O LEU A 69 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 294 through 297 Processing sheet with id= C, first strand: chain 'A' and resid 131 through 135 removed outlier: 3.926A pdb=" N GLY A 205 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N TYR A 193 " --> pdb=" O ARG A 203 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ARG A 203 " --> pdb=" O TYR A 193 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLU A 195 " --> pdb=" O CYS A 201 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N CYS A 201 " --> pdb=" O GLU A 195 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 336 through 338 Processing sheet with id= E, first strand: chain 'A' and resid 141 through 143 Processing sheet with id= F, first strand: chain 'B' and resid 360 through 362 removed outlier: 6.533A pdb=" N VAL B 328 " --> pdb=" O VAL B 67 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N LEU B 69 " --> pdb=" O VAL B 328 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N LEU B 330 " --> pdb=" O LEU B 69 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 230 through 240 Processing sheet with id= H, first strand: chain 'B' and resid 131 through 135 removed outlier: 3.693A pdb=" N GLY B 205 " --> pdb=" O VAL B 191 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N TYR B 193 " --> pdb=" O ARG B 203 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ARG B 203 " --> pdb=" O TYR B 193 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N GLU B 195 " --> pdb=" O CYS B 201 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N CYS B 201 " --> pdb=" O GLU B 195 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 139 through 141 Processing sheet with id= J, first strand: chain 'C' and resid 67 through 69 removed outlier: 6.275A pdb=" N LEU C 360 " --> pdb=" O LEU C 68 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'C' and resid 230 through 240 Processing sheet with id= L, first strand: chain 'C' and resid 132 through 135 removed outlier: 3.740A pdb=" N GLY C 205 " --> pdb=" O VAL C 191 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N TYR C 193 " --> pdb=" O ARG C 203 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ARG C 203 " --> pdb=" O TYR C 193 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 158 through 163 Processing sheet with id= N, first strand: chain 'C' and resid 299 through 302 removed outlier: 6.780A pdb=" N ILE C 327 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ILE C 302 " --> pdb=" O ILE C 327 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL C 329 " --> pdb=" O ILE C 302 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'C' and resid 336 through 338 Processing sheet with id= P, first strand: chain 'D' and resid 354 through 358 removed outlier: 6.660A pdb=" N VAL D 323 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N ILE D 75 " --> pdb=" O VAL D 323 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N MET D 325 " --> pdb=" O ILE D 75 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N GLY D 77 " --> pdb=" O MET D 325 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU D 295 " --> pdb=" O ILE D 322 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 288 through 292 Processing sheet with id= R, first strand: chain 'D' and resid 168 through 173 removed outlier: 3.826A pdb=" N GLY D 158 " --> pdb=" O MET D 173 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LYS D 163 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N VAL D 142 " --> pdb=" O LYS D 163 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 331 through 333 Processing sheet with id= T, first strand: chain 'D' and resid 190 through 194 removed outlier: 3.772A pdb=" N GLY D 205 " --> pdb=" O ILE D 191 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N SER D 193 " --> pdb=" O LYS D 203 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N LYS D 203 " --> pdb=" O SER D 193 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 354 through 357 removed outlier: 6.646A pdb=" N VAL E 323 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ILE E 75 " --> pdb=" O VAL E 323 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N MET E 325 " --> pdb=" O ILE E 75 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA E 326 " --> pdb=" O ILE E 297 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 290 through 292 removed outlier: 3.614A pdb=" N VAL E 237 " --> pdb=" O GLU E 133 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 168 through 172 removed outlier: 6.479A pdb=" N LYS E 163 " --> pdb=" O VAL E 142 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N VAL E 142 " --> pdb=" O LYS E 163 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 331 through 333 Processing sheet with id= Y, first strand: chain 'F' and resid 354 through 356 removed outlier: 6.810A pdb=" N VAL F 323 " --> pdb=" O VAL F 73 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N ILE F 75 " --> pdb=" O VAL F 323 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N MET F 325 " --> pdb=" O ILE F 75 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU F 295 " --> pdb=" O ILE F 322 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'F' and resid 289 through 292 removed outlier: 3.666A pdb=" N LYS F 235 " --> pdb=" O SER F 135 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'F' and resid 201 through 203 removed outlier: 7.034A pdb=" N THR F 161 " --> pdb=" O VAL F 143 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ILE F 145 " --> pdb=" O LYS F 159 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LYS F 159 " --> pdb=" O ILE F 145 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N ILE F 147 " --> pdb=" O GLN F 157 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N GLN F 157 " --> pdb=" O ILE F 147 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 331 through 333 Processing sheet with id= AC, first strand: chain 'G' and resid 1081 through 1084 removed outlier: 6.387A pdb=" N PHE G1024 " --> pdb=" O MET G1082 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N THR G1084 " --> pdb=" O PHE G1024 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL G1026 " --> pdb=" O THR G1084 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N TYR G1103 " --> pdb=" O LEU G1025 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL G1027 " --> pdb=" O TYR G1103 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ILE G1105 " --> pdb=" O VAL G1027 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ASN G1130 " --> pdb=" O MET G1104 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N LEU G1106 " --> pdb=" O ASN G1130 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU G1132 " --> pdb=" O LEU G1106 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'G' and resid 1213 through 1219 removed outlier: 7.028A pdb=" N VAL G1671 " --> pdb=" O ILE G1214 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N ILE G1216 " --> pdb=" O VAL G1671 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N VAL G1673 " --> pdb=" O ILE G1216 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N VAL G1218 " --> pdb=" O VAL G1673 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ARG G1675 " --> pdb=" O VAL G1218 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'G' and resid 1312 through 1314 removed outlier: 6.606A pdb=" N GLU G1475 " --> pdb=" O TYR G1313 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain 'G' and resid 1596 through 1599 removed outlier: 6.451A pdb=" N ILE G1623 " --> pdb=" O CYS G1597 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N LEU G1599 " --> pdb=" O ILE G1623 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N LEU G1625 " --> pdb=" O LEU G1599 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF Processing sheet with id= AG, first strand: chain 'H' and resid 449 through 452 Processing sheet with id= AH, first strand: chain 'J' and resid 80 through 82 removed outlier: 7.484A pdb=" N ILE J 61 " --> pdb=" O PRO J 155 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL J 157 " --> pdb=" O ILE J 61 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'J' and resid 86 through 91 Processing sheet with id= AJ, first strand: chain 'J' and resid 203 through 208 Processing sheet with id= AK, first strand: chain 'J' and resid 295 through 297 Processing sheet with id= AL, first strand: chain 'J' and resid 686 through 688 1396 hydrogen bonds defined for protein. 4044 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 255 hydrogen bonds 510 hydrogen bond angles 0 basepair planarities 102 basepair parallelities 215 stacking parallelities Total time for adding SS restraints: 24.55 Time building geometry restraints manager: 18.