Starting phenix.real_space_refine (version: 1.21rc1) on Wed Apr 26 01:50:53 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d6x_27225/04_2023/8d6x_27225.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d6x_27225/04_2023/8d6x_27225.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d6x_27225/04_2023/8d6x_27225.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d6x_27225/04_2023/8d6x_27225.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d6x_27225/04_2023/8d6x_27225.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d6x_27225/04_2023/8d6x_27225.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.122 sd= 1.501 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 178 5.16 5 C 42947 2.51 5 N 12014 2.21 5 O 13223 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 466": "OE1" <-> "OE2" Residue "B GLU 443": "OE1" <-> "OE2" Residue "C GLU 557": "OE1" <-> "OE2" Residue "D GLU 557": "OE1" <-> "OE2" Residue "E GLU 536": "OE1" <-> "OE2" Residue "F GLU 506": "OE1" <-> "OE2" Residue "k TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 10": "OE1" <-> "OE2" Residue "n GLU 15": "OE1" <-> "OE2" Residue "o GLU 44": "OE1" <-> "OE2" Residue "H TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 144": "OD1" <-> "OD2" Residue "H PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 161": "OE1" <-> "OE2" Residue "M TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 113": "OE1" <-> "OE2" Residue "R GLU 507": "OE1" <-> "OE2" Residue "V TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 338": "OD1" <-> "OD2" Residue "Z TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 461": "OD1" <-> "OD2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 68362 Number of models: 1 Model: "" Number of chains: 41 Chain: "A" Number of atoms: 3650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3650 Classifications: {'peptide': 466} Link IDs: {'PTRANS': 22, 'TRANS': 443} Chain breaks: 3 Chain: "B" Number of atoms: 3719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3719 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 22, 'TRANS': 453} Chain breaks: 1 Chain: "C" Number of atoms: 3629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3629 Classifications: {'peptide': 464} Link IDs: {'PTRANS': 22, 'TRANS': 441} Chain breaks: 2 Chain: "D" Number of atoms: 3542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3542 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 22, 'TRANS': 429} Chain breaks: 3 Chain: "E" Number of atoms: 3719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3719 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 22, 'TRANS': 453} Chain breaks: 1 Chain: "F" Number of atoms: 3723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3723 Classifications: {'peptide': 477} Link IDs: {'PTRANS': 22, 'TRANS': 454} Chain breaks: 1 Chain: "k" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "l" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "m" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "n" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "o" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "G" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "H" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "I" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "J" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "K" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "L" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "M" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "N" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "P" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "Q" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "R" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "S" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "T" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1636 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "U" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "V" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "W" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "X" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "Y" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "Z" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "a" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "b" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "c" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "d" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Link IDs: {'TRANS': 3} Chain: "e" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Link IDs: {'TRANS': 3} Chain: "f" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Link IDs: {'TRANS': 3} Chain: "g" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Link IDs: {'TRANS': 3} Chain: "h" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Link IDs: {'TRANS': 3} Chain: "i" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Link IDs: {'TRANS': 3} Chain: "j" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Link IDs: {'TRANS': 3} Chain: "O" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Time building chain proxies: 28.19, per 1000 atoms: 0.41 Number of scatterers: 68362 At special positions: 0 Unit cell: (151.536, 160.72, 298.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 178 16.00 O 13223 8.00 N 12014 7.00 C 42947 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: 25.68 Conformation dependent library (CDL) restraints added in 8.7 seconds 17650 Ramachandran restraints generated. 8825 Oldfield, 0 Emsley, 8825 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16392 Finding SS restraints... Secondary structure from input PDB file: 298 helices and 88 sheets defined 44.4% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.13 Creating SS restraints... Processing helix chain 'A' and resid 237 through 243 removed outlier: 3.507A pdb=" N LEU A 241 " --> pdb=" O GLU A 237 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL A 242 " --> pdb=" O VAL A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 274 removed outlier: 4.465A pdb=" N LEU A 270 " --> pdb=" O ASP A 266 " (cutoff:3.500A) Proline residue: A 271 - end of helix Processing helix chain 'A' and resid 274 through 281 removed outlier: 3.856A pdb=" N TYR A 278 " --> pdb=" O HIS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 318 Processing helix chain 'A' and resid 335 through 338 removed outlier: 3.557A pdb=" N LEU A 338 " --> pdb=" O PRO A 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 335 through 338' Processing helix chain 'A' and resid 344 through 362 removed outlier: 3.914A pdb=" N ILE A 349 " --> pdb=" O THR A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 404 removed outlier: 4.133A pdb=" N VAL A 393 " --> pdb=" O GLU A 389 " (cutoff:3.500A) Proline residue: A 394 - end of helix Processing helix chain 'A' and resid 441 through 453 Processing helix chain 'A' and resid 460 through 466 removed outlier: 3.712A pdb=" N GLU A 466 " --> pdb=" O ASP A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 488 Processing helix chain 'A' and resid 490 through 492 No H-bonds generated for 'chain 'A' and resid 490 through 492' Processing helix chain 'A' and resid 511 through 514 Processing helix chain 'A' and resid 515 through 537 Processing helix chain 'A' and resid 543 through 558 removed outlier: 3.848A pdb=" N LEU A 547 " --> pdb=" O ARG A 543 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL A 552 " --> pdb=" O LEU A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 565 removed outlier: 4.375A pdb=" N THR A 564 " --> pdb=" O LEU A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 578 Processing helix chain 'B' and resid 131 through 135 Processing helix chain 'B' and resid 236 through 240 Processing helix chain 'B' and resid 250 through 254 Processing helix chain 'B' and resid 258 through 274 removed outlier: 3.678A pdb=" N GLU B 262 " --> pdb=" O SER B 258 " (cutoff:3.500A) Proline residue: B 271 - end of helix Processing helix chain 'B' and resid 274 through 281 Processing helix chain 'B' and resid 298 through 318 Processing helix chain 'B' and resid 334 through 338 removed outlier: 3.928A pdb=" N LEU B 337 " --> pdb=" O GLY B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 360 Processing helix chain 'B' and resid 391 through 401 Processing helix chain 'B' and resid 441 through 453 Processing helix chain 'B' and resid 460 through 467 removed outlier: 3.544A pdb=" N PHE B 467 " --> pdb=" O ASP B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 488 Processing helix chain 'B' and resid 490 through 492 No H-bonds generated for 'chain 'B' and resid 490 through 492' Processing helix chain 'B' and resid 511 through 514 removed outlier: 3.597A pdb=" N ASN B 514 " --> pdb=" O LYS B 511 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 511 