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 9269 1.33 - 1.45: 10737 1.45 - 1.57: 23915 1.57 - 1.69: 597 1.69 - 1.81: 277 Bond restraints: 44795 Sorted by residual: bond pdb=" C4 ATP J 801 " pdb=" C5 ATP J 801 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.69e+01 bond pdb=" C5 ATP J 801 " pdb=" C6 ATP J 801 " ideal model delta sigma weight residual 1.409 1.473 -0.064 1.00e-02 1.00e+04 4.15e+01 bond pdb=" CZ ARG J 112 " pdb=" NH1 ARG J 112 " ideal model delta sigma weight residual 1.323 1.411 -0.088 1.40e-02 5.10e+03 3.92e+01 bond pdb=" CG ARG J 112 " pdb=" CD ARG J 112 " ideal model delta sigma weight residual 1.520 1.350 0.170 3.00e-02 1.11e+03 3.20e+01 bond pdb=" C4 ATP J 801 " pdb=" N9 ATP J 801 " ideal model delta sigma weight residual 1.374 1.322 0.052 1.00e-02 1.00e+04 2.74e+01 ... (remaining 44790 not shown) Histogram of bond angle deviations from ideal: 96.66 - 104.60: 1709 104.60 - 112.54: 24290 112.54 - 120.48: 19955 120.48 - 128.42: 15355 128.42 - 136.36: 517 Bond angle restraints: 61826 Sorted by residual: angle pdb=" PB ATP J 801 " pdb=" O3B ATP J 801 " pdb=" PG ATP J 801 " ideal model delta sigma weight residual 139.87 119.67 20.20 1.00e+00 1.00e+00 4.08e+02 angle pdb=" PA ATP J 801 " pdb=" O3A ATP J 801 " pdb=" PB ATP J 801 " ideal model delta sigma weight residual 136.83 119.30 17.53 1.00e+00 1.00e+00 3.07e+02 angle pdb=" C5 ATP J 801 " pdb=" C4 ATP J 801 " pdb=" N3 ATP J 801 " ideal model delta sigma weight residual 126.80 119.35 7.45 1.00e+00 1.00e+00 5.56e+01 angle pdb=" O3' DA L 63 " pdb=" P DT L 64 " pdb=" O5' DT L 64 " ideal model delta sigma weight residual 104.00 115.07 -11.07 1.50e+00 4.44e-01 5.45e+01 angle pdb=" OP1 DG K 23 " pdb=" P DG K 23 " pdb=" OP2 DG K 23 " ideal model delta sigma weight residual 120.00 99.36 20.64 3.00e+00 1.11e-01 4.73e+01 ... (remaining 61821 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.57: 25152 35.57 - 71.14: 1298 71.14 - 106.71: 20 106.71 - 142.28: 11 142.28 - 177.84: 4 Dihedral angle restraints: 26485 sinusoidal: 12603 harmonic: 13882 Sorted by residual: dihedral pdb=" CA ILE G1701 " pdb=" C ILE G1701 " pdb=" N THR G1702 " pdb=" CA THR G1702 " ideal model delta harmonic sigma weight residual 180.00 136.34 43.66 0 5.00e+00 4.00e-02 7.62e+01 dihedral pdb=" CA THR G1550 " pdb=" C THR G1550 " pdb=" N ASP G1551 " pdb=" CA ASP G1551 " ideal model delta harmonic sigma weight residual -180.00 -140.04 -39.96 0 5.00e+00 4.00e-02 6.39e+01 dihedral pdb=" CA PHE G1548 " pdb=" C PHE G1548 " pdb=" N VAL G1549 " pdb=" CA VAL G1549 " ideal model delta harmonic sigma weight residual -180.00 -140.58 -39.42 0 5.00e+00 4.00e-02 6.22e+01 ... (remaining 26482 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 6138 0.084 - 0.169: 845 0.169 - 0.253: 54 0.253 - 0.337: 3 0.337 - 0.421: 5 Chirality restraints: 7045 Sorted by residual: chirality pdb=" CB ILE G1083 " pdb=" CA ILE G1083 " pdb=" CG1 ILE G1083 " pdb=" CG2 ILE G1083 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.42 2.00e-01 2.50e+01 4.44e+00 chirality pdb=" CB ILE C 324 " pdb=" CA ILE C 324 " pdb=" CG1 ILE C 324 " pdb=" CG2 ILE C 324 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" CB ILE J 39 " pdb=" CA ILE J 39 " pdb=" CG1 ILE J 39 " pdb=" CG2 ILE J 39 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.32e+00 ... (remaining 7042 not shown) Planarity restraints: 6957 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP O 72 " -0.046 2.00e-02 2.50e+03 9.21e-02 8.48e+01 pdb=" CG ASP O 72 " 0.159 2.00e-02 2.50e+03 pdb=" OD1 ASP O 72 " -0.058 2.00e-02 2.50e+03 pdb=" OD2 ASP O 72 " -0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP Q 77 " 0.043 2.00e-02 2.50e+03 8.52e-02 7.26e+01 pdb=" CG ASP Q 77 " -0.147 2.00e-02 2.50e+03 pdb=" OD1 ASP Q 77 " 0.056 2.00e-02 2.50e+03 pdb=" OD2 ASP Q 77 " 0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE G1701 " -0.031 2.00e-02 2.50e+03 6.07e-02 3.69e+01 pdb=" C ILE G1701 " 0.105 2.00e-02 2.50e+03 pdb=" O ILE G1701 " -0.040 2.00e-02 2.50e+03 pdb=" N THR G1702 " -0.034 2.00e-02 2.50e+03 ... (remaining 6954 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 2410 2.71 - 3.26: 40537 3.26 - 3.81: 73706 3.81 - 4.35: 89973 4.35 - 4.90: 143516 Nonbonded interactions: 350142 Sorted by model distance: nonbonded pdb=" O SER C 100 " pdb=" OG1 THR F 116 " model vdw 2.165 2.440 nonbonded pdb=" OH TYR G1095 " pdb=" OP1 DG K 21 " model vdw 2.204 2.440 nonbonded pdb=" OE1 GLU E 245 " pdb=" OH TYR G1313 " model vdw 2.254 2.440 nonbonded pdb=" OD2 ASP B 256 " pdb=" OG SER B 259 " model vdw 2.264 2.440 nonbonded pdb=" NE2 HIS G1270 " pdb=" O VAL G1549 " model vdw 2.267 2.520 ... (remaining 350137 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 144 or resid 156 through 462 or resid 501)) selection = chain 'B' selection = (chain 'C' and (resid 14 through 144 or resid 156 through 462 or resid 501)) } ncs_group { reference = (chain 'D' and (resid 20 through 150 or resid 156 through 458 or resid 501)) selection = (chain 'E' and (resid 20 through 150 or resid 156 through 458 or resid 501)) selection = (chain 'F' and (resid 20 through 458 or resid 501)) } ncs_group { reference = (chain 'M' and (resid 40 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 58 or (resid 59 and (name N or nam \ e CA or name C or name O or name CB )) or resid 60 through 63 or (resid 64 and ( \ name N or name CA or name C or name O or name CB )) or resid 65 through 134)) selection = (chain 'Q' and (resid 40 through 41 or (resid 42 and (name N or name CA or name \ C or name O or name CB )) or resid 43 through 82 or (resid 83 and (name N or nam \ e CA or name C or name O or name CB )) or resid 84 through 133 or (resid 134 and \ (name N or name CA or name C or name O or name CB )))) } ncs_group { reference = (chain 'N' and (resid 24 through 58 or (resid 59 and (name N or name CA or name \ C or name O or name CB )) or resid 60 through 76 or (resid 77 and (name N or nam \ e CA or name C or name O or name CB )) or resid 78 or (resid 79 and (name N or n \ ame CA or name C or name O or name CB )) or resid 80 through 102)) selection = (chain 'R' and (resid 24 through 43 or (resid 44 and (name N or name CA or name \ C or name O or name CB )) or resid 45 through 102)) } ncs_group { reference = (chain 'O' and (resid 16 through 74 or (resid 75 and (name N or name CA or name \ C or name O or name CB )) or resid 76 through 118)) selection = (chain 'S' and (resid 16 through 19 or (resid 20 through 21 and (name N or name \ CA or name C or name O or name CB )) or resid 22 through 34 or (resid 35 through \ 36 and (name N or name CA or name C or name O or name CB )) or resid 37 through \ 94 or (resid 95 and (name N or name CA or name C or name O or name CB )) or res \ id 96 through 118)) } ncs_group { reference = (chain 'P' and (resid 31 through 84 or (resid 85 and (name N or name CA or name \ C or name O or name CB )) or resid 86 through 125)) selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.730 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: 0.060 Extract box with map and model: 10.820 Check model and map are aligned: 0.720 Set scattering table: 0.410 Process input model: 130.080 Find NCS groups from input model: 2.550 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 149.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 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 : 0.009 0.170 44795 Z= 0.591 Angle : 1.013 20.639 61826 Z= 0.568 Chirality : 0.057 0.421 7045 Planarity : 0.008 0.092 6957 Dihedral : 16.662 177.844 17533 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.68 % Favored : 93.19 % Rotamer: Outliers : 0.13 % Allowed : 2.16 % Favored : 97.71 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -3.82 (0.10), residues: 4686 helix: -2.40 (0.08), residues: 2114 sheet: -2.22 (0.19), residues: 610 loop : -2.63 (0.12), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP G1650 HIS 0.018 0.003 HIS B 306 PHE 0.033 0.004 PHE G1576 TYR 0.074 0.004 TYR J 89 ARG 0.016 0.001 ARG O 88 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1223 residues out of total 3969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1218 time to evaluate : 4.337 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: 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: 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: 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: A 62 MET cc_start: 0.6285 (tmm) cc_final: 0.5668 (tmm) REVERT: A 85 SER cc_start: 0.9137 (p) cc_final: 0.8846 (t) REVERT: A 103 TYR cc_start: 0.7820 (m-80) cc_final: 0.7343 (m-80) REVERT: A 137 THR cc_start: 0.9304 (m) cc_final: 0.9099 (p) REVERT: A 155 ILE cc_start: 0.9418 (mt) cc_final: 0.9159 (tt) REVERT: A 177 ILE cc_start: 0.9396 (mt) cc_final: 0.9186 (mm) REVERT: A 309 ASP cc_start: 0.8669 (p0) cc_final: 0.8408 (p0) REVERT: A 359 LEU cc_start: 0.8760 (mt) cc_final: 0.8528 (mm) REVERT: A 416 ILE cc_start: 0.9256 (mm) cc_final: 0.9049 (mt) REVERT: B 100 SER cc_start: 0.9249 (m) cc_final: 0.8590 (t) REVERT: B 158 LEU cc_start: 0.7933 (tt) cc_final: 0.7227 (tt) REVERT: B 178 TYR cc_start: 0.7925 (t80) cc_final: 0.7707 (t80) REVERT: B 260 MET cc_start: 0.8437 (ptt) cc_final: 0.8202 (ptm) REVERT: B 280 ILE cc_start: 0.9531 (mt) cc_final: 0.9251 (tt) REVERT: B 304 GLU cc_start: 0.8488 (mt-10) cc_final: 0.7954 (mt-10) REVERT: B 309 ASP cc_start: 0.7915 (p0) cc_final: 0.7506 (p0) REVERT: B 356 LEU cc_start: 0.8788 (tp) cc_final: 0.8577 (tt) REVERT: B 361 ILE cc_start: 0.9423 (mt) cc_final: 0.8862 (tt) REVERT: B 409 GLN cc_start: 0.7847 (mt0) cc_final: 0.7277 (mm-40) REVERT: C 8 ARG cc_start: 0.6893 (mtt180) cc_final: 0.6628 (mtt-85) REVERT: C 44 CYS cc_start: 0.7937 (m) cc_final: 0.6739 (t) REVERT: C 95 CYS cc_start: 0.8781 (t) cc_final: 0.8203 (m) REVERT: C 101 GLU cc_start: 0.7838 (tt0) cc_final: 0.7635 (tm-30) REVERT: C 110 THR cc_start: 0.8654 (p) cc_final: 0.8332 (p) REVERT: C 136 VAL cc_start: 0.7719 (t) cc_final: 0.7430 (t) REVERT: C 146 ASN cc_start: 0.9195 (m-40) cc_final: 0.8660 (p0) REVERT: C 159 LEU cc_start: 0.8877 (mp) cc_final: 0.8645 (tp) REVERT: C 160 ILE cc_start: 0.9207 (mt) cc_final: 0.8811 (mt) REVERT: C 197 ASN cc_start: 0.9326 (p0) cc_final: 0.9061 (p0) REVERT: C 364 THR cc_start: 0.8679 (m) cc_final: 0.8422 (p) REVERT: C 416 ILE cc_start: 0.8828 (mm) cc_final: 0.8535 (tt) REVERT: D 106 SER cc_start: 0.7964 (m) cc_final: 0.7315 (m) REVERT: D 107 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7352 (tm-30) REVERT: D 181 MET cc_start: 0.9334 (mmt) cc_final: 0.8720 (mmm) REVERT: D 247 ASP cc_start: 0.7893 (m-30) cc_final: 0.7582 (m-30) REVERT: D 253 THR cc_start: 0.8452 (m) cc_final: 0.8189 (m) REVERT: D 256 PHE cc_start: 0.6668 (m-80) cc_final: 0.6217 (m-80) REVERT: D 350 LEU cc_start: 0.8255 (mt) cc_final: 0.7903 (tp) REVERT: E 217 MET cc_start: 0.6572 (mmm) cc_final: 0.5486 (tpp) REVERT: E 307 CYS cc_start: 0.8480 (m) cc_final: 0.7988 (t) REVERT: E 369 ILE cc_start: 0.9268 (mt) cc_final: 0.8986 (mm) REVERT: E 407 THR cc_start: 0.8156 (m) cc_final: 0.7796 (t) REVERT: F 106 SER cc_start: 0.9287 (m) cc_final: 0.8046 (m) REVERT: F 112 GLU cc_start: 0.7819 (tt0) cc_final: 0.7585 (tt0) REVERT: F 138 MET cc_start: 