through 514' Processing helix chain 'B' and resid 515 through 537 Processing helix chain 'B' and resid 543 through 559 Processing helix chain 'B' and resid 567 through 578 Processing helix chain 'C' and resid 236 through 242 removed outlier: 4.146A pdb=" N ASP C 240 " --> pdb=" O ALA C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 274 removed outlier: 5.124A pdb=" N LEU C 270 " --> pdb=" O ASP C 266 " (cutoff:3.500A) Proline residue: C 271 - end of helix Processing helix chain 'C' and resid 274 through 281 Processing helix chain 'C' and resid 298 through 314 Processing helix chain 'C' and resid 343 through 361 Processing helix chain 'C' and resid 388 through 401 removed outlier: 3.653A pdb=" N VAL C 393 " --> pdb=" O GLU C 389 " (cutoff:3.500A) Proline residue: C 394 - end of helix Processing helix chain 'C' and resid 422 through 427 removed outlier: 3.502A pdb=" N LEU C 426 " --> pdb=" O ASP C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 453 Processing helix chain 'C' and resid 460 through 467 Processing helix chain 'C' and resid 470 through 487 Processing helix chain 'C' and resid 490 through 492 No H-bonds generated for 'chain 'C' and resid 490 through 492' Processing helix chain 'C' and resid 511 through 513 No H-bonds generated for 'chain 'C' and resid 511 through 513' Processing helix chain 'C' and resid 515 through 538 Processing helix chain 'C' and resid 543 through 554 removed outlier: 3.750A pdb=" N LEU C 547 " --> pdb=" O ARG C 543 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL C 552 " --> pdb=" O LEU C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 566 through 578 removed outlier: 3.667A pdb=" N TRP C 570 " --> pdb=" O ASN C 566 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 242 removed outlier: 4.052A pdb=" N VAL D 242 " --> pdb=" O GLU D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 268 Processing helix chain 'D' and resid 268 through 274 Processing helix chain 'D' and resid 274 through 281 Processing helix chain 'D' and resid 300 through 314 Processing helix chain 'D' and resid 334 through 338 removed outlier: 3.531A pdb=" N LEU D 338 " --> pdb=" O GLY D 334 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 334 through 338' Processing helix chain 'D' and resid 343 through 361 removed outlier: 3.822A pdb=" N ARG D 347 " --> pdb=" O GLY D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 376 Processing helix chain 'D' and resid 392 through 403 Processing helix chain 'D' and resid 422 through 427 Processing helix chain 'D' and resid 441 through 453 Processing helix chain 'D' and resid 460 through 466 removed outlier: 4.316A pdb=" N GLU D 466 " --> pdb=" O ASP D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 487 Processing helix chain 'D' and resid 490 through 494 Processing helix chain 'D' and resid 515 through 537 Processing helix chain 'D' and resid 543 through 559 removed outlier: 3.508A pdb=" N LEU D 547 " --> pdb=" O ARG D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 578 Processing helix chain 'E' and resid 236 through 243 removed outlier: 4.216A pdb=" N ASP E 240 " --> pdb=" O ALA E 236 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU E 243 " --> pdb=" O GLU E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 254 removed outlier: 3.522A pdb=" N ILE E 254 " --> pdb=" O TYR E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 269 Processing helix chain 'E' and resid 269 through 274 Processing helix chain 'E' and resid 274 through 281 Processing helix chain 'E' and resid 298 through 318 removed outlier: 3.820A pdb=" N ALA E 307 " --> pdb=" O ALA E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 328 removed outlier: 3.676A pdb=" N ALA E 325 " --> pdb=" O ASP E 321 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TYR E 328 " --> pdb=" O GLU E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 334 through 338 removed outlier: 3.865A pdb=" N LEU E 337 " --> pdb=" O GLY E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 343 through 360 Processing helix chain 'E' and resid 388 through 401 Proline residue: E 394 - end of helix Processing helix chain 'E' and resid 441 through 453 Processing helix chain 'E' and resid 460 through 466 removed outlier: 3.821A pdb=" N GLU E 466 " --> pdb=" O ASP E 462 " (cutoff:3.500A) Processing helix chain 'E' and resid 470 through 487 Processing helix chain 'E' and resid 490 through 492 No H-bonds generated for 'chain 'E' and resid 490 through 492' Processing helix chain 'E' and resid 515 through 537 Processing helix chain 'E' and resid 543 through 558 Processing helix chain 'E' and resid 569 through 578 removed outlier: 3.919A pdb=" N ILE E 573 " --> pdb=" O ASP E 569 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 193 Processing helix chain 'F' and resid 250 through 254 Processing helix chain 'F' and resid 257 through 274 removed outlier: 4.251A pdb=" N LEU F 270 " --> pdb=" O ASP F 266 " (cutoff:3.500A) Proline residue: F 271 - end of helix Processing helix chain 'F' and resid 274 through 281 removed outlier: 3.930A pdb=" N TYR F 278 " --> pdb=" O HIS F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 317 Processing helix chain 'F' and resid 323 through 328 removed outlier: 3.672A pdb=" N TYR F 328 " --> pdb=" O GLU F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 334 through 338 Processing helix chain 'F' and resid 344 through 360 Processing helix chain 'F' and resid 388 through 400 Proline residue: F 394 - end of helix Processing helix chain 'F' and resid 422 through 427 removed outlier: 3.831A pdb=" N LEU F 426 " --> pdb=" O ASP F 422 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG F 427 " --> pdb=" O PRO F 423 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 422 through 427' Processing helix chain 'F' and resid 441 through 453 Processing helix chain 'F' and resid 460 through 466 removed outlier: 4.074A pdb=" N GLU F 466 " --> pdb=" O ASP F 462 " (cutoff:3.500A) Processing helix chain 'F' and resid 470 through 487 Processing helix chain 'F' and resid 511 through 514 removed outlier: 3.582A pdb=" N ASN F 514 " --> pdb=" O LYS F 511 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 511 through 514' Processing helix chain 'F' and resid 515 through 537 Processing helix chain 'F' and resid 543 through 558 Processing helix chain 'F' and resid 569 through 578 removed outlier: 4.399A pdb=" N GLY F 575 " --> pdb=" O ALA F 571 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N LYS F 576 " --> pdb=" O ARG F 572 " (cutoff:3.500A) Processing helix chain 'k' and resid 9 through 26 Processing helix chain 'k' and resid 67 through 89 Processing helix chain 'k' and resid 90 through 94 Processing helix chain 'k' and resid 95 through 113 removed outlier: 3.518A pdb=" N LEU k 99 " --> pdb=" O THR k 95 " (cutoff:3.500A) Processing helix chain 'k' and resid 159 through 171 removed outlier: 4.330A pdb=" N ILE k 163 " --> pdb=" O THR k 159 " (cutoff:3.500A) Processing helix chain 'k' and resid 176 through 190 removed outlier: 3.667A pdb=" N ALA k 190 " --> pdb=" O ALA k 186 " (cutoff:3.500A) Processing helix chain 'k' and resid 227 through 234 Processing helix chain 'l' and resid 9 through 26 Processing helix chain 'l' and resid 67 through 89 Processing helix chain 'l' and resid 95 through 114 Processing helix chain 'l' and resid 159 through 171 removed outlier: 4.156A pdb=" N ILE l 163 " --> pdb=" O THR l 159 " (cutoff:3.500A) Processing helix chain 'l' and resid 176 through 190 Processing helix chain 'l' and resid 227 through 233 Processing helix chain 'm' and resid 9 through 26 Processing helix chain 'm' and resid 67 through 89 Processing helix chain 'm' and resid 90 through 94 Processing helix chain 'm' and resid 95 through 114 Processing helix chain 'm' and resid 159 through 171 removed outlier: 4.459A pdb=" N ILE m 163 " --> pdb=" O THR m 159 " (cutoff:3.500A) Processing helix chain 'm' and resid 176 through 190 removed outlier: 3.718A pdb=" N ALA m 190 " --> pdb=" O ALA m 186 " (cutoff:3.500A) Processing helix chain 'm' and resid 227 through 234 Processing helix chain 'n' and resid 9 through 26 Processing helix chain 'n' and resid 67 through 89 Processing helix chain 'n' and resid 95 through 114 Processing helix chain 'n' and resid 159 through 171 removed outlier: 4.342A pdb=" N ILE n 163 " --> pdb=" O THR n 159 " (cutoff:3.500A) Processing helix chain 'n' and resid 176 through 190 removed outlier: 3.609A pdb=" N ALA n 190 " --> pdb=" O ALA n 186 " (cutoff:3.500A) Processing helix chain 'n' and resid 227 through 234 Processing helix chain 'o' and resid 9 through 26 Processing helix chain 'o' and resid 67 through 89 Processing helix chain 'o' and resid 90 through 94 Processing helix chain 'o' and resid 95 through 114 Processing helix chain 'o' and resid 159 through 171 removed outlier: 4.062A pdb=" N ILE o 163 " --> pdb=" O THR o 159 " (cutoff:3.500A) Processing helix chain 'o' and resid 176 through 190 removed outlier: 3.650A pdb=" N ALA o 190 " --> pdb=" O ALA o 186 " (cutoff:3.500A) Processing helix chain 'o' and resid 227 through 234 Processing helix chain 'G' and resid 9 through 26 Processing helix chain 'G' and resid 67 through 89 Processing helix chain 'G' and resid 90 through 94 Processing helix chain 'G' and resid 95 through 114 Processing helix chain 'G' and resid 159 through 171 removed outlier: 4.287A pdb=" N ILE G 163 " --> pdb=" O THR G 159 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 190 Processing helix chain 'G' and resid 227 through 234 Processing helix chain 'H' and resid 9 through 26 Processing helix chain 'H' and resid 67 through 89 Processing helix chain 'H' and resid 95 through 114 Processing helix chain 'H' and resid 159 through 171 removed outlier: 3.984A pdb=" N ILE H 163 " --> pdb=" O THR H 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 190 removed outlier: 3.618A pdb=" N ALA H 190 " --> pdb=" O ALA H 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 234 Processing helix chain 'I' and resid 9 through 26 Processing helix chain 'I' and resid 67 through 89 Processing helix chain 'I' and resid 95 through 113 Processing helix chain 'I' and resid 159 through 171 removed outlier: 3.910A pdb=" N ILE I 163 " --> pdb=" O THR I 159 " (cutoff:3.500A) Processing helix chain 'I' and resid 176 through 190 removed outlier: 3.811A pdb=" N ALA I 190 " --> pdb=" O ALA I 186 " (cutoff:3.500A) Processing helix chain 'I' and resid 227 through 234 Processing helix chain 'J' and resid 9 through 26 Processing helix chain 'J' and resid 67 through 89 removed outlier: 3.590A pdb=" N PHE J 71 " --> pdb=" O LYS J 67 " (cutoff:3.500A) Processing helix chain 'J' and resid 90 through 94 Processing helix chain 'J' and resid 95 through 114 removed outlier: 3.555A pdb=" N LEU J 99 " --> pdb=" O THR J 95 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN J 114 " --> pdb=" O ILE J 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 171 removed outlier: 4.191A pdb=" N ILE J 163 " --> pdb=" O THR J 159 " (cutoff:3.500A) Processing helix chain 'J' and resid 176 through 190 Processing helix chain 'J' and resid 226 through 234 removed outlier: 3.684A pdb=" N LEU J 230 " --> pdb=" O THR J 226 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 26 Processing helix chain 'K' and resid 67 through 89 removed outlier: 3.572A pdb=" N PHE K 71 " --> pdb=" O LYS K 67 " (cutoff:3.500A) Processing helix chain 'K' and resid 95 through 114 Processing helix chain 'K' and resid 159 through 171 removed outlier: 4.592A pdb=" N ILE K 163 " --> pdb=" O THR K 159 " (cutoff:3.500A) Processing helix chain 'K' and resid 176 through 190 Processing helix chain 'K' and resid 226 through 234 removed outlier: 3.522A pdb=" N LEU K 230 " --> pdb=" O THR K 226 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 26 Processing helix chain 'L' and resid 67 through 89 Processing helix chain 'L' and resid 90 through 94 Processing helix chain 'L' and resid 95 through 114 Processing helix chain 'L' and resid 159 through 171 removed outlier: 4.532A pdb=" N ILE L 163 " --> pdb=" O THR L 159 " (cutoff:3.500A) Processing helix chain 'L' and resid 176 through 190 Processing helix chain 'L' and resid 227 through 234 Processing helix chain 'M' and resid 9 through 26 Processing helix chain 'M' and resid 67 through 89 Processing helix chain 'M' and resid 95 through 114 removed outlier: 3.513A pdb=" N LEU M 99 " --> pdb=" O THR M 95 " (cutoff:3.500A) Processing helix chain 'M' and resid 160 through 171 Processing helix chain 'M' and resid 176 through 190 Processing helix chain 'M' and resid 226 through 234 Processing helix chain 'N' and resid 9 through 26 Processing helix chain 'N' and resid 67 through 89 removed outlier: 3.511A pdb=" N PHE N 71 " --> pdb=" O LYS N 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 90 through 94 Processing helix chain 'N' and resid 95 through 114 Processing helix chain 'N' and resid 160 through 171 Processing helix chain 'N' and resid 176 through 190 Processing helix chain 'N' and resid 227 through 234 Processing helix chain 'P' and resid 348 through 371 Processing helix chain 'P' and resid 375 through 390 Processing helix chain 'P' and resid 390 through 395 Processing helix chain 'P' and resid 413 through 416 Processing helix chain 'P' and resid 442 through 454 removed outlier: 3.696A pdb=" N LYS P 452 " --> pdb=" O SER P 448 " (cutoff:3.500A) Processing helix chain 'P' and resid 455 through 457 No H-bonds generated for 'chain 'P' and resid 455 through 457' Processing helix chain 'P' and resid 459 through 478 Processing helix chain 'P' and resid 506 through 522 Processing helix chain 'Q' and resid 348 through 371 Processing helix chain 'Q' and resid 375 through 390 Processing helix chain 'Q' and resid 390 through 396 removed outlier: 3.722A pdb=" N GLN Q 396 " --> pdb=" O ALA Q 392 " (cutoff:3.500A) Processing helix chain 'Q' and resid 442 through 454 removed outlier: 3.563A pdb=" N LYS Q 452 " --> pdb=" O SER Q 448 " (cutoff:3.500A) Processing helix chain 'Q' and resid 455 through 457 No H-bonds generated for 'chain 'Q' and resid 455 through 457' Processing helix chain 'Q' and resid 459 through 478 Processing helix chain 'Q' and resid 506 through 522 removed outlier: 3.698A pdb=" N ILE Q 510 " --> pdb=" O PRO Q 506 " (cutoff:3.500A) Processing helix chain 'R' and resid 348 through 371 Processing helix chain 'R' and resid 375 through 390 Processing helix chain 'R' and resid 390 through 395 Processing helix chain 'R' and resid 413 through 416 Processing helix chain 'R' and resid 442 through 454 removed outlier: 3.772A pdb=" N LYS R 452 " --> pdb=" O SER R 448 " (cutoff:3.500A) Processing helix chain 'R' and resid 455 through 457 No H-bonds generated for 'chain 'R' and resid 455 through 457' Processing helix chain 'R' and resid 459 through 478 Processing helix chain 'R' and resid 506 through 522 Processing helix chain 'S' and resid 348 through 371 Processing helix chain 'S' and resid 375 through 390 Processing helix chain 'S' and resid 390 through 397 Processing helix chain 'S' and resid 413 through 416 Processing helix chain 'S' and resid 442 through 454 removed outlier: 3.582A pdb=" N LYS S 452 " --> pdb=" O SER S 448 " (cutoff:3.500A) Processing helix chain 'S' and resid 455 through 457 No H-bonds generated for 'chain 'S' and resid 455 through 457' Processing helix chain 'S' and resid 459 through 478 Processing helix chain 'S' and resid 506 through 522 Processing helix chain 'T' and resid 348 through 371 Processing helix chain 'T' and resid 375 through 390 Processing helix chain 'T' and resid 390 through 396 removed outlier: 3.770A pdb=" N GLN T 396 " --> pdb=" O ALA T 392 " (cutoff:3.500A) Processing helix chain 'T' and resid 413 through 416 Processing helix chain 'T' and resid 442 through 454 removed outlier: 3.841A pdb=" N LYS T 452 " --> pdb=" O SER T 448 " (cutoff:3.500A) Processing helix chain 'T' and resid 455 through 457 No H-bonds generated for 'chain 'T' and resid 455 through 457' Processing helix chain 'T' and resid 459 through 478 Processing helix chain 'T' and resid 506 through 522 Processing helix chain 'U' and resid 348 through 371 Processing helix chain 'U' and resid 375 through 390 Processing helix chain 'U' and resid 390 through 396 removed outlier: 3.529A pdb=" N GLN U 396 " --> pdb=" O ALA U 392 " (cutoff:3.500A) Processing helix chain 'U' and resid 413 through 416 Processing helix chain 'U' and resid 442 through 454 removed outlier: 3.704A pdb=" N LYS U 452 " --> pdb=" O SER U 448 " (cutoff:3.500A) Processing helix chain 'U' and resid 459 through 478 Processing helix chain 'U' and resid 506 through 522 Processing helix chain 'V' and resid 348 through 371 Processing helix chain 'V' and resid 375 through 390 Processing helix chain 'V' and resid 390 through 397 removed outlier: 3.870A pdb=" N GLN V 396 " --> pdb=" O ALA V 392 " (cutoff:3.500A) Processing helix chain 'V' and resid 413 through 416 Processing helix chain 'V' and resid 442 through 454 removed outlier: 4.456A pdb=" N LYS V 452 " --> pdb=" O SER V 448 " (cutoff:3.500A) Processing helix chain 'V' and resid 455 through 457 No H-bonds generated for 'chain 'V' and resid 455 through 457' Processing helix chain 'V' and resid 459 through 478 Processing helix chain 'V' and resid 506 through 522 Processing helix chain 'W' and resid 348 through 371 Processing helix chain 'W' and resid 375 through 390 Processing helix chain 'W' and resid 390 through 395 Processing helix chain 'W' and resid 413 through 416 Processing helix chain 'W' and resid 442 through 454 removed outlier: 4.268A pdb=" N