0.8370 (ttp) cc_final: 0.8071 (ptm) REVERT: F 160 LEU cc_start: 0.8400 (tp) cc_final: 0.7974 (tt) REVERT: F 162 ILE cc_start: 0.7924 (pt) cc_final: 0.7616 (pt) REVERT: F 173 MET cc_start: 0.8092 (mtm) cc_final: 0.7728 (mpp) REVERT: F 179 ASP cc_start: 0.8728 (m-30) cc_final: 0.8221 (t70) REVERT: F 208 TYR cc_start: 0.7898 (m-80) cc_final: 0.7672 (m-80) REVERT: G 1033 LEU cc_start: 0.9015 (mt) cc_final: 0.8754 (tt) REVERT: G 1110 GLN cc_start: 0.8430 (pt0) cc_final: 0.8019 (tm-30) REVERT: G 1263 GLN cc_start: 0.6490 (tp-100) cc_final: 0.6278 (tp40) REVERT: G 1346 MET cc_start: 0.8263 (mmm) cc_final: 0.7882 (mmt) REVERT: G 1349 ILE cc_start: 0.9536 (pp) cc_final: 0.9246 (pp) REVERT: G 1694 GLU cc_start: 0.9281 (tt0) cc_final: 0.9024 (tm-30) REVERT: H 462 PRO cc_start: 0.8863 (Cg_exo) cc_final: 0.8059 (Cg_endo) REVERT: I 20 LEU cc_start: 0.9331 (mt) cc_final: 0.8513 (mm) REVERT: J 129 TRP cc_start: 0.7975 (m100) cc_final: 0.7693 (m100) REVERT: J 168 SER cc_start: 0.9524 (m) cc_final: 0.9323 (p) REVERT: J 284 TYR cc_start: 0.8564 (t80) cc_final: 0.8015 (t80) REVERT: M 64 LYS cc_start: 0.8703 (mmtm) cc_final: 0.8461 (mmtt) REVERT: M 67 PHE cc_start: 0.8448 (t80) cc_final: 0.6742 (t80) REVERT: M 113 HIS cc_start: 0.7682 (t70) cc_final: 0.5856 (t70) REVERT: N 49 LEU cc_start: 0.9183 (mt) cc_final: 0.8601 (mm) REVERT: N 81 VAL cc_start: 0.9035 (OUTLIER) cc_final: 0.8712 (p) REVERT: N 84 MET cc_start: 0.8254 (mmm) cc_final: 0.8023 (tpt) REVERT: O 25 PHE cc_start: 0.9291 (m-80) cc_final: 0.8596 (m-10) REVERT: O 27 VAL cc_start: 0.9014 (t) cc_final: 0.8513 (t) REVERT: P 59 MET cc_start: 0.9059 (tmm) cc_final: 0.8676 (tpp) REVERT: P 64 SER cc_start: 0.9645 (m) cc_final: 0.8914 (p) REVERT: P 80 LEU cc_start: 0.9577 (mt) cc_final: 0.9293 (tp) REVERT: P 93 GLU cc_start: 0.9264 (mp0) cc_final: 0.9000 (mp0) REVERT: Q 61 LEU cc_start: 0.8790 (mp) cc_final: 0.8133 (pt) REVERT: Q 62 ILE cc_start: 0.9013 (mt) cc_final: 0.8783 (mm) REVERT: Q 87 SER cc_start: 0.9248 (p) cc_final: 0.9044 (p) REVERT: Q 89 VAL cc_start: 0.9238 (t) cc_final: 0.9014 (p) REVERT: Q 100 LEU cc_start: 0.9514 (mt) cc_final: 0.9143 (pp) REVERT: R 37 LEU cc_start: 0.9473 (mt) cc_final: 0.8962 (mt) REVERT: R 43 VAL cc_start: 0.8294 (t) cc_final: 0.7417 (t) REVERT: R 84 MET cc_start: 0.8812 (mmm) cc_final: 0.8308 (tpp) REVERT: R 98 TYR cc_start: 0.8457 (m-10) cc_final: 0.7879 (m-10) REVERT: S 33 LEU cc_start: 0.9324 (mt) cc_final: 0.9096 (mt) REVERT: S 79 ILE cc_start: 0.8454 (pt) cc_final: 0.8162 (pt) REVERT: S 107 VAL cc_start: 0.8511 (m) cc_final: 0.8269 (t) REVERT: T 113 GLU cc_start: 0.8602 (mm-30) cc_final: 0.7818 (mt-10) outliers start: 5 outliers final: 1 residues processed: 1219 average time/residue: 0.6136 time to fit residues: 1176.5579 Evaluate side-chains 633 residues out of total 3969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 631 time to evaluate : 4.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 417 optimal weight: 10.0000 chunk 374 optimal weight: 0.8980 chunk 207 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 252 optimal weight: 1.9990 chunk 200 optimal weight: 0.7980 chunk 387 optimal weight: 0.9990 chunk 149 optimal weight: 0.9990 chunk 235 optimal weight: 5.9990 chunk 288 optimal weight: 0.8980 chunk 448 optimal weight: 20.0000 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 HIS A 237 GLN A 248 ASN ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 28 ASN ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN B 381 GLN C 28 ASN C 237 GLN C 242 HIS D 250 ASN D 274 GLN D 301 HIS D 394 GLN D 443 GLN D 452 ASN E 92 GLN E 250 ASN E 394 GLN E 409 GLN F 24 HIS F 250 ASN F 328 ASN G 964 GLN G 969 ASN ** G1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1130 ASN G1140 GLN G1191 HIS ** G1269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1402 HIS G1419 HIS G1570 HIS G1616 GLN G1692 GLN ** G1697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 19 GLN ** J 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 214 HIS J 633 ASN ** J 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 762 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 68 GLN R 25 ASN T 63 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 44795 Z= 0.192 Angle : 0.634 9.436 61826 Z= 0.333 Chirality : 0.042 0.225 7045 Planarity : 0.005 0.060 6957 Dihedral : 21.034 176.630 8508 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.78 % Favored : 95.13 % Rotamer: Outliers : 0.08 % Allowed : 2.85 % Favored : 97.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.11), residues: 4686 helix: -0.89 (0.10), residues: 2132 sheet: -1.89 (0.20), residues: 600 loop : -2.16 (0.13), residues: 1954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 282 HIS 0.007 0.001 HIS P 109 PHE 0.031 0.002 PHE G1158 TYR 0.023 0.002 TYR F 400 ARG 0.008 0.001 ARG D 335 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 827 residues out of total 3969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 824 time to evaluate : 4.680 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 SER cc_start: 0.9275 (p) cc_final: 0.9018 (t) REVERT: A 130 ASP cc_start: 0.8765 (m-30) cc_final: 0.7919 (p0) REVERT: A 137 THR cc_start: 0.9043 (m) cc_final: 0.8787 (t) REVERT: A 278 MET cc_start: 0.8608 (tmm) cc_final: 0.8332 (tmm) REVERT: B 100 SER cc_start: 0.9103 (m) cc_final: 0.8457 (t) REVERT: B 158 LEU cc_start: 0.7779 (tt) cc_final: 0.7100 (tt) REVERT: B 162 LEU cc_start: 0.8886 (mt) cc_final: 0.8623 (tp) REVERT: B 178 TYR cc_start: 0.7969 (t80) cc_final: 0.7592 (t80) REVERT: B 248 ASN cc_start: 0.8338 (t0) cc_final: 0.7793 (t0) REVERT: B 276 LEU cc_start: 0.8599 (tp) cc_final: 0.8370 (tt) REVERT: B 287 TYR cc_start: 0.8049 (m-10) cc_final: 0.7305 (m-80) REVERT: B 306 HIS cc_start: 0.8113 (p-80) cc_final: 0.7521 (p90) REVERT: C 44 CYS cc_start: 0.7697 (m) cc_final: 0.6749 (t) REVERT: C 77 LYS cc_start: 0.8900 (mtmm) cc_final: 0.8440 (mtmm) REVERT: C 95 CYS cc_start: 0.8747 (t) cc_final: 0.8134 (m) REVERT: C 101 GLU cc_start: 0.7725 (tt0) cc_final: 0.7349 (tm-30) REVERT: C 216 LEU cc_start: 0.8950 (mt) cc_final: 0.8533 (mt) REVERT: C 261 MET cc_start: 0.7586 (mmt) cc_final: 0.7314 (mmt) REVERT: C 364 THR cc_start: 0.8737 (m) cc_final: 0.8500 (p) REVERT: C 416 ILE cc_start: 0.8786 (mm) cc_final: 0.8568 (tt) REVERT: D 30 LEU cc_start: 0.7792 (tt) cc_final: 0.7332 (tp) REVERT: D 46 LEU cc_start: 0.9032 (tp) cc_final: 0.8791 (tp) REVERT: D 113 MET cc_start: 0.8607 (ptt) cc_final: 0.8364 (ptt) REVERT: D 181 MET cc_start: 0.9294 (mmt) cc_final: 0.8813 (mmm) REVERT: E 187 MET cc_start: 0.8747 (ttt) cc_final: 0.8481 (ttp) REVERT: E 217 MET cc_start: 0.6153 (mmm) cc_final: 0.5290 (tpp) REVERT: E 369 ILE cc_start: 0.9282 (mt) cc_final: 0.8921 (mm) REVERT: E 407 THR cc_start: 0.8273 (m) cc_final: 0.7895 (t) REVERT: F 138 MET cc_start: 0.8209 (ttp) cc_final: 0.7998 (ptp) REVERT: F 173 MET cc_start: 0.8031 (mtm) cc_final: 0.7528 (mpp) REVERT: F 400 TYR cc_start: 0.8308 (t80) cc_final: 0.7526 (t80) REVERT: F 404 LEU cc_start: 0.9214 (mm) cc_final: 0.8902 (mm) REVERT: G 1050 LEU cc_start: 0.9459 (tp) cc_final: 0.9226 (tp) REVERT: G 1104 MET cc_start: 0.7864 (ttm) cc_final: 0.7322 (mtm) REVERT: G 1110 GLN cc_start: 0.8227 (pt0) cc_final: 0.7997 (tp40) REVERT: G 1128 CYS cc_start: 0.5167 (m) cc_final: 0.3272 (m) REVERT: G 1198 MET cc_start: 0.8458 (tmm) cc_final: 0.8253 (tmm) REVERT: G 1262 MET cc_start: 0.8774 (mtp) cc_final: 0.8373 (mtp) REVERT: G 1452 LYS cc_start: 0.8772 (tttt) cc_final: 0.8325 (tppt) REVERT: G 1694 GLU cc_start: 0.9236 (tt0) cc_final: 0.8992 (tm-30) REVERT: J 129 TRP cc_start: 0.7863 (m100) cc_final: 0.7124 (m100) REVERT: J 168 SER cc_start: 0.9481 (m) cc_final: 0.9242 (p) REVERT: J 284 TYR cc_start: 0.8538 (t80) cc_final: 0.7822 (t80) REVERT: M 67 PHE cc_start: 0.8470 (t80) cc_final: 0.8220 (t80) REVERT: N 49 LEU cc_start: 0.9323 (mt) cc_final: 0.9067 (mm) REVERT: O 25 PHE cc_start: 0.9384 (m-80) cc_final: 0.8830 (m-10) REVERT: O 73 ASN cc_start: 0.8453 (m110) cc_final: 0.8193 (m110) REVERT: P 64 SER cc_start: 0.9508 (m) cc_final: 0.9047 (p) REVERT: P 93 GLU cc_start: 0.9169 (mp0) cc_final: 0.8890 (mp0) REVERT: P 100 LEU cc_start: 0.9554 (mt) cc_final: 0.9260 (mm) REVERT: Q 67 PHE cc_start: 0.8780 (t80) cc_final: 0.8463 (t80) REVERT: Q 119 ILE cc_start: 0.9377 (mt) cc_final: 0.8902 (mm) REVERT: Q 122 LYS cc_start: 0.9233 (mppt) cc_final: 0.8943 (mppt) REVERT: R 50 ILE cc_start: 0.9246 (mm) cc_final: 0.9022 (mm) REVERT: R 55 ARG cc_start: 0.8789 (mtt180) cc_final: 0.8280 (mmt90) REVERT: R 84 MET cc_start: 0.9005 (mmm) cc_final: 0.8413 (tpp) REVERT: R 96 THR cc_start: 0.8447 (m) cc_final: 0.8067 (p) REVERT: R 98 TYR cc_start: 0.8354 (m-10) cc_final: 0.7732 (m-10) REVERT: S 30 VAL cc_start: 0.9436 (t) cc_final: 0.9210 (t) REVERT: S 39 TYR cc_start: 0.9060 (m-80) cc_final: 0.7849 (m-80) REVERT: S 89 ASN cc_start: 0.7916 (m-40) cc_final: 0.7334 (t0) REVERT: S 92 GLU cc_start: 0.8108 (pm20) cc_final: 0.7576 (mp0) REVERT: T 113 GLU cc_start: 0.8631 (mm-30) cc_final: 0.7903 (mt-10) outliers start: 3 outliers final: 0 residues processed: 825 average time/residue: 0.5437 time to fit residues: 740.0608 Evaluate side-chains 573 residues out of total 3969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 573 time to evaluate : 4.