LYS W 452 " --> pdb=" O SER W 448 " (cutoff:3.500A) Processing helix chain 'W' and resid 455 through 457 No H-bonds generated for 'chain 'W' and resid 455 through 457' Processing helix chain 'W' and resid 459 through 478 Processing helix chain 'W' and resid 506 through 522 Processing helix chain 'X' and resid 348 through 371 Processing helix chain 'X' and resid 375 through 390 Processing helix chain 'X' and resid 390 through 395 Processing helix chain 'X' and resid 413 through 416 Processing helix chain 'X' and resid 442 through 454 removed outlier: 3.732A pdb=" N LYS X 452 " --> pdb=" O SER X 448 " (cutoff:3.500A) Processing helix chain 'X' and resid 459 through 478 Processing helix chain 'X' and resid 506 through 522 Processing helix chain 'Y' and resid 348 through 371 Processing helix chain 'Y' and resid 375 through 390 Processing helix chain 'Y' and resid 390 through 396 Processing helix chain 'Y' and resid 413 through 416 Processing helix chain 'Y' and resid 442 through 454 removed outlier: 3.633A pdb=" N LYS Y 452 " --> pdb=" O SER Y 448 " (cutoff:3.500A) Processing helix chain 'Y' and resid 455 through 457 No H-bonds generated for 'chain 'Y' and resid 455 through 457' Processing helix chain 'Y' and resid 459 through 478 Processing helix chain 'Y' and resid 506 through 522 Processing helix chain 'Z' and resid 348 through 371 Processing helix chain 'Z' and resid 375 through 390 Processing helix chain 'Z' and resid 390 through 397 Processing helix chain 'Z' and resid 413 through 416 Processing helix chain 'Z' and resid 442 through 454 removed outlier: 3.557A pdb=" N LYS Z 452 " --> pdb=" O SER Z 448 " (cutoff:3.500A) Processing helix chain 'Z' and resid 455 through 457 No H-bonds generated for 'chain 'Z' and resid 455 through 457' Processing helix chain 'Z' and resid 459 through 478 Processing helix chain 'Z' and resid 506 through 522 Processing helix chain 'a' and resid 348 through 371 Processing helix chain 'a' and resid 375 through 390 Processing helix chain 'a' and resid 390 through 395 Processing helix chain 'a' and resid 413 through 416 Processing helix chain 'a' and resid 442 through 454 removed outlier: 3.503A pdb=" N LYS a 452 " --> pdb=" O SER a 448 " (cutoff:3.500A) Processing helix chain 'a' and resid 455 through 457 No H-bonds generated for 'chain 'a' and resid 455 through 457' Processing helix chain 'a' and resid 459 through 478 Processing helix chain 'a' and resid 506 through 522 Processing helix chain 'b' and resid 348 through 371 Processing helix chain 'b' and resid 375 through 390 Processing helix chain 'b' and resid 390 through 395 Processing helix chain 'b' and resid 413 through 416 Processing helix chain 'b' and resid 442 through 454 removed outlier: 3.507A pdb=" N LYS b 452 " --> pdb=" O SER b 448 " (cutoff:3.500A) Processing helix chain 'b' and resid 455 through 457 No H-bonds generated for 'chain 'b' and resid 455 through 457' Processing helix chain 'b' and resid 459 through 478 Processing helix chain 'b' and resid 506 through 522 Processing helix chain 'c' and resid 348 through 371 Processing helix chain 'c' and resid 375 through 390 Processing helix chain 'c' and resid 390 through 395 Processing helix chain 'c' and resid 442 through 454 Processing helix chain 'c' and resid 459 through 478 Processing helix chain 'c' and resid 506 through 522 Processing helix chain 'O' and resid 9 through 26 Processing helix chain 'O' and resid 67 through 89 Processing helix chain 'O' and resid 90 through 94 Processing helix chain 'O' and resid 95 through 113 Processing helix chain 'O' and resid 159 through 171 removed outlier: 4.747A pdb=" N ILE O 163 " --> pdb=" O THR O 159 " (cutoff:3.500A) Processing helix chain 'O' and resid 176 through 190 Processing helix chain 'O' and resid 226 through 234 Processing sheet with id=AA1, first strand: chain 'A' and resid 120 through 125 removed outlier: 7.149A pdb=" N THR A 112 " --> pdb=" O THR A 107 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N THR A 107 " --> pdb=" O THR A 112 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ASP A 114 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU A 151 " --> pdb=" O ARG A 142 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 160 through 167 removed outlier: 6.986A pdb=" N LEU A 175 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N ILE A 167 " --> pdb=" O ARG A 173 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ARG A 173 " --> pdb=" O ILE A 167 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 183 through 188 current: chain 'A' and resid 228 through 232 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 228 through 232 current: chain 'C' and resid 173 through 177 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 183 through 188 current: chain 'C' and resid 228 through 233 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 228 through 233 current: chain 'D' and resid 173 through 177 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 183 through 188 current: chain 'D' and resid 228 through 233 Processing sheet with id=AA3, first strand: chain 'A' and resid 330 through 333 removed outlier: 6.735A pdb=" N LEU A 330 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ASP A 371 " --> pdb=" O LEU A 330 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE A 332 " --> pdb=" O ASP A 371 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA A 414 " --> pdb=" O PHE A 370 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N GLY A 288 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ILE A 435 " --> pdb=" O GLY A 288 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N LEU A 290 " --> pdb=" O ILE A 435 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 506 through 509 removed outlier: 3.901A pdb=" N LEU A 496 " --> pdb=" O MET A 508 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N TYR A 583 " --> pdb=" O THR A 499 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 99 through 107 removed outlier: 6.563A pdb=" N ASP B 114 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N THR B 107 " --> pdb=" O THR B 112 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N THR B 112 " --> pdb=" O THR B 107 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 120 through 125 current: chain 'B' and resid 151 through 155 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 151 through 155 current: chain 'E' and resid 112 through 117 removed outlier: 3.541A pdb=" N MET E 122 " --> pdb=" O VAL E 115 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 120 through 125 current: chain 'E' and resid 151 through 153 Processing sheet with id=AA6, first strand: chain 'B' and resid 159 through 167 removed outlier: 5.709A pdb=" N LEU B 164 " --> pdb=" O VAL B 177 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N VAL B 177 " --> pdb=" O LEU B 164 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 183 through 188 current: chain 'B' and resid 228 through 232 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 228 through 232 current: chain 'E' and resid 173 through 177 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 183 through 188 current: chain 'E' and resid 228 through 232 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 228 through 232 current: chain 'F' and resid 173 through 177 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 183 through 188 current: chain 'F' and resid 228 through 232 Processing sheet with id=AA7, first strand: chain 'B' and resid 329 through 332 removed outlier: 6.374A pdb=" N LEU B 330 " --> pdb=" O PHE B 369 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ASP B 371 " --> pdb=" O LEU B 330 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE B 332 " --> pdb=" O ASP B 371 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N GLY B 288 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N ILE B 435 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N LEU B 290 " --> pdb=" O ILE B 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 506 through 509 removed outlier: 4.089A pdb=" N VAL B 498 " --> pdb=" O GLU B 506 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N MET B 508 " --> pdb=" O LEU B 496 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU B 496 " --> pdb=" O MET B 508 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 101 through 107 removed outlier: 6.644A pdb=" N ASP C 114 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N THR C 107 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N THR C 112 " --> pdb=" O THR C 107 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 120 through 125 current: chain 'C' and resid 151 through 152 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 151 through 152 current: chain 'F' and resid 112 through 117 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 120 