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 249 optimal weight: 9.9990 chunk 139 optimal weight: 5.9990 chunk 373 optimal weight: 20.0000 chunk 305 optimal weight: 9.9990 chunk 123 optimal weight: 9.9990 chunk 449 optimal weight: 0.7980 chunk 485 optimal weight: 9.9990 chunk 400 optimal weight: 10.0000 chunk 445 optimal weight: 7.9990 chunk 153 optimal weight: 1.9990 chunk 360 optimal weight: 9.9990 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 289 ASN B 14 HIS B 60 HIS ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 10 ASN ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 GLN D 49 GLN D 368 GLN ** D 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 GLN F 24 HIS F 250 ASN ** G1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1287 HIS ** G1383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1657 GLN G1692 GLN ** G1697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 19 GLN I 168 HIS ** I 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 610 HIS J 676 GLN ** J 762 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 31 HIS ** P 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 76 GLN ** R 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 63 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 44795 Z= 0.474 Angle : 0.839 10.697 61826 Z= 0.439 Chirality : 0.046 0.215 7045 Planarity : 0.006 0.073 6957 Dihedral : 21.272 178.354 8508 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 19.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.17 % Favored : 92.79 % Rotamer: Outliers : 0.15 % Allowed : 4.02 % Favored : 95.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.12), residues: 4686 helix: -0.40 (0.11), residues: 2112 sheet: -1.68 (0.20), residues: 638 loop : -2.08 (0.13), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP G1415 HIS 0.017 0.002 HIS A 306 PHE 0.034 0.003 PHE F 349 TYR 0.028 0.003 TYR E 339 ARG 0.012 0.001 ARG N 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 3969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 628 time to evaluate : 4.544 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 CYS cc_start: 0.8644 (m) cc_final: 0.7923 (t) REVERT: A 100 SER cc_start: 0.8848 (m) cc_final: 0.8397 (t) REVERT: A 130 ASP cc_start: 0.8717 (m-30) cc_final: 0.8028 (p0) REVERT: A 190 ASP cc_start: 0.8437 (m-30) cc_final: 0.8015 (p0) REVERT: A 193 TYR cc_start: 0.7424 (OUTLIER) cc_final: 0.6423 (p90) REVERT: A 278 MET cc_start: 0.8654 (tmm) cc_final: 0.8215 (tmm) REVERT: A 279 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7782 (mm-30) REVERT: B 62 MET cc_start: 0.6967 (ttp) cc_final: 0.6324 (ppp) REVERT: B 100 SER cc_start: 0.9296 (m) cc_final: 0.8917 (t) REVERT: B 158 LEU cc_start: 0.7903 (tt) cc_final: 0.7674 (tt) REVERT: B 248 ASN cc_start: 0.8784 (t0) cc_final: 0.8015 (t0) REVERT: B 309 ASP cc_start: 0.7766 (p0) cc_final: 0.7559 (p0) REVERT: B 361 ILE cc_start: 0.9533 (mt) cc_final: 0.9107 (tt) REVERT: C 44 CYS cc_start: 0.8045 (m) cc_final: 0.6974 (t) REVERT: C 101 GLU cc_start: 0.7984 (tt0) cc_final: 0.7091 (tm-30) REVERT: C 159 LEU cc_start: 0.8981 (mp) cc_final: 0.8727 (mt) REVERT: C 216 LEU cc_start: 0.8883 (mt) cc_final: 0.8467 (mt) REVERT: C 261 MET cc_start: 0.8110 (mmt) cc_final: 0.7723 (mmt) REVERT: D 46 LEU cc_start: 0.9232 (tp) cc_final: 0.8893 (tp) REVERT: D 160 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8940 (tt) REVERT: D 179 ASP cc_start: 0.8417 (m-30) cc_final: 0.8190 (m-30) REVERT: D 247 ASP cc_start: 0.8523 (m-30) cc_final: 0.8148 (m-30) REVERT: E 113 MET cc_start: 0.9140 (ptt) cc_final: 0.8891 (ptt) REVERT: E 217 MET cc_start: 0.6772 (mmm) cc_final: 0.6004 (tpp) REVERT: E 304 ASP cc_start: 0.8598 (p0) cc_final: 0.8338 (p0) REVERT: E 307 CYS cc_start: 0.8389 (m) cc_final: 0.7745 (t) REVERT: F 138 MET cc_start: 0.8529 (ttp) cc_final: 0.8087 (ptp) REVERT: F 173 MET cc_start: 0.8155 (mtm) cc_final: 0.7660 (mpp) REVERT: F 190 ASP cc_start: 0.7948 (m-30) cc_final: 0.7376 (m-30) REVERT: G 1011 MET cc_start: 0.8914 (mmp) cc_final: 0.8662 (mmp) REVERT: G 1092 ASP cc_start: 0.8536 (t0) cc_final: 0.8236 (m-30) REVERT: G 1104 MET cc_start: 0.7821 (ttm) cc_final: 0.7530 (ttp) REVERT: G 1143 MET cc_start: 0.9014 (mmp) cc_final: 0.8603 (mmp) REVERT: G 1171 ASP cc_start: 0.8593 (t70) cc_final: 0.8255 (t0) REVERT: G 1237 ILE cc_start: 0.6623 (pt) cc_final: 0.6224 (pt) REVERT: G 1346 MET cc_start: 0.8056 (mmm) cc_final: 0.7581 (mmt) REVERT: G 1349 ILE cc_start: 0.9346 (pt) cc_final: 0.9090 (pt) REVERT: G 1496 MET cc_start: 0.8251 (mtp) cc_final: 0.7932 (mtp) REVERT: G 1675 ARG cc_start: 0.7615 (mtm180) cc_final: 0.7367 (mtp180) REVERT: G 1684 GLU cc_start: 0.8813 (mt-10) cc_final: 0.8462 (mt-10) REVERT: G 1694 GLU cc_start: 0.9259 (tt0) cc_final: 0.8948 (tm-30) REVERT: I 193 ILE cc_start: 0.9525 (mp) cc_final: 0.9307 (mm) REVERT: J 168 SER cc_start: 0.9567 (m) cc_final: 0.9259 (p) REVERT: J 284 TYR cc_start: 0.8890 (t80) cc_final: 0.8325 (t80) REVERT: J 700 GLU cc_start: 0.8434 (mp0) cc_final: 0.8059 (mp0) REVERT: M 67 PHE cc_start: 0.8720 (t80) cc_final: 0.8139 (t80) REVERT: N 39 ARG cc_start: 0.8977 (mmt180) cc_final: 0.8633 (mmt180) REVERT: N 50 ILE cc_start: 0.9041 (mm) cc_final: 0.8782 (mm) REVERT: N 53 GLU cc_start: 0.9254 (mp0) cc_final: 0.8702 (mp0) REVERT: N 59 LYS cc_start: 0.9582 (ptmt) cc_final: 0.9335 (ptmm) REVERT: N 63 GLU cc_start: 0.9503 (pt0) cc_final: 0.9093 (pt0) REVERT: N 84 MET cc_start: 0.8862 (tpt) cc_final: 0.8642 (tpp) REVERT: N 92 ARG cc_start: 0.8446 (ptm-80) cc_final: 0.8221 (ttp80) REVERT: O 25 PHE cc_start: 0.9557 (m-80) cc_final: 0.8324 (m-10) REVERT: O 38 ASN cc_start: 0.8473 (m110) cc_final: 0.7922 (m-40) REVERT: O 56 GLU cc_start: 0.8904 (tm-30) cc_final: 0.8354 (tt0) REVERT: O 61 GLU cc_start: 0.8738 (mp0) cc_final: 0.8401 (mp0) REVERT: O 73 ASN cc_start: 0.8618 (m110) cc_final: 0.8399 (m110) REVERT: O 78 ILE cc_start: 0.9684 (mm) cc_final: 0.9288 (tp) REVERT: O 115 LEU cc_start: 0.9354 (mp) cc_final: 0.8715 (tt) REVERT: P 63 ASN cc_start: 0.9452 (m-40) cc_final: 0.9157 (m110) REVERT: Q 61 LEU cc_start: 0.9081 (mp) cc_final: 0.8842 (mm) REVERT: Q 90 MET cc_start: 0.9278 (mmp) cc_final: 0.8934 (mmm) REVERT: Q 97 GLU cc_start: 0.9304 (mt-10) cc_final: 0.8826 (pt0) REVERT: R 39 ARG cc_start: 0.8969 (mmt-90) cc_final: 0.8682 (mmt-90) REVERT: R 55 ARG cc_start: 0.8934 (mtt90) cc_final: 0.8375 (mmt90) REVERT: R 84 MET cc_start: 0.9041 (mmm) cc_final: 0.8609 (tpp) REVERT: S 89 ASN cc_start: 0.8263 (m-40) cc_final: 0.7786 (t0) REVERT: S 92 GLU cc_start: 0.8114 (pm20) cc_final: 0.7639 (mp0) outliers start: 6 outliers final: 2 residues processed: 632 average time/residue: 0.5615 time to fit residues: 589.7397 Evaluate side-chains 463 residues out of total 3969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 459 time to evaluate : 4.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 444 optimal weight: 4.9990 chunk 337 optimal weight: 9.9990 chunk 233 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 chunk 214 optimal weight: 10.0000 chunk 301 optimal weight: 0.9990 chunk 451 optimal weight: 7.9990 chunk 477 optimal weight: 6.9990 chunk 235 optimal weight: 0.7980 chunk 427 optimal weight: 20.0000 chunk 128 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 381 GLN ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 GLN F 24 HIS F 250 ASN ** G 992 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1006 GLN G1034 HIS ** G1151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1593 ASN ** G1616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 19 GLN ** I 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 762 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 766 ASN O 84 GLN P 47 GLN Q 93 GLN ** S 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 63 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.4356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 44795 Z= 0.248 Angle : 0.636 14.023 61826 Z= 0.334 Chirality : 0.042 0.229 7045 Planarity : 0.004 0.050 6957 Dihedral : 21.179 179.087 8508 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.12 % Favored : 94.84 % Rotamer: Outliers : 0.03 % Allowed : 2.80 % Favored : 97.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.12), residues: 4686 helix: 0.05 (0.11), residues: 2116 sheet: -1.57 (0.20), residues: 637 loop : -1.86 (0.14), residues: 1933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G1415 HIS 0.014 0.001 HIS G1151 PHE 0.026 0.002 PHE P 65 TYR 0.021 0.002 TYR N 98 ARG 0.019 0.000 ARG J 48 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 3969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 619 time to evaluate : 4.638 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: 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: symmetry clash revert: symmetry clash REVERT: A 44 CYS cc_start: 0.8585 (m) cc_final: 0.8248 (m) REVERT: A 100 SER cc_start: 0.8815 (m) cc_final: 0.8267 (t) REVERT: A 130 ASP cc_start: 0.8668 (m-30) cc_final: 0.8056 (p0) REVERT: A 278 MET cc_start: 0.8498 (tmm) cc_final: 0.8160 (tmm) REVERT: A 279 GLU cc_start: 0.8305 (mm-30) cc_final: 0.7703 (mm-30) REVERT: B 100 SER cc_start: 0.9198 (m) cc_final: 0.8736 (t) REVERT: B 173 LEU cc_start: 0.8579 (mm) cc_final: 0.8177 (pp) REVERT: B 309 ASP cc_start: 0.7902 (p0) cc_final: 0.7513 (p0) REVERT: B 361 ILE cc_start: 0.9507 (mt) cc_final: 0.9020 (tt) REVERT: C 44 CYS cc_start: 0.8087 (m) cc_final: 0.6856 (t) REVERT: C 101 GLU cc_start: 0.7867 (tt0) cc_final: 0.7033 (tm-30) REVERT: C 139 MET cc_start: 0.8668 (mmm) cc_final: 0.8328 (mmp) REVERT: C 159 LEU cc_start: 0.8950 (mp) cc_final: 0.8711 (mt) REVERT: C 179 GLU cc_start: 0.8465 (pm20) cc_final: 0.7091 (tp30) REVERT: C 197 ASN cc_start: 0.9429 (p0) cc_final: 0.8964 (p0) REVERT: C 261 MET cc_start: 0.7799 (mmt) cc_final: 0.7473 (mmt) REVERT: D 46 LEU cc_start: 0.9192 (tp) cc_final: 0.8908 (tp) REVERT: D 113 MET cc_start: 0.8927 (ptt) cc_final: 0.8575 (ptt) REVERT: D 179 ASP cc_start: 0.8388 (m-30) cc_final: 0.8095 (m-30) REVERT: D 181 MET cc_start: 0.9362 (mmm) cc_final: 0.8820 (mmt) REVERT: E 217 MET cc_start: 0.6754 (mmm) cc_final: 0.6014 (tpp) REVERT: E 325 MET cc_start: 0.8729 (mtp) cc_final: 0.8525 (mtt) REVERT: F 113 MET cc_start: 0.7341 (pmm) cc_final: 0.7036 (pmm) REVERT: F 138 MET cc_start: 0.8391 (ttp) cc_final: 0.8001 (ptp) REVERT: F 162 ILE cc_start: 0.7934 (pt) cc_final: 0.7537 (pt) REVERT: F 173 MET cc_start: 0.8320 (mtm) cc_final: 0.7710 (mpp) REVERT: F 190 ASP cc_start: 0.8017 (m-30) cc_final: 0.7500 (m-30) REVERT: G 1014 LEU cc_start: 0.9104 (tp) cc_final: 0.8867 (tp) REVERT: G 1099 MET cc_start: 0.7659 (mtt) cc_final: 0.7446 (mtt) REVERT: G 1143 MET cc_start: 0.8980 (mmp) cc_final: 0.8438 (mmp) REVERT: G 1171 ASP cc_start: 0.8563 (t70) cc_final: 0.8168 (t0) REVERT: G 1346 MET cc_start: 0.8010 (mmm) cc_final: 0.7690 (mmt) REVERT: G 1491 MET cc_start: 0.8874 (mmp) cc_final: 0.8613 (mmp) REVERT: G 1496 MET cc_start: 0.8314 (mtp) cc_final: 0.7912 (mtp) REVERT: G 1585 MET cc_start: 0.9400 (tpp) cc_final: 0.9124 (tpp) REVERT: G 1684 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8250 (mt-10) REVERT: G 1694 GLU cc_start: 0.9231 (tt0) cc_final: 0.8917 (tm-30) REVERT: H 474 PHE cc_start: 0.8725 (m-80) cc_final: 0.8413 (m-80) REVERT: I 169 TYR cc_start: 0.8241 (m-10) cc_final: 0.8032 (m-10) REVERT: J 168 SER cc_start: 0.9508 (m) cc_final: 0.9099 (p) REVERT: J 284 TYR cc_start: 0.8795 (t80) cc_final: 0.8137 (t80) REVERT: J 639 VAL cc_start: 0.9638 (t) cc_final: 0.9398 (t) REVERT: M 67 PHE cc_start: 0.8641 (t80) cc_final: 0.8356 (t80) REVERT: N 50 ILE cc_start: 0.8840 (mm) cc_final: 0.8463 (mm) REVERT: N 53 GLU cc_start: 0.9093 (mp0) cc_final: 0.8636 (mp0) REVERT: N 59 LYS cc_start: 0.9553 (ptmt) cc_final: 0.9276 (ptmm) REVERT: N 63 GLU cc_start: 0.9409 (pt0) cc_final: 0.8953 (pt0) REVERT: N 84 MET cc_start: 0.8741 (tpt) cc_final: 0.8530 (tpp) REVERT: N 92 ARG cc_start: 0.8575 (ptm-80) cc_final: 0.8138 (ttp80) REVERT: O 25 PHE cc_start: 0.9446 (m-80) cc_final: 0.8958 (m-10) REVERT: O 78 ILE cc_start: 0.9657 (mm) cc_final: 0.9290 (tp) REVERT: O 84 GLN cc_start: 0.9329 (tm130) cc_final: 0.7439 (tm-30) REVERT: O 115 LEU cc_start: 0.9327 (mp) cc_final: 0.9046 (mt) REVERT: Q 61 LEU cc_start: 0.8850 (mp) cc_final: 0.8475 (mt) REVERT: Q 73 GLU cc_start: 0.8878 (tp30) cc_final: 0.8670 (tp30) REVERT: Q 90 MET cc_start: 0.9297 (mmp) cc_final: 0.8979 (mmm) REVERT: Q 97 GLU cc_start: 0.9342 (mt-10) cc_final: 0.8582 (pt0) REVERT: R 39 ARG cc_start: 0.9019 (mmt-90) cc_final: 0.8622 (mmt-90) REVERT: R 55 ARG cc_start: 0.8953 (mtt90) cc_final: 0.8337 (mmt90) REVERT: R 84 MET cc_start: 0.9047 (mmm) cc_final: 0.8808 (tpp) REVERT: S 89 ASN cc_start: 0.8293 (m-40) cc_final: 0.7911 (t0) REVERT: S 92 GLU cc_start: 0.8136 (pm20) cc_final: 0.7861 (pm20) REVERT: T 108 LYS cc_start: 0.8740 (ttpt) cc_final: 0.8498 (mmtm) REVERT: T 113 GLU cc_start: 0.8568 (mm-30) cc_final: 0.8182 (mt-10) outliers start: 1 outliers final: 0 residues processed: 620 average time/residue: 0.5389 time to fit residues: 553.2612 Evaluate side-chains 456 residues out of total 3969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 456 time to evaluate : 4.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 397 optimal weight: 10.0000 chunk 271 optimal weight: 8.9990 chunk 6 optimal weight: 5.9990 chunk 355 optimal weight: 0.4980 chunk 197 optimal weight: 1.9990 chunk 407 optimal weight: 10.0000 chunk 330 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 243 optimal weight: 8.9990 chunk 428 optimal weight: 3.9990 chunk 120 optimal weight: 0.4980 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 281 ASN ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 381 GLN C 43 GLN ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 250 ASN D 452 ASN E 92 GLN F 368 GLN ** G 992 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1364 ASN ** G1383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1697 GLN I 19 GLN ** J 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 762 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 766 ASN O 24 GLN P 47 GLN ** S 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 63 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.4667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 44795 Z= 0.260 Angle : 0.639 10.925 61826 Z= 0.336 Chirality : 0.042 0.243 7045 Planarity : 0.004 0.137 6957 Dihedral : 21.136 178.939 8508 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.36 % Favored : 93.60 % Rotamer: Outliers : 0.03 % Allowed : 2.14 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.12), residues: 4686 helix: 0.19 (0.11), residues: 2106 sheet: -1.48 (0.20), residues: 629 loop : -1.77 (0.14), residues: 1951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 129 HIS 0.010 0.001 HIS G1151 PHE 0.018 0.002 PHE P 65 TYR 0.027 0.002 TYR D 400 ARG 0.026 0.001 ARG O 88 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 3969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 581 time to evaluate : 4.665 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: 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: symmetry clash revert: symmetry clash REVERT: A 44 CYS cc_start: 0.8549 (m) cc_final: 0.8209 (m) REVERT: A 100 SER cc_start: 0.8865 (m) cc_final: 0.8360 (t) REVERT: A 130 ASP cc_start: 0.8635 (m-30) cc_final: 0.8030 (p0) REVERT: A 278 MET cc_start: 0.8453 (tmm) cc_final: 0.8191 (tmm) REVERT: A 359 LEU cc_start: 0.8906 (mm) cc_final: 0.8702 (mm) REVERT: B 100 SER cc_start: 0.9160 (m) cc_final: 0.8802 (t) REVERT: B 361 ILE cc_start: 0.9513 (mt) cc_final: 0.9027 (tt) REVERT: C 44 CYS cc_start: 0.7759 (m) cc_final: 0.6738 (t) REVERT: C 101 GLU cc_start: 0.7898 (tt0) cc_final: 0.7067 (tm-30) REVERT: C 159 LEU cc_start: 0.9086 (mp) cc_final: 0.8793 (tp) REVERT: C 197 ASN cc_start: 0.9427 (p0) cc_final: 0.8969 (p0) REVERT: C 261 MET cc_start: 0.8338 (mmt) cc_final: 0.7861 (mmt) REVERT: D 46 LEU cc_start: 0.9132 (tp) cc_final: 0.8814 (tp) REVERT: D 113 MET cc_start: 0.8954 (ptt) cc_final: 0.8559 (ptt) REVERT: D 179 ASP cc_start: 0.8346 (m-30) cc_final: 0.8064 (m-30) REVERT: D 181 MET cc_start: 0.9184 (mmm) cc_final: 0.8802 (mmm) REVERT: D 247 ASP cc_start: 0.8329 (m-30) cc_final: 0.8068 (m-30) REVERT: D 301 HIS cc_start: 0.9015 (p90) cc_final: 0.8681 (p90) REVERT: E 217 MET cc_start: 0.6845 (mmm) cc_final: 0.6050 (tpp) REVERT: F 138 MET cc_start: 0.8376 (ttp) cc_final: 0.8018 (ptp) REVERT: F 173 MET cc_start: 0.8124 (mtm) cc_final: 0.7763 (mpp) REVERT: F 190 ASP cc_start: 0.7962 (m-30) cc_final: 0.7339 (m-30) REVERT: F 202 THR cc_start: 0.9300 (t) cc_final: 0.9003 (p) REVERT: G 1104 MET cc_start: 0.8217 (ttm) cc_final: 0.7991 (ttm) REVERT: G 1346 MET cc_start: 0.8026 (mmm) cc_final: 0.7670 (mmt) REVERT: G 1496 MET cc_start: 0.8315 (mtp) cc_final: 0.7879 (mtp) REVERT: G 1585 MET cc_start: 0.9414 (tpp) cc_final: 0.9155 (tpp) REVERT: G 1684 GLU cc_start: 0.8696 (mt-10) cc_final: 0.8266 (mt-10) REVERT: H 447 MET cc_start: 0.9050 (mmp) cc_final: 0.8629 (mmp) REVERT: I 169 TYR cc_start: 0.8193 (m-10) cc_final: 0.7958 (m-10) REVERT: J 168 SER cc_start: 0.9521 (m) cc_final: 0.9170 (p) REVERT: M 50 GLU cc_start: 0.9158 (mp0) cc_final: 0.8841 (mp0) REVERT: M 67 PHE cc_start: 0.8572 (t80) cc_final: 0.8192 (t80) REVERT: N 50 ILE cc_start: 0.8881 (mm) cc_final: 0.8391 (mm) REVERT: N 53 GLU cc_start: 0.9137 (mp0) cc_final: 0.8495 (mp0) REVERT: N 59 LYS cc_start: 0.9558 (ptmt) cc_final: 0.9258 (ptmm) REVERT: N 63 GLU cc_start: 0.9373 (pt0) cc_final: 0.8889 (pt0) REVERT: N 84 MET cc_start: 0.8781 (tpt) cc_final: 0.8487 (tpp) REVERT: N 92 ARG cc_start: 0.8627 (ptm-80) cc_final: 0.8156 (ttp80) REVERT: N 98 TYR cc_start: 0.7878 (m-80) cc_final: 0.7537 (m-80) REVERT: O 25 PHE cc_start: 0.9512 (m-80) cc_final: 0.8981 (m-10) REVERT: O 38 ASN cc_start: 0.8325 (m110) cc_final: 0.7810 (m-40) REVERT: P 40 TYR cc_start: 0.8872 (m-80) cc_final: 0.8408 (m-80) REVERT: Q 61 LEU cc_start: 0.8856 (mp) cc_final: 0.8316 (mt) REVERT: Q 73 GLU cc_start: 0.8886 (tp30) cc_final: 0.8657 (tp30) REVERT: Q 90 MET cc_start: 0.9297 (mmp) cc_final: 0.8943 (mmm) REVERT: Q 97 GLU cc_start: 0.9370 (mt-10) cc_final: 0.8701 (pt0) REVERT: R 39 ARG cc_start: 0.8986 (mmt-90) cc_final: 0.8572 (mmt-90) REVERT: R 49 LEU cc_start: 0.8952 (mp) cc_final: 0.8749 (mm) REVERT: R 55 ARG cc_start: 0.8972 (mtt90) cc_final: 0.8367 (mmt90) REVERT: R 84 MET cc_start: 0.9078 (mmm) cc_final: 0.8790 (tpp) REVERT: R 88 TYR cc_start: 0.8732 (m-10) cc_final: 0.8509 (m-80) REVERT: R 97 LEU cc_start: 0.9214 (tt) cc_final: 0.8669 (mp) REVERT: S 89 ASN cc_start: 0.8353 (m-40) cc_final: 0.8037 (t0) REVERT: S 92 GLU cc_start: 0.8069 (pm20) cc_final: 0.7577 (mp0) REVERT: T 108 LYS cc_start: 0.8896 (ttpt) cc_final: 0.8639 (mmtm) REVERT: T 113 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8269 (mt-10) outliers start: 1 outliers final: 0 residues processed: 582 average time/residue: 0.5249 time to fit residues: 513.7300 Evaluate side-chains 448 residues out of total 3969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 448 time to evaluate : 4.