through 125 current: chain 'F' and resid 151 through 152 Processing sheet with id=AB1, first strand: chain 'C' and resid 328 through 332 removed outlier: 6.772A pdb=" N TYR C 328 " --> pdb=" O ILE C 367 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N PHE C 369 " --> pdb=" O TYR C 328 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU C 330 " --> pdb=" O PHE C 369 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N GLY C 288 " --> pdb=" O VAL C 433 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N ILE C 435 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N LEU C 290 " --> pdb=" O ILE C 435 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 506 through 509 removed outlier: 4.010A pdb=" N TYR C 583 " --> pdb=" O THR C 499 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 120 through 125 removed outlier: 6.645A pdb=" N ASP D 114 " --> pdb=" O LEU D 105 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU D 151 " --> pdb=" O ARG D 142 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 328 through 333 removed outlier: 7.068A pdb=" N ILE D 412 " --> pdb=" O VAL D 366 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N VAL D 368 " --> pdb=" O ILE D 412 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N ALA D 414 " --> pdb=" O VAL D 368 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N PHE D 370 " --> pdb=" O ALA D 414 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N GLY D 288 " --> pdb=" O VAL D 433 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N ILE D 435 " --> pdb=" O GLY D 288 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N LEU D 290 " --> pdb=" O ILE D 435 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 505 through 508 removed outlier: 3.928A pdb=" N TYR D 583 " --> pdb=" O THR D 499 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 329 through 331 removed outlier: 6.307A pdb=" N LEU E 330 " --> pdb=" O PHE E 369 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N ASP E 371 " --> pdb=" O LEU E 330 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N VAL E 366 " --> pdb=" O ILE E 410 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ILE E 412 " --> pdb=" O VAL E 366 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N VAL E 368 " --> pdb=" O ILE E 412 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ALA E 414 " --> pdb=" O VAL E 368 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N PHE E 370 " --> pdb=" O ALA E 414 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLY E 288 " --> pdb=" O VAL E 433 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N ILE E 435 " --> pdb=" O GLY E 288 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N LEU E 290 " --> pdb=" O ILE E 435 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 506 through 509 removed outlier: 6.037A pdb=" N GLU E 506 " --> pdb=" O GLU E 497 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N GLU E 497 " --> pdb=" O GLU E 506 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N MET E 508 " --> pdb=" O PHE E 495 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N THR E 499 " --> pdb=" O VAL E 582 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 330 through 332 removed outlier: 6.108A pdb=" N LEU F 290 " --> pdb=" O ILE F 435 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 505 through 509 Processing sheet with id=AC1, first strand: chain 'k' and resid 153 through 156 Processing sheet with id=AC2, first strand: chain 'k' and resid 53 through 57 removed outlier: 6.430A pdb=" N VAL k 60 " --> pdb=" O LEU k 56 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA k 125 " --> pdb=" O GLY k 61 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU k 138 " --> pdb=" O GLU k 150 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'l' and resid 153 through 156 Processing sheet with id=AC4, first strand: chain 'l' and resid 53 through 57 removed outlier: 6.377A pdb=" N VAL l 60 " --> pdb=" O LEU l 56 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA l 125 " --> pdb=" O GLY l 61 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'm' and resid 153 through 156 Processing sheet with id=AC6, first strand: chain 'm' and resid 53 through 57 removed outlier: 6.405A pdb=" N VAL m 60 " --> pdb=" O LEU m 56 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA m 125 " --> pdb=" O GLY m 61 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA m 63 " --> pdb=" O CYS m 123 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA m 65 " --> pdb=" O GLU m 121 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU m 121 " --> pdb=" O ALA m 65 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU m 138 " --> pdb=" O GLU m 150 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'n' and resid 153 through 156 Processing sheet with id=AC8, first strand: chain 'n' and resid 53 through 57 removed outlier: 6.339A pdb=" N VAL n 60 " --> pdb=" O LEU n 56 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA n 125 " --> pdb=" O GLY n 61 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA n 63 " --> pdb=" O CYS n 123 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU n 138 " --> pdb=" O GLU n 150 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'o' and resid 153 through 154 Processing sheet with id=AD1, first strand: chain 'o' and resid 53 through 57 removed outlier: 6.386A pdb=" N VAL o 60 " --> pdb=" O LEU o 56 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA o 125 " --> pdb=" O GLY o 61 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA o 63 " --> pdb=" O CYS o 123 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 153 through 156 Processing sheet with id=AD3, first strand: chain 'G' and resid 54 through 57 removed outlier: 6.285A pdb=" N VAL G 60 " --> pdb=" O LEU G 56 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ALA G 125 " --> pdb=" O GLY G 61 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA G 63 " --> pdb=" O CYS G 123 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU G 138 " --> pdb=" O GLU G 150 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 153 through 156 Processing sheet with id=AD5, first strand: chain 'H' and resid 53 through 57 removed outlier: 6.745A pdb=" N VAL H 60 " --> pdb=" O LEU H 56 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA H 125 " --> pdb=" O GLY H 61 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 153 through 156 Processing sheet with id=AD7, first strand: chain 'I' and resid 53 through 57 removed outlier: 6.263A pdb=" N VAL I 60 " --> pdb=" O LEU I 56 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA I 125 " --> pdb=" O GLY I 61 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU I 138 " --> pdb=" O GLU I 150 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 153 through 156 Processing sheet with id=AD9, first strand: chain 'J' and resid 53 through 57 removed outlier: 6.418A pdb=" N VAL J 60 " --> pdb=" O LEU J 56 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA J 125 " --> pdb=" O GLY J 61 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU J 138 " --> pdb=" O GLU J 150 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 153 through 156 Processing sheet with id=AE2, first strand: chain 'K' and resid 54 through 57 removed outlier: 6.405A pdb=" N VAL K 60 " --> pdb=" O LEU K 56 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA K 125 " --> pdb=" O GLY K 61 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA K 63 " --> pdb=" O CYS K 123 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU K 138 " --> pdb=" O GLU K 150 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 153 through 156 Processing sheet with id=AE4, first strand: chain 'L' and resid 53 through 57 removed outlier: 6.483A pdb=" N VAL L 60 " --> pdb=" O LEU L 56 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA L 125 " --> pdb=" O GLY L 61 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'M' and resid 153 through 156 Processing sheet with id=AE6, first strand: chain 'M' and resid 53 through 57 removed outlier: 6.345A pdb=" N VAL M 60 " --> pdb=" O LEU M 56 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA M 125 " --> pdb=" O GLY M 61 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU M 138 " --> pdb=" O GLU M 150 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'N' and resid 153 through 156 Processing sheet with id=AE8, first strand: chain 'N' and resid 53 through 57 removed outlier: 6.383A pdb=" N VAL N 60 " --> pdb=" O LEU N 56 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ALA N 125 " --> pdb=" O GLY N 61 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU N 138 " --> pdb=" O GLU N 150 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'P' and resid 436 through 440 Processing sheet with id=AF1, first strand: chain 'P' and resid 320 through 