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 160 optimal weight: 4.9990 chunk 430 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 280 optimal weight: 10.0000 chunk 117 optimal weight: 7.9990 chunk 477 optimal weight: 5.9990 chunk 396 optimal weight: 10.0000 chunk 221 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 158 optimal weight: 4.9990 chunk 250 optimal weight: 2.9990 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 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 250 ASN F 24 HIS F 250 ASN ** G 992 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 19 GLN ** I 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 762 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 766 ASN P 109 HIS ** S 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 63 ASN ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.5140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 44795 Z= 0.345 Angle : 0.695 9.889 61826 Z= 0.365 Chirality : 0.043 0.212 7045 Planarity : 0.005 0.111 6957 Dihedral : 21.235 178.369 8508 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.96 % Favored : 93.00 % Rotamer: Outliers : 0.03 % Allowed : 2.39 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.12), residues: 4686 helix: 0.12 (0.11), residues: 2112 sheet: -1.50 (0.20), residues: 635 loop : -1.89 (0.14), residues: 1939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP J 129 HIS 0.009 0.001 HIS D 343 PHE 0.019 0.002 PHE H 474 TYR 0.033 0.002 TYR G1591 ARG 0.012 0.001 ARG O 88 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 3969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 562 time to evaluate : 4.292 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 CYS cc_start: 0.8494 (m) cc_final: 0.8251 (m) REVERT: A 130 ASP cc_start: 0.8583 (m-30) cc_final: 0.7997 (p0) REVERT: A 278 MET cc_start: 0.8607 (tmm) cc_final: 0.8403 (tmm) REVERT: B 100 SER cc_start: 0.9180 (m) cc_final: 0.8861 (t) REVERT: C 44 CYS cc_start: 0.8020 (m) cc_final: 0.7179 (t) REVERT: C 101 GLU cc_start: 0.8006 (tt0) cc_final: 0.7143 (tm-30) REVERT: C 139 MET cc_start: 0.8851 (mmm) cc_final: 0.8569 (mmp) REVERT: C 159 LEU cc_start: 0.9103 (mp) cc_final: 0.8757 (tp) REVERT: C 197 ASN cc_start: 0.9448 (p0) cc_final: 0.9017 (p0) REVERT: C 261 MET cc_start: 0.8245 (mmt) cc_final: 0.7931 (mmt) REVERT: C 311 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7849 (tm-30) REVERT: D 46 LEU cc_start: 0.9143 (tp) cc_final: 0.8795 (tp) REVERT: D 181 MET cc_start: 0.9199 (mmm) cc_final: 0.8811 (mmm) REVERT: D 247 ASP cc_start: 0.8414 (m-30) cc_final: 0.8056 (m-30) REVERT: D 301 HIS cc_start: 0.9032 (p90) cc_final: 0.8636 (p90) REVERT: E 164 THR cc_start: 0.8181 (p) cc_final: 0.7588 (p) REVERT: E 217 MET cc_start: 0.6981 (mmm) cc_final: 0.6173 (tpp) REVERT: E 231 LEU cc_start: 0.9027 (tt) cc_final: 0.8806 (tt) REVERT: F 138 MET cc_start: 0.8349 (ttp) cc_final: 0.7795 (ptp) REVERT: F 171 TYR cc_start: 0.8238 (m-80) cc_final: 0.7861 (m-80) REVERT: F 173 MET cc_start: 0.8236 (mtm) cc_final: 0.7744 (mpp) REVERT: F 190 ASP cc_start: 0.8248 (m-30) cc_final: 0.7860 (m-30) REVERT: F 202 THR cc_start: 0.9271 (t) cc_final: 0.9004 (p) REVERT: G 1066 TRP cc_start: 0.7710 (t-100) cc_final: 0.7311 (t-100) REVERT: G 1092 ASP cc_start: 0.8382 (t0) cc_final: 0.8165 (m-30) REVERT: G 1143 MET cc_start: 0.9072 (mmp) cc_final: 0.8359 (mmm) REVERT: G 1198 MET cc_start: 0.8541 (tmm) cc_final: 0.8334 (tmm) REVERT: G 1272 ASP cc_start: 0.8577 (m-30) cc_final: 0.8290 (m-30) REVERT: G 1346 MET cc_start: 0.7929 (mmm) cc_final: 0.7602 (mmt) REVERT: G 1496 MET cc_start: 0.8358 (mtp) cc_final: 0.7940 (mtp) REVERT: G 1578 MET cc_start: 0.8806 (mtm) cc_final: 0.8468 (mtp) REVERT: G 1585 MET cc_start: 0.9410 (tpp) cc_final: 0.9173 (tpp) REVERT: G 1684 GLU cc_start: 0.8603 (mt-10) cc_final: 0.8316 (mt-10) REVERT: H 447 MET cc_start: 0.9087 (mmp) cc_final: 0.8743 (mmp) REVERT: I 188 TYR cc_start: 0.9115 (p90) cc_final: 0.8854 (p90) REVERT: J 168 SER cc_start: 0.9511 (m) cc_final: 0.9197 (p) REVERT: J 768 PHE cc_start: 0.7329 (t80) cc_final: 0.7115 (t80) REVERT: M 67 PHE cc_start: 0.8657 (t80) cc_final: 0.8226 (t80) REVERT: N 50 ILE cc_start: 0.8789 (mm) cc_final: 0.8259 (mm) REVERT: N 53 GLU cc_start: 0.9121 (mp0) cc_final: 0.8626 (mp0) REVERT: N 58 LEU cc_start: 0.9793 (tp) cc_final: 0.9592 (tp) REVERT: N 59 LYS cc_start: 0.9578 (ptmt) cc_final: 0.9230 (ptmm) REVERT: N 63 GLU cc_start: 0.9375 (pt0) cc_final: 0.8865 (pt0) REVERT: N 84 MET cc_start: 0.8847 (tpt) cc_final: 0.8645 (tpp) REVERT: N 92 ARG cc_start: 0.8819 (ptm-80) cc_final: 0.8477 (ttp80) REVERT: N 98 TYR cc_start: 0.7716 (m-80) cc_final: 0.7396 (m-80) REVERT: O 25 PHE cc_start: 0.9533 (m-80) cc_final: 0.8852 (m-10) REVERT: O 38 ASN cc_start: 0.8340 (m110) cc_final: 0.7869 (m-40) REVERT: O 78 ILE cc_start: 0.9652 (mm) cc_final: 0.9426 (tp) REVERT: P 40 TYR cc_start: 0.9079 (m-80) cc_final: 0.8610 (m-80) REVERT: Q 61 LEU cc_start: 0.8941 (mp) cc_final: 0.8451 (mt) REVERT: Q 77 ASP cc_start: 0.8832 (t70) cc_final: 0.8606 (t70) REVERT: Q 90 MET cc_start: 0.9318 (mmp) cc_final: 0.8988 (mmm) REVERT: Q 97 GLU cc_start: 0.9364 (mt-10) cc_final: 0.8716 (pt0) REVERT: R 49 LEU cc_start: 0.9102 (mp) cc_final: 0.8828 (tp) REVERT: R 55 ARG cc_start: 0.9029 (mtt90) cc_final: 0.8420 (mmt90) REVERT: R 75 HIS cc_start: 0.9148 (t-90) cc_final: 0.8915 (t70) REVERT: R 84 MET cc_start: 0.9122 (mmm) cc_final: 0.8815 (tpp) REVERT: S 89 ASN cc_start: 0.8488 (m-40) cc_final: 0.8186 (t0) REVERT: S 92 GLU cc_start: 0.8136 (pm20) cc_final: 0.7637 (mp0) REVERT: T 108 LYS cc_start: 0.9126 (ttpt) cc_final: 0.8904 (mmtm) outliers start: 1 outliers final: 0 residues processed: 563 average time/residue: 0.5414 time to fit residues: 511.2627 Evaluate side-chains 421 residues out of total 3969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 421 time to evaluate : 5.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 460 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 272 optimal weight: 20.0000 chunk 349 optimal weight: 4.9990 chunk 270 optimal weight: 20.0000 chunk 402 optimal weight: 10.0000 chunk 266 optimal weight: 7.9990 chunk 476 optimal weight: 4.9990 chunk 297 optimal weight: 0.0670 chunk 290 optimal weight: 0.3980 chunk 219 optimal weight: 7.9990 overall best weight: 3.2924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 381 GLN ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN ** G 992 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 19 GLN ** I 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 762 HIS J 766 ASN ** S 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 63 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.5361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 44795 Z= 0.302 Angle : 0.660 10.370 61826 Z= 0.347 Chirality : 0.042 0.245 7045 Planarity : 0.004 0.064 6957 Dihedral : 21.250 178.044 8508 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.53 % Favored : 93.43 % Rotamer: Outliers : 0.03 % Allowed : 1.73 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.12), residues: 4686 helix: 0.26 (0.11), residues: 2113 sheet: -1.43 (0.20), residues: 632 loop : -1.90 (0.14), residues: 1941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP J 129 HIS 0.007 0.001 HIS G1151 PHE 0.032 0.002 PHE B 355 TYR 0.024 0.002 TYR B 178 ARG 0.009 0.001 ARG Q 128 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 3969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 548 time to evaluate : 4.549 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 CYS cc_start: 0.8425 (m) cc_final: 0.8149 (m) REVERT: A 130 ASP cc_start: 0.8540 (m-30) cc_final: 0.8054 (p0) REVERT: A 273 THR cc_start: 0.9208 (p) cc_final: 0.8891 (m) REVERT: B 100 SER cc_start: 0.9203 (m) cc_final: 0.8810 (t) REVERT: B 287 TYR cc_start: 0.8386 (m-10) cc_final: 0.7876 (m-10) REVERT: C 44 CYS cc_start: 0.8107 (m) cc_final: 0.6696 (t) REVERT: C 159 LEU cc_start: 0.9124 (mp) cc_final: 0.8739 (tp) REVERT: C 197 ASN cc_start: 0.9443 (p0) cc_final: 0.9032 (p0) REVERT: C 261 MET cc_start: 0.8039 (mmt) cc_final: 0.7754 (mmt) REVERT: C 311 GLU cc_start: 0.8139 (tm-30) cc_final: 0.7749 (tm-30) REVERT: D 46 LEU cc_start: 0.9100 (tp) cc_final: 0.8755 (tp) REVERT: D 113 MET cc_start: 0.8953 (ptt) cc_final: 0.8588 (ptt) REVERT: D 181 MET cc_start: 0.9184 (mmm) cc_final: 0.8784 (mmm) REVERT: D 247 ASP cc_start: 0.8402 (m-30) cc_final: 0.8051 (m-30) REVERT: D 301 HIS cc_start: 0.9038 (p90) cc_final: 0.8653 (p90) REVERT: E 88 MET cc_start: 0.8836 (tpp) cc_final: 0.8549 (tpt) REVERT: E 164 THR cc_start: 0.8033 (p) cc_final: 0.7638 (p) REVERT: E 217 MET cc_start: 0.6909 (mmm) cc_final: 0.6093 (tpp) REVERT: E 325 MET cc_start: 0.8724 (mtp) cc_final: 0.8515 (mtt) REVERT: F 173 MET cc_start: 0.8078 (mtm) cc_final: 0.7771 (mpp) REVERT: F 190 ASP cc_start: 0.8334 (m-30) cc_final: 0.7877 (m-30) REVERT: G 1050 LEU cc_start: 0.9593 (tp) cc_final: 0.9313 (tt) REVERT: G 1066 TRP cc_start: 0.7638 (t-100) cc_final: 0.7432 (t-100) REVERT: G 1088 LEU cc_start: 0.9494 (mt) cc_final: 0.9241 (mt) REVERT: G 1104 MET cc_start: 0.8219 (ttm) cc_final: 0.7971 (mtt) REVERT: G 1262 MET cc_start: 0.8931 (mmm) cc_final: 0.8695 (mmm) REVERT: G 1272 ASP cc_start: 0.8623 (m-30) cc_final: 0.8276 (m-30) REVERT: G 1346 MET cc_start: 0.7857 (mmm) cc_final: 0.7494 (mmt) REVERT: G 1496 MET cc_start: 0.8259 (mtp) cc_final: 0.7894 (mtp) REVERT: G 1545 MET cc_start: 0.7947 (ppp) cc_final: 0.7619 (ppp) REVERT: G 1659 MET cc_start: 0.9523 (mtp) cc_final: 0.9311 (mtp) REVERT: G 1684 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8204 (mt-10) REVERT: H 447 MET cc_start: 0.9097 (mmp) cc_final: 0.8801 (mmp) REVERT: H 474 PHE cc_start: 0.8807 (m-80) cc_final: 0.8582 (m-10) REVERT: J 168 SER cc_start: 0.9551 (m) cc_final: 0.9207 (p) REVERT: J 768 PHE cc_start: 0.7320 (t80) cc_final: 0.6990 (t80) REVERT: M 50 GLU cc_start: 0.9324 (mp0) cc_final: 0.8943 (mp0) REVERT: M 67 PHE cc_start: 0.8647 (t80) cc_final: 0.8228 (t80) REVERT: N 50 ILE cc_start: 0.8780 (mm) cc_final: 0.8205 (mm) REVERT: N 53 GLU cc_start: 0.9157 (mp0) cc_final: 0.8517 (mp0) REVERT: N 59 LYS cc_start: 0.9587 (ptmt) cc_final: 0.9244 (ptmm) REVERT: N 63 GLU cc_start: 0.9331 (pt0) cc_final: 0.8878 (pt0) REVERT: N 84 MET cc_start: 0.8898 (tpt) cc_final: 0.8622 (tpt) REVERT: N 92 ARG cc_start: 0.8820 (ptm-80) cc_final: 0.8379 (ttp80) REVERT: O 25 PHE cc_start: 0.9493 (m-80) cc_final: 0.8835 (m-10) REVERT: O 38 ASN cc_start: 0.8366 (m110) cc_final: 0.7886 (m-40) REVERT: O 78 ILE cc_start: 0.9636 (mm) cc_final: 0.9426 (tp) REVERT: P 40 TYR cc_start: 0.9006 (m-80) cc_final: 0.8713 (m-80) REVERT: P 101 LEU cc_start: 0.9239 (mm) cc_final: 0.8955 (mm) REVERT: Q 61 LEU cc_start: 0.8964 (mp) cc_final: 0.8626 (pp) REVERT: Q 90 MET cc_start: 0.9318 (mmp) cc_final: 0.8979 (mmm) REVERT: Q 97 GLU cc_start: 0.9373 (mt-10) cc_final: 0.9162 (pt0) REVERT: Q 103 LEU cc_start: 0.9384 (pp) cc_final: 0.9183 (pp) REVERT: R 49 LEU cc_start: 0.8996 (mp) cc_final: 0.8773 (tp) REVERT: R 55 ARG cc_start: 0.9039 (mtt90) cc_final: 0.8450 (mmt90) REVERT: R 84 MET cc_start: 0.9084 (mmm) cc_final: 0.8693 (tpp) REVERT: S 89 ASN cc_start: 0.8521 (m-40) cc_final: 0.8246 (t0) REVERT: S 92 GLU cc_start: 0.8185 (pm20) cc_final: 0.7688 (mp0) REVERT: S 99 LYS cc_start: 0.8982 (mttm) cc_final: 0.8756 (mmmt) outliers start: 1 outliers final: 0 residues processed: 549 average time/residue: 0.5085 time to fit residues: 475.5412 Evaluate side-chains 402 residues out of total 3969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 402 time to evaluate : 5.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 294 optimal weight: 9.9990 chunk 190 optimal weight: 0.7980 chunk 284 optimal weight: 7.9990 chunk 143 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 302 optimal weight: 5.9990 chunk 324 optimal weight: 8.9990 chunk 235 optimal weight: 0.9980 chunk 44 optimal weight: 10.0000 chunk 374 optimal weight: 20.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 289 ASN ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN F 250 ASN ** G 992 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 19 GLN ** I 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 631 HIS J 766 ASN S 31 HIS T 63 ASN T 67 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.5484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 44795 Z= 0.230 Angle : 0.626 9.553 61826 Z= 0.328 Chirality : 0.042 0.260 7045 Planarity : 0.004 0.043 6957 Dihedral : 21.216 177.963 8508 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.87 % Favored : 94.09 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.12), residues: 4686 helix: 0.43 (0.12), residues: 2098 sheet: -1.39 (0.20), residues: 642 loop : -1.80 (0.14), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP J 129 HIS 0.019 0.001 HIS G1151 PHE 0.021 0.001 PHE Q 67 TYR 0.022 0.002 TYR A 193 ARG 0.010 0.000 ARG M 128 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 3969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 548 time to evaluate : 4.332 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: 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: symmetry clash revert: symmetry clash REVERT: A 130 ASP cc_start: 0.8565 (m-30) cc_final: 0.8072 (p0) REVERT: A 278 MET cc_start: 0.8048 (tmm) cc_final: 0.7599 (tmm) REVERT: A 279 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7716 (mm-30) REVERT: B 100 SER cc_start: 0.9188 (m) cc_final: 0.8795 (t) REVERT: B 371 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7858 (mp0) REVERT: C 101 GLU cc_start: 0.8072 (tt0) cc_final: 0.7124 (tm-30) REVERT: C 159 LEU cc_start: 0.9107 (mp) cc_final: 0.8813 (tp) REVERT: C 197 ASN cc_start: 0.9430 (p0) cc_final: 0.8998 (p0) REVERT: C 311 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7666 (tm-30) REVERT: D 46 LEU cc_start: 0.9119 (tp) cc_final: 0.8739 (tp) REVERT: D 113 MET cc_start: 0.9028 (ptt) cc_final: 0.8551 (ptt) REVERT: D 181 MET cc_start: 0.9200 (mmm) cc_final: 0.8842 (mmm) REVERT: D 301 HIS cc_start: 0.9059 (p90) cc_final: 0.8694 (p90) REVERT: E 88 MET cc_start: 0.8746 (tpp) cc_final: 0.8502 (tpt) REVERT: E 164 THR cc_start: 0.8058 (p) cc_final: 0.7835 (p) REVERT: E 217 MET cc_start: 0.6805 (mmm) cc_final: 0.6018 (tpp) REVERT: E 226 CYS cc_start: 0.8823 (t) cc_final: 0.8598 (t) REVERT: F 173 MET cc_start: 0.8029 (mtm) cc_final: 0.7778 (mpp) REVERT: F 190 ASP cc_start: 0.8429 (m-30) cc_final: 0.8015 (m-30) REVERT: G 1050 LEU cc_start: 0.9589 (tp) cc_final: 0.9305 (tt) REVERT: G 1104 MET cc_start: 0.8238 (ttm) cc_final: 0.7993 (mtt) REVERT: G 1240 MET cc_start: 0.3830 (mtt) cc_final: 0.3213 (mtt) REVERT: G 1262 MET cc_start: 0.8876 (mmm) cc_final: 0.8554 (mmt) REVERT: G 1272 ASP cc_start: 0.8623 (m-30) cc_final: 0.8265 (m-30) REVERT: G 1307 THR cc_start: 0.8998 (m) cc_final: 0.8779 (m) REVERT: G 1346 MET cc_start: 0.7946 (mmm) cc_final: 0.7711 (mmt) REVERT: G 1496 MET cc_start: 0.8228 (mtp) cc_final: 0.7829 (mtp) REVERT: G 1581 MET cc_start: 0.8712 (tpp) cc_final: 0.8217 (tmm) REVERT: G 1659 MET cc_start: 0.9512 (mtp) cc_final: 0.9308 (mtm) REVERT: G 1684 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8166 (mt-10) REVERT: H 447 MET cc_start: 0.9124 (mmp) cc_final: 0.8736 (mmp) REVERT: H 474 PHE cc_start: 0.8780 (m-80) cc_final: 0.8558 (m-10) REVERT: J 168 SER cc_start: 0.9518 (m) cc_final: 0.9205 (p) REVERT: J 768 PHE cc_start: 0.7400 (t80) cc_final: 0.7037 (t80) REVERT: M 67 PHE cc_start: 0.8629 (t80) cc_final: 0.8344 (t80) REVERT: N 50 ILE cc_start: 0.8716 (mm) cc_final: 0.8183 (mm) REVERT: N 53 GLU cc_start: 0.9130 (mp0) cc_final: 0.8545 (mp0) REVERT: N 59 LYS cc_start: 0.9588 (ptmt) cc_final: 0.9258 (ptmm) REVERT: N 61 PHE cc_start: 0.9185 (t80) cc_final: 0.8968 (t80) REVERT: N 63 GLU cc_start: 0.9309 (pt0) cc_final: 0.8839 (pt0) REVERT: N 84 MET cc_start: 0.8790 (tpt) cc_final: 0.8554 (tpt) REVERT: N 92 ARG cc_start: 0.8763 (ptm-80) cc_final: 0.8295 (ttp80) REVERT: O 25 PHE cc_start: 0.9427 (m-80) cc_final: 0.8810 (m-80) REVERT: O 38 ASN cc_start: 0.8320 (m110) cc_final: 0.7855 (m-40) REVERT: O 61 GLU cc_start: 0.8895 (mp0) cc_final: 0.8654 (mp0) REVERT: O 73 ASN cc_start: 0.9099 (t0) cc_final: 0.8780 (t0) REVERT: O 78 ILE cc_start: 0.9642 (mm) cc_final: 0.9345 (tp) REVERT: P 40 TYR cc_start: 0.8962 (m-80) cc_final: 0.8661 (m-80) REVERT: Q 60 LEU cc_start: 0.9359 (mp) cc_final: 0.9153 (mt) REVERT: Q 61 LEU cc_start: 0.8881 (mp) cc_final: 0.8570 (pp) REVERT: Q 90 MET cc_start: 0.9301 (mmp) cc_final: 0.8954 (mmm) REVERT: Q 97 GLU cc_start: 0.9309 (mt-10) cc_final: 0.9090 (pt0) REVERT: Q 122 LYS cc_start: 0.9213 (mppt) cc_final: 0.8909 (ttpt) REVERT: R 55 ARG cc_start: 0.9054 (mtt90) cc_final: 0.8468 (mmt90) REVERT: R 84 MET cc_start: 0.9051 (mmm) cc_final: 0.8660 (tpp) REVERT: S 89 ASN cc_start: 0.8559 (m-40) cc_final: 0.8248 (t0) REVERT: S 92 GLU cc_start: 0.8176 (pm20) cc_final: 0.7665 (mp0) REVERT: T 76 GLU cc_start: 0.8878 (mm-30) cc_final: 0.8677 (mm-30) outliers start: 0 outliers final: 0 residues processed: 548 average time/residue: 0.5175 time to fit residues: 479.6252 Evaluate side-chains 408 residues out of total 3969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 408 time to evaluate : 4.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 433 optimal weight: 9.9990 chunk 456 optimal weight: 9.9990 chunk 416 optimal weight: 10.0000 chunk 443 optimal weight: 0.7980 chunk 267 optimal weight: 6.9990 chunk 193 optimal weight: 3.9990 chunk 348 optimal weight: 9.9990 chunk 136 optimal weight: 0.8980 chunk 400 optimal weight: 10.0000 chunk 419 optimal weight: 10.0000 chunk 442 optimal weight: 0.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 24 HIS F 250 ASN ** G 992 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1489 ASN ** G1593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 19 GLN ** I 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 766 ASN ** S 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 63 ASN ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.5667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 44795 Z= 0.268 Angle : 0.644 9.468 61826 Z= 0.337 Chirality : 0.042 0.238 7045 Planarity : 0.004 0.058 6957 Dihedral : 21.206 178.351 8508 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.51 % Favored : 93.45 % Rotamer: Outliers : 0.05 % Allowed : 0.64 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.12), residues: 4686 helix: 0.42 (0.12), residues: 2101 sheet: -1.40 (0.20), residues: 655 loop : -1.77 (0.14), residues: 1930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP J 129 HIS 0.018 0.001 HIS G1151 PHE 0.019 0.002 PHE M 104 TYR 0.023 0.002 TYR A 193 ARG 0.014 0.001 ARG N 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 3969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 536 time to evaluate : 4.672 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ASP cc_start: 0.8619 (m-30) cc_final: 0.8085 (p0) REVERT: A 135 GLU cc_start: 0.7596 (tp30) cc_final: 0.7243 (tp30) REVERT: A 279 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7824 (mm-30) REVERT: B 62 MET cc_start: 0.6589 (ppp) cc_final: 0.6211 (ppp) REVERT: B 100 SER cc_start: 0.9196 (m) cc_final: 0.8814 (t) REVERT: B 269 MET cc_start: 0.7812 (mtm) cc_final: 0.7531 (ttp) REVERT: C 101 GLU cc_start: 0.8050 (tt0) cc_final: 0.7091 (tm-30) REVERT: C 159 LEU cc_start: 0.9102 (mp) cc_final: 0.8738 (tp) REVERT: C 197 ASN cc_start: 0.9445 (p0) cc_final: 0.9028 (p0) REVERT: D 46 LEU cc_start: 0.9125 (tp) cc_final: 0.8775 (tp) REVERT: D 113 MET cc_start: 0.9003 (ptt) cc_final: 0.8590 (ptt) REVERT: D 301 HIS cc_start: 0.9036 (p90) cc_final: 0.8616 (p90) REVERT: E 88 MET cc_start: 0.8752 (tpp) cc_final: 0.8445 (tpt) REVERT: E 164 THR cc_start: 0.8059 (p) cc_final: 0.7736 (p) REVERT: E 217 MET cc_start: 0.6925 (mmm) cc_final: 0.6140 (tpp) REVERT: E 325 MET cc_start: 0.8762 (mtp) cc_final: 0.8536 (mtt) REVERT: F 173 MET cc_start: 0.8044 (mtm) cc_final: 0.7742 (mpp) REVERT: F 190 ASP cc_start: 0.8464 (m-30) cc_final: 0.8123 (m-30) REVERT: G 1014 LEU cc_start: 0.8862 (tp) cc_final: 0.8656 (tp) REVERT: G 1050 LEU cc_start: 0.9610 (tp) cc_final: 0.9400 (tp) REVERT: G 1066 TRP cc_start: 0.7529 (t-100) cc_final: 0.7240 (t-100) REVERT: G 1104 MET cc_start: 0.8293 (ttm) cc_final: 0.7890 (mtt) REVERT: G 1240 MET cc_start: 0.3897 (mtt) cc_final: 0.3266 (mtt) REVERT: G 1262 MET cc_start: 0.8879 (mmm) cc_final: 0.8616 (mmt) REVERT: G 1272 ASP cc_start: 0.8665 (m-30) cc_final: 0.8306 (m-30) REVERT: G 1307 THR cc_start: 0.9026 (m) cc_final: 0.8799 (m) REVERT: G 1346 MET cc_start: 0.7965 (mmm) cc_final: 0.7722 (mmt) REVERT: G 1496 MET cc_start: 0.8211 (mtp) cc_final: 0.7916 (mtp) REVERT: G 1576 PHE cc_start: 0.6961 (t80) cc_final: 0.6457 (t80) REVERT: G 1581 MET cc_start: 0.8805 (tpp) cc_final: 0.7920 (tmm) REVERT: G 1684 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8213 (mt-10) REVERT: H 447 MET cc_start: 0.9124 (mmp) cc_final: 0.8804 (mmp) REVERT: H 474 PHE cc_start: 0.8798 (m-80) cc_final: 0.8577 (m-10) REVERT: J 168 SER cc_start: 0.9555 (m) cc_final: 0.9232 (p) REVERT: M 59 GLU cc_start: 0.8811 (pm20) cc_final: 0.8389 (pm20) REVERT: M 67 PHE cc_start: 0.8646 (t80) cc_final: 0.8230 (t80) REVERT: N 39 ARG cc_start: 0.9042 (tpp80) cc_final: 0.8186 (tpp-160) REVERT: N 50 ILE cc_start: 0.8784 (mm) cc_final: 0.8283 (mm) REVERT: N 53 GLU cc_start: 0.9133 (mp0) cc_final: 0.8512 (mp0) REVERT: N 59 LYS cc_start: 0.9586 (ptmt) cc_final: 0.9228 (ptmm) REVERT: N 63 GLU cc_start: 0.9282 (pt0) cc_final: 0.8812 (pt0) REVERT: N 84 MET cc_start: 0.8776 (tpt) cc_final: 0.8570 (tpt) REVERT: N 92 ARG cc_start: 0.8714 (ptm-80) cc_final: 0.8508 (ttp80) REVERT: O 25 PHE cc_start: 0.9407 (m-80) cc_final: 0.8858 (m-10) REVERT: O 38 ASN cc_start: 0.8323 (m110) cc_final: 0.7864 (m-40) REVERT: O 59 THR cc_start: 0.9600 (p) cc_final: 0.9387 (p) REVERT: O 61 GLU cc_start: 0.9033 (mp0) cc_final: 0.8593 (mp0) REVERT: O 73 ASN cc_start: 0.9094 (t0) cc_final: 0.8787 (t0) REVERT: O 78 ILE cc_start: 0.9681 (mm) cc_final: 0.9370 (tp) REVERT: P 40 TYR cc_start: 0.9014 (m-80) cc_final: 0.8712 (m-80) REVERT: P 69 ILE cc_start: 0.9572 (pt) cc_final: 0.9233 (pt) REVERT: Q 60 LEU cc_start: 0.9376 (mp) cc_final: 0.9165 (mt) REVERT: Q 61 LEU cc_start: 0.8917 (mp) cc_final: 0.8556 (pp) REVERT: Q 90 MET cc_start: 0.9307 (mmp) cc_final: 0.8948 (mmm) REVERT: Q 97 GLU cc_start: 0.9341 (mt-10) cc_final: 0.9010 (pt0) REVERT: Q 122 LYS cc_start: 0.9295 (mppt) cc_final: 0.8984 (pttm) REVERT: R 39 ARG cc_start: 0.8911 (mmt-90) cc_final: 0.8240 (mmt-90) REVERT: R 55 ARG cc_start: 0.9047 (mtt90) cc_final: 0.8455 (mmt90) REVERT: R 84 MET cc_start: 0.9061 (mmm) cc_final: 0.8729 (tpp) REVERT: R 88 TYR cc_start: 0.8728 (m-10) cc_final: 0.8464 (m-80) REVERT: S 89 ASN cc_start: 0.8633 (m-40) cc_final: 0.8410 (t0) REVERT: S 92 GLU cc_start: 0.8085 (pm20) cc_final: 0.7577 (mp0) REVERT: T 113 GLU cc_start: 0.8778 (mm-30) cc_final: 0.8403 (mt-10) outliers start: 2 outliers final: 0 residues processed: 537 average time/residue: 0.5267 time to fit residues: 483.9628 Evaluate side-chains 408 residues out of total 3969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 408 time to evaluate : 4.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 291 optimal weight: 7.9990 chunk 469 optimal weight: 4.9990 chunk 286 optimal weight: 20.0000 chunk 222 optimal weight: 10.0000 chunk 326 optimal weight: 0.9980 chunk 492 optimal weight: 2.9990 chunk 452 optimal weight: 5.9990 chunk 391 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 302 optimal weight: 0.0970 chunk 240 optimal weight: 9.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 ASN ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN F 24 HIS F 232 GLN ** G 992 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1151 HIS ** G1236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1489 ASN I 19 GLN ** I 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 766 ASN ** S 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 63 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.5803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 44795 Z= 0.235 Angle : 0.634 9.787 61826 Z= 0.331 Chirality : 0.042 0.249 7045 Planarity : 0.004 0.051 6957 Dihedral : 21.188 178.449 8508 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.68 % Favored : 94.28 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.12), residues: 4686 helix: 0.45 (0.12), residues: 2098 sheet: -1.43 (0.20), residues: 659 loop : -1.68 (0.14), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP J 129 HIS 0.017 0.001 HIS G1151 PHE 0.033 0.001 PHE B 355 TYR 0.030 0.002 TYR B 406 ARG 0.006 0.000 ARG M 49 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 3969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 541 time to evaluate : 4.829 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 CYS cc_start: 0.8158 (m) cc_final: 0.7852 (m) REVERT: A 130 ASP cc_start: 0.8646 (m-30) cc_final: 0.8070 (p0) REVERT: A 135 GLU cc_start: 0.7587 (tp30) cc_final: 0.7281 (tp30) REVERT: B 100 SER cc_start: 0.9155 (m) cc_final: 0.8722 (t) REVERT: B 269 MET cc_start: 0.7791 (mtm) cc_final: 0.7444 (ttp) REVERT: B 371 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7989 (mp0) REVERT: C 101 GLU cc_start: 0.7983 (tt0) cc_final: 0.7041 (tm-30) REVERT: C 159 LEU cc_start: 0.9115 (mp) cc_final: 0.8767 (tp) REVERT: C 197 ASN cc_start: 0.9459 (p0) cc_final: 0.9049 (p0) REVERT: C 311 GLU cc_start: 0.8054 (tm-30) cc_final: 0.7660 (tm-30) REVERT: D 46 LEU cc_start: 0.9166 (tp) cc_final: 0.8805 (tp) REVERT: D 113 MET cc_start: 0.9023 (ptt) cc_final: 0.8577 (ptt) REVERT: D 181 MET cc_start: 0.9202 (mmm) cc_final: 0.8850 (mmm) REVERT: D 301 HIS cc_start: 0.9062 (p90) cc_final: 0.8643 (p90) REVERT: E 88 MET cc_start: 0.8722 (tpp) cc_final: 0.8410 (tpt) REVERT: E 164 THR cc_start: 0.8173 (p) cc_final: 0.7861 (p) REVERT: E 217 MET cc_start: 0.6850 (mmm) cc_final: 0.6082 (tpp) REVERT: E 226 CYS cc_start: 0.8855 (t) cc_final: 0.8643 (t) REVERT: E 231 LEU cc_start: 0.9060 (tt) cc_final: 0.8858 (tt) REVERT: F 190 ASP cc_start: 0.8480 (m-30) cc_final: 0.8276 (m-30) REVERT: G 1050 LEU cc_start: 0.9598 (tp) cc_final: 0.9397 (tt) REVERT: G 1104 MET cc_start: 0.8217 (ttm) cc_final: 0.7815 (mtt) REVERT: G 1192 MET cc_start: 0.8867 (ptp) cc_final: 0.8661 (ppp) REVERT: G 1240 MET cc_start: 0.3920 (mtt) cc_final: 0.3353 (mtt) REVERT: G 1272 ASP cc_start: 0.8650 (m-30) cc_final: 0.8262 (m-30) REVERT: G 1307 THR cc_start: 0.9058 (m) cc_final: 0.8841 (m) REVERT: G 1346 MET cc_start: 0.7874 (mmm) cc_final: 0.7669 (mmt) REVERT: G 1496 MET cc_start: 0.8177 (mtp) cc_final: 0.7884 (mtp) REVERT: G 1501 PHE cc_start: 0.8299 (m-80) cc_final: 0.7712 (m-10) REVERT: G 1545 MET cc_start: 0.8131 (ppp) cc_final: 0.7470 (ppp) REVERT: G 1581 MET cc_start: 0.8785 (tpp) cc_final: 0.7984 (tmm) REVERT: G 1684 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8216 (mt-10) REVERT: H 447 MET cc_start: 0.9119 (mmp) cc_final: 0.8732 (mmp) REVERT: H 474 PHE cc_start: 0.8771 (m-80) cc_final: 0.8554 (m-10) REVERT: J 168 SER cc_start: 0.9477 (m) cc_final: 0.9083 (p) REVERT: M 51 ILE cc_start: 0.8414 (mm) cc_final: 0.8186 (mm) REVERT: M 54 TYR cc_start: 0.9278 (m-10) cc_final: 0.8982 (m-10) REVERT: M 67 PHE cc_start: 0.8652 (t80) cc_final: 0.8251 (t80) REVERT: N 50 ILE cc_start: 0.8812 (mm) cc_final: 0.8306 (mm) REVERT: N 53 GLU cc_start: 0.9102 (mp0) cc_final: 0.8589 (mp0) REVERT: N 61 PHE cc_start: 0.9155 (t80) cc_final: 0.8925 (t80) REVERT: N 75 HIS cc_start: 0.8754 (t-90) cc_final: 0.8512 (t-90) REVERT: N 84 MET cc_start: 0.8778 (tpt) cc_final: 0.8545 (tpt) REVERT: N 92 ARG cc_start: 0.8697 (ptm-80) cc_final: 0.8237 (ttp80) REVERT: O 25 PHE cc_start: 0.9425 (m-80) cc_final: 0.8931 (m-80) REVERT: O 38 ASN cc_start: 0.8318 (m110) cc_final: 0.7849 (m-40) REVERT: O 61 GLU cc_start: 0.9020 (mp0) cc_final: 0.8479 (mp0) REVERT: O 73 ASN cc_start: 0.9065 (t0) cc_final: 0.8760 (t0) REVERT: O 78 ILE cc_start: 0.9663 (mm) cc_final: 0.9369 (tp) REVERT: P 40 TYR cc_start: 0.8923 (m-80) cc_final: 0.8675 (m-80) REVERT: P 71 GLU cc_start: 0.9025 (tm-30) cc_final: 0.8822 (tp30) REVERT: Q 50 GLU cc_start: 0.9314 (tt0) cc_final: 0.9035 (tt0) REVERT: Q 61 LEU cc_start: 0.8912 (mp) cc_final: 0.8606 (pp) REVERT: Q 90 MET cc_start: 0.9291 (mmp) cc_final: 0.8931 (mmm) REVERT: Q 97 GLU cc_start: 0.9328 (mt-10) cc_final: 0.9053 (mt-10) REVERT: Q 122 LYS cc_start: 0.9304 (mppt) cc_final: 0.8916 (pttm) REVERT: R 39 ARG cc_start: 0.8860 (mmt-90) cc_final: 0.8104 (mmt-90) REVERT: R 49 LEU cc_start: 0.8588 (tp) cc_final: 0.8330 (tp) REVERT: R 55 ARG cc_start: 0.9057 (mtt90) cc_final: 0.8468 (mmt90) REVERT: R 84 MET cc_start: 0.9044 (mmm) cc_final: 0.8754 (tpp) REVERT: R 88 TYR cc_start: 0.8703 (m-10) cc_final: 0.8482 (m-80) REVERT: S 92 GLU cc_start: 0.8067 (pm20) cc_final: 0.7588 (mp0) REVERT: T 51 ASP cc_start: 0.8309 (p0) cc_final: 0.7898 (p0) REVERT: T 113 GLU cc_start: 0.8773 (mm-30) cc_final: 0.8421 (mt-10) outliers start: 0 outliers final: 0 residues processed: 541 average time/residue: 0.5057 time to fit residues: 467.1926 Evaluate side-chains 408 residues out of total 3969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 408 time to evaluate : 4.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 311 optimal weight: 0.9990 chunk 417 optimal weight: 10.0000 chunk 120 optimal weight: 8.9990 chunk 361 optimal weight: 7.9990 chunk 57 optimal weight: 6.9990 chunk 108 optimal weight: 7.9990 chunk 392 optimal weight: 0.5980 chunk 164 optimal weight: 3.9990 chunk 403 optimal weight: 10.0000 chunk 49 optimal weight: 8.9990 chunk 72 optimal weight: 0.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 381 GLN ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN F 232 GLN F 250 ASN ** G 992 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1489 ASN I 19 GLN ** I 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 766 ASN ** N 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 38 ASN T 63 ASN ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.075709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.054727 restraints weight = 173733.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.056137 restraints weight = 102274.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.057101 restraints weight = 69592.120| |-----------------------------------------------------------------------------| r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.5986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 44795 Z= 0.268 Angle : 0.652 9.667 61826 Z= 0.340 Chirality : 0.042 0.238 7045 Planarity : 0.004 0.057 6957 Dihedral : 21.173 178.806 8508 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.53 % Favored : 93.43 % Rotamer: Outliers : 0.03 % Allowed : 0.56 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.12), residues: 4686 helix: 0.48 (0.12), residues: 2084 sheet: -1.42 (0.20), residues: 649 loop : -1.67 (0.14), residues: 1953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 282 HIS 0.006 0.001 HIS E 301 PHE 0.024 0.002 PHE Q 67 TYR 0.025 0.002 TYR A 287 ARG 0.005 0.000 ARG E 367 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10360.17 seconds wall clock time: 187 minutes 7.62 seconds (11227.62 seconds total)