322 removed outlier: 5.990A pdb=" N GLN P 322 " --> pdb=" O ILE P 326 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N ILE P 326 " --> pdb=" O GLN P 322 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'P' and resid 335 through 336 removed outlier: 3.854A pdb=" N PHE P 423 " --> pdb=" O PRO P 402 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Q' and resid 436 through 440 Processing sheet with id=AF4, first strand: chain 'Q' and resid 320 through 322 removed outlier: 6.380A pdb=" N SER Q 320 " --> pdb=" O SER Q 327 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Q' and resid 334 through 338 removed outlier: 6.774A pdb=" N THR Q 341 " --> pdb=" O THR Q 337 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N PHE Q 423 " --> pdb=" O PRO Q 402 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'R' and resid 436 through 440 Processing sheet with id=AF7, first strand: chain 'R' and resid 320 through 322 removed outlier: 6.248A pdb=" N SER R 320 " --> pdb=" O SER R 327 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'R' and resid 334 through 338 removed outlier: 6.783A pdb=" N THR R 341 " --> pdb=" O THR R 337 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N PHE R 423 " --> pdb=" O PRO R 402 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'S' and resid 436 through 440 Processing sheet with id=AG1, first strand: chain 'S' and resid 320 through 322 removed outlier: 5.847A pdb=" N GLN S 322 " --> pdb=" O ILE S 326 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N ILE S 326 " --> pdb=" O GLN S 322 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'S' and resid 334 through 338 removed outlier: 6.817A pdb=" N THR S 341 " --> pdb=" O THR S 337 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N PHE S 423 " --> pdb=" O PRO S 402 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'T' and resid 436 through 440 Processing sheet with id=AG4, first strand: chain 'T' and resid 320 through 322 removed outlier: 6.237A pdb=" N SER T 320 " --> pdb=" O SER T 327 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'T' and resid 335 through 338 removed outlier: 7.021A pdb=" N THR T 341 " --> pdb=" O THR T 337 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N PHE T 423 " --> pdb=" O PRO T 402 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'U' and resid 436 through 440 Processing sheet with id=AG7, first strand: chain 'U' and resid 320 through 322 removed outlier: 6.250A pdb=" N SER U 320 " --> pdb=" O SER U 327 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'U' and resid 341 through 347 removed outlier: 3.782A pdb=" N PHE U 423 " --> pdb=" O PRO U 402 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'V' and resid 436 through 440 Processing sheet with id=AH1, first strand: chain 'V' and resid 320 through 322 removed outlier: 5.867A pdb=" N GLN V 322 " --> pdb=" O ILE V 326 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ILE V 326 " --> pdb=" O GLN V 322 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'V' and resid 341 through 347 removed outlier: 4.017A pdb=" N PHE V 423 " --> pdb=" O PRO V 402 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'W' and resid 436 through 440 Processing sheet with id=AH4, first strand: chain 'W' and resid 320 through 322 removed outlier: 6.411A pdb=" N GLN W 322 " --> pdb=" O ILE W 326 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ILE W 326 " --> pdb=" O GLN W 322 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'W' and resid 335 through 338 removed outlier: 6.746A pdb=" N THR W 341 " --> pdb=" O THR W 337 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU W 404 " --> pdb=" O VAL W 421 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'X' and resid 436 through 440 Processing sheet with id=AH7, first strand: chain 'X' and resid 320 through 322 removed outlier: 6.082A pdb=" N GLN X 322 " --> pdb=" O ILE X 326 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ILE X 326 " --> pdb=" O GLN X 322 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'X' and resid 341 through 347 removed outlier: 3.996A pdb=" N PHE X 423 " --> pdb=" O PRO X 402 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'Y' and resid 436 through 440 Processing sheet with id=AI1, first strand: chain 'Y' and resid 320 through 322 removed outlier: 6.408A pdb=" N SER Y 320 " --> pdb=" O SER Y 327 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'Y' and resid 335 through 336 removed outlier: 4.319A pdb=" N PHE Y 423 " --> pdb=" O PRO Y 402 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'Z' and resid 436 through 440 Processing sheet with id=AI4, first strand: chain 'Z' and resid 320 through 322 removed outlier: 6.206A pdb=" N GLN Z 322 " --> pdb=" O ILE Z 326 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ILE Z 326 " --> pdb=" O GLN Z 322 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'Z' and resid 335 through 338 removed outlier: 6.395A pdb=" N THR Z 341 " --> pdb=" O THR Z 337 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE Z 423 " --> pdb=" O PRO Z 402 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'a' and resid 436 through 440 Processing sheet with id=AI7, first strand: chain 'a' and resid 320 through 322 removed outlier: 5.998A pdb=" N GLN a 322 " --> pdb=" O ILE a 326 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N ILE a 326 " --> pdb=" O GLN a 322 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'a' and resid 335 through 338 removed outlier: 6.665A pdb=" N THR a 341 " --> pdb=" O THR a 337 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N PHE a 423 " --> pdb=" O PRO a 402 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'b' and resid 436 through 440 Processing sheet with id=AJ1, first strand: chain 'b' and resid 320 through 322 removed outlier: 6.041A pdb=" N GLN b 322 " --> pdb=" O ILE b 326 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N ILE b 326 " --> pdb=" O GLN b 322 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'b' and resid 335 through 338 removed outlier: 6.544A pdb=" N THR b 341 " --> pdb=" O THR b 337 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N PHE b 423 " --> pdb=" O PRO b 402 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'c' and resid 436 through 440 Processing sheet with id=AJ4, first strand: chain 'c' and resid 320 through 322 removed outlier: 6.263A pdb=" N SER c 320 " --> pdb=" O SER c 327 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'c' and resid 341 through 347 removed outlier: 4.162A pdb=" N PHE c 423 " --> pdb=" O PRO c 402 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'O' and resid 153 through 156 Processing sheet with id=AJ7, first strand: chain 'O' and resid 53 through 57 removed outlier: 6.365A pdb=" N VAL O 60 " --> pdb=" O LEU O 56 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA O 125 " --> pdb=" O GLY O 61 " (cutoff:3.500A) 3880 hydrogen bonds defined for protein. 11091 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 32.70 Time building geometry restraints manager: 28.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 22712 1.34 - 1.46: 10691 1.46 - 1.58: 35684 1.58 - 1.70: 1 1.70 - 1.82: 324 Bond restraints: 69412 Sorted by residual: bond pdb=" CA GLN P 322 " pdb=" CB GLN P 322 " ideal model delta sigma weight residual 1.526 1.589 -0.063 1.53e-02 4.27e+03 1.70e+01 bond pdb=" N VAL o 120 " pdb=" CA VAL o 120 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.11e-02 8.12e+03 1.26e+01 bond pdb=" N VAL W 421 " pdb=" CA VAL W 421 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.18e-02 7.18e+03 1.15e+01 bond pdb=" N ILE W 420 " pdb=" CA ILE W 420 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.19e-02 7.06e+03 1.07e+01 bond pdb=" N ILE H 141 " pdb=" CA ILE H 141 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.14e-02 7.69e+03 1.06e+01 ... (remaining 69407 not shown) Histogram of bond angle deviations from ideal: 96.58 - 104.07: 869 104.07 - 111.56: 30690 111.56 - 119.05: 25147 119.05 - 126.55: 36706 126.55 - 134.04: 518 Bond angle restraints: 93930 Sorted by residual: angle pdb=" N GLU Z 433 " pdb=" CA GLU Z 433 " pdb=" C GLU Z 433 " ideal model delta sigma weight residual 113.50 107.93 5.57 1.23e+00 6.61e-01 2.05e+01 angle pdb=" CB LYS C 275 " pdb=" CG LYS C 275 " pdb=" CD LYS C 275 " ideal model delta sigma weight residual 111.30 101.71 9.59 2.30e+00 1.89e-01 1.74e+01 angle pdb=" N GLU V 433 " pdb=" CA GLU V 433 " pdb=" C GLU V 433 " ideal model delta sigma weight residual 113.50 108.60 4.90 1.23e+00 6.61e-01 1.59e+01 angle pdb=" N GLY M 145 " pdb=" CA GLY M 145 " pdb=" C GLY M 145 " ideal model delta sigma weight residual 115.36 110.27 5.09 1.33e+00 5.65e-01 1.46e+01 angle pdb=" CA GLU o 119 " pdb=" C GLU o 119 " pdb=" O GLU o 119 " ideal model delta sigma weight residual 122.64 118.09 4.55 1.25e+00 6.40e-01 1.32e+01 ... (remaining 93925 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 39119 17.99 - 35.98: 2474 35.98 - 53.96: 368 53.96 - 71.95: 51 71.95 - 89.94: 49 Dihedral angle restraints: 42061 sinusoidal: 16427 harmonic: 25634 Sorted by residual: dihedral pdb=" CA MET T 450 " pdb=" C MET T 450 " pdb=" N LYS T 451 " pdb=" CA LYS T 451 " ideal model delta harmonic sigma weight residual 180.00 153.22 26.78 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA MET D 508 " pdb=" C MET D 508 " pdb=" N TYR D 509 " pdb=" CA TYR D 509 " ideal model delta harmonic sigma weight residual -180.00 -157.22 -22.78 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA MET X 450 " pdb=" C MET X 450 " pdb=" N LYS X 451 " pdb=" CA LYS X 451 " ideal model delta harmonic sigma weight residual 180.00 159.08 20.92 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 42058 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 8413 0.050 - 0.100: 1739 0.100 - 0.150: 519 0.150 - 0.199: 23 0.199 - 0.249: 10 Chirality restraints: 10704 Sorted by residual: chirality pdb=" CA MET X 450 " pdb=" N MET X 450 " pdb=" C MET X 450 " pdb=" CB MET X 450 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA ILE I 141 " pdb=" N ILE I 141 " pdb=" C ILE I 141 " pdb=" CB ILE I 141 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA ILE Z 431 " pdb=" N ILE Z 431 " pdb=" C ILE Z 431 " pdb=" CB ILE Z 431 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 10701 not shown) Planarity restraints: 12361 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE S 355 " -0.030 2.00e-02 2.50e+03 2.30e-02 9.26e+00 pdb=" CG PHE S 355 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE S 355 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE S 355 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE S 355 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE S 355 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE S 355 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE N 111 " 0.012 2.00e-02 2.50e+03 2.36e-02 5.56e+00 pdb=" C PHE N 111 " -0.041 2.00e-02 2.50e+03 pdb=" O PHE N 111 " 0.015 2.00e-02 2.50e+03 pdb=" N THR N 112 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP R 413 " 0.038 5.00e-02 4.00e+02 5.88e-02 5.54e+00 pdb=" N PRO R 414 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO R 414 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO R 414 " 0.033 5.00e-02 4.00e+02 ... (remaining 12358 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 4894 2.74 - 3.28: 73751 3.28 - 3.82: 124356 3.82 - 4.36: 145610 4.36 - 4.90: 245273 Nonbonded interactions: 593884 Sorted by model distance: nonbonded pdb=" OG1 THR W 337 " pdb=" OG1 THR W 341 " model vdw 2.195 2.440 nonbonded pdb=" ND2 ASN m 45 " pdb=" O LEU m 50 " model vdw 2.200 2.520 nonbonded pdb=" NH2 ARG H 135 " pdb=" O PRO H 151 " model vdw 2.201 2.520 nonbonded pdb=" O ILE I 53 " pdb=" NH2 ARG I 224 " model vdw 2.201 2.520 nonbonded pdb=" O SER Q 416 " pdb=" NH1 ARG Q 419 " model vdw 2.204 2.520 ... (remaining 593879 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 97 through 315 or resid 326 through 377 or resid 390 throu \ gh 587)) selection = (chain 'B' and (resid 97 through 315 or resid 326 through 377 or resid 390 throu \ gh 587)) selection = (chain 'C' and (resid 97 through 377 or resid 390 through 587)) selection = chain 'D' selection = (chain 'E' and (resid 97 through 315 or resid 326 through 377 or resid 390 throu \ gh 587)) selection = (chain 'F' and (resid 97 through 315 or resid 326 through 377 or resid 390 throu \ gh 587)) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' } ncs_group { reference = (chain 'P' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'Q' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'R' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'S' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = chain 'T' selection = (chain 'U' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'V' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'W' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'X' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'Y' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'Z' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'a' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'b' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'c' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) } ncs_group { reference = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.040 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: 0.050 Extract box with map and model: 5.650 Check model and map are aligned: 0.780 Set scattering table: 0.470 Process input model: 153.830 Find NCS groups from input model: 4.750 Set up NCS constraints: 0.560 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 168.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4313 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 : 0.003 0.063 69412 Z= 0.203 Angle : 0.617 9.922 93930 Z= 0.360 Chirality : 0.044 0.249 10704 Planarity : 0.004 0.059 12361 Dihedral : 12.145 89.941 25669 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.61 % Favored : 97.38 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.09), residues: 8825 helix: 1.89 (0.09), residues: 3496 sheet: 0.11 (0.11), residues: 1976 loop : 0.12 (0.11), residues: 3353 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17650 Ramachandran restraints generated. 8825 Oldfield, 0 Emsley, 8825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17650 Ramachandran restraints generated. 8825 Oldfield, 0 Emsley, 8825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 7024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 366 time to evaluate : 6.277 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: 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 outliers start: 4 outliers final: 0 residues processed: 370 average time/residue: 0.8017 time to fit residues: 484.4969 Evaluate side-chains 275 residues out of total 7024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 275 time to evaluate : 6.317 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.2910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 880 random chunks: chunk 743 optimal weight: 20.0000 chunk 666 optimal weight: 8.9990 chunk 370 optimal weight: 5.9990 chunk 227 optimal weight: 10.0000 chunk 449 optimal weight: 9.9990 chunk 356 optimal weight: 10.0000 chunk 689 optimal weight: 10.0000 chunk 266 optimal weight: 8.9990 chunk 419 optimal weight: 9.9990 chunk 513 optimal weight: 40.0000 chunk 799 optimal weight: 9.9990 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 HIS ** C 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 ASN D 558 ASN E 274 HIS ** F 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 395 GLN ** m 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 165 ASN G 98 GLN ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 98 GLN J 101 ASN ** K 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 114 GLN ** L 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 415 GLN ** R 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 415 GLN ** T 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 437 GLN ** U 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 415 GLN ** X 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 216 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4595 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.064 69412 Z= 0.328 Angle : 0.687 11.698 93930 Z= 0.372 Chirality : 0.046 0.207 10704 Planarity : 0.006 0.074 12361 Dihedral : 4.643 26.741 9913 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 31.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer Outliers : 0.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.09), residues: 8825 helix: 1.29 (0.08), residues: 3514 sheet: -0.50 (0.11), residues: 2022 loop : -0.07 (0.12), residues: 3289 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17650 Ramachandran restraints generated. 8825 Oldfield, 0 Emsley, 8825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17650 Ramachandran restraints generated. 8825 Oldfield, 0 Emsley, 8825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 7024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 277 time to evaluate : 6.412 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: symmetry clash outliers start: 44 outliers final: 19 residues processed: 318 average time/residue: 0.7443 time to fit residues: 395.4195 Evaluate side-chains 271 residues out of total 7024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 252 time to evaluate : 6.325 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.5280 time to fit residues: 27.8297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 880 random chunks: chunk 444 optimal weight: 20.0000 chunk 248 optimal weight: 8.9990 chunk 665 optimal weight: 40.0000 chunk 544 optimal weight: 20.0000 chunk 220 optimal weight: 2.9990 chunk 800 optimal weight: 8.9990 chunk 864 optimal weight: 8.9990 chunk 712 optimal weight: 8.9990 chunk 793 optimal weight: 20.0000 chunk 272 optimal weight: 9.9990 chunk 642 optimal weight: 30.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 493 ASN F 308 ASN ** F 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 105 GLN ** m 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 165 ASN ** n 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 165 ASN ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 98 GLN K 98 GLN ** K 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4615 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.078 69412 Z= 0.272 Angle : 0.614 8.006 93930 Z= 0.334 Chirality : 0.045 0.188 10704 Planarity : 0.005 0.052 12361 Dihedral : 4.601 33.221 9913 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 29.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer Outliers : 1.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.09), residues: 8825 helix: 1.30 (0.08), residues: 3495 sheet: -0.72 (0.11), residues: 2039 loop : -0.12 (0.12), residues: 3291 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17650 Ramachandran restraints generated. 8825 Oldfield, 0 Emsley, 8825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17650 Ramachandran restraints generated. 8825 Oldfield, 0 Emsley, 8825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 7024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 269 time to evaluate : 6.369 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 outliers start: 84 outliers final: 38 residues processed: 340 average time/residue: 0.7255 time to fit residues: 417.0988 Evaluate side-chains 274 residues out of total 7024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 236 time to evaluate : 6.329 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.6356 time to fit residues: 51.7280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 880 random chunks: chunk 790 optimal weight: 30.0000 chunk 601 optimal weight: 9.9990 chunk 415 optimal weight: 9.9990 chunk 88 optimal weight: 50.0000 chunk 382 optimal weight: 9.9990 chunk 537 optimal weight: 20.0000 chunk 803 optimal weight: 0.5980 chunk 850 optimal weight: 7.9990 chunk 419 optimal weight: 3.9990 chunk 761 optimal weight: 2.9990 chunk 229 optimal weight: 20.0000 overall best weight: 5.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 114 GLN ** n 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 129 HIS J 98 GLN ** K 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 114 GLN K 216 ASN ** L 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 381 ASN ** Z 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 381 ASN ** a 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 390 ASN ** c 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4593 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 69412 Z= 0.218 Angle : 0.575 10.437 93930 Z= 0.308 Chirality : 0.044 0.174 10704 Planarity : 0.004 0.062 12361 Dihedral : 4.495 39.770 9913 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 27.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer Outliers : 1.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.09), residues: 8825 helix: 1.42 (0.08), residues: 3519 sheet: -0.57 (0.12), residues: 1966 loop : -0.15 (0.11), residues: 3340 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17650 Ramachandran restraints generated. 8825 Oldfield, 0 Emsley, 8825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17650 Ramachandran restraints generated. 8825 Oldfield, 0 Emsley, 8825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 7024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 253 time to evaluate : 6.313 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 outliers start: 77 outliers final: 25 residues processed: 326 average time/residue: 0.7160 time to fit residues: 400.4076 Evaluate side-chains 256 residues out of total 7024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 231 time to evaluate : 6.226 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 25 outliers final: 1 residues processed: 25 average time/residue: 0.5037 time to fit residues: 32.4274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 880 random chunks: chunk 708 optimal weight: 5.9990 chunk 482 optimal weight: 20.0000 chunk 12 optimal weight: 30.0000 chunk 633 optimal weight: 2.9990 chunk 350 optimal weight: 8.9990 chunk 725 optimal weight: 20.0000 chunk 587 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 434 optimal weight: 10.0000 chunk 763 optimal weight: 9.9990 chunk 214 optimal weight: 50.0000 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 HIS B 408 ASN ** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 HIS ** C 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 73 ASN ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 165 ASN ** K 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 98 GLN ** L 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 415 GLN ** T 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 415 GLN Y 415 GLN ** Z 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 415 GLN ** f 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4728 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.070 69412 Z= 0.293 Angle : 0.666 13.153 93930 Z= 0.357 Chirality : 0.046 0.260 10704 Planarity : 0.006 0.064 12361 Dihedral : 4.824 46.302 9913 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 35.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer Outliers : 1.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.09), residues: 8825 helix: 1.01 (0.08), residues: 3530 sheet: -0.71 (0.12), residues: 1933 loop : -0.36 (0.11), residues: 3362 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17650 Ramachandran restraints generated. 8825 Oldfield, 0 Emsley, 8825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17650 Ramachandran restraints generated. 8825 Oldfield, 0 Emsley, 8825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 7024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 245 time to evaluate : 7.016 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 outliers start: 108 outliers final: 46 residues processed: 346 average time/residue: 0.7222 time to fit residues: 428.9829 Evaluate side-chains 267 residues out of total 7024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 221 time to evaluate : 6.339 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 0 residues processed: 46 average time/residue: 0.5933 time to fit residues: 57.3953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 880 random chunks: chunk 286 optimal weight: 10.0000 chunk 766 optimal weight: 20.0000 chunk 168 optimal weight: 0.0570 chunk 499 optimal weight: 9.9990 chunk 209 optimal weight: 50.0000 chunk 851 optimal weight: 8.9990 chunk 706 optimal weight: 30.0000 chunk 394 optimal weight: 8.9990 chunk 70 optimal weight: 40.0000 chunk 281 optimal weight: 40.0000 chunk 446 optimal weight: 0.7980 overall best weight: 5.7704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 529 ASN ** D 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4680 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.065 69412 Z= 0.231 Angle : 0.609 11.713 93930 Z= 0.323 Chirality : 0.044 0.289 10704 Planarity : 0.005 0.048 12361 Dihedral : 4.720 52.376 9913 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 31.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer Outliers : 1.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.09), residues: 8825 helix: 1.18 (0.09), residues: 3529 sheet: -0.59 (0.12), residues: 1877 loop : -0.35 (0.11), residues: 3419 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17650 Ramachandran restraints generated. 8825 Oldfield, 0 Emsley, 8825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17650 Ramachandran restraints generated. 8825 Oldfield, 0 Emsley, 8825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 7024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 236 time to evaluate : 6.435 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 outliers start: 73 outliers final: 39 residues processed: 306 average time/residue: 0.7096 time to fit residues: 372.6897 Evaluate side-chains 261 residues out of total 7024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 222 time to evaluate : 6.370 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.5614 time to fit residues: 48.7276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 880 random chunks: chunk 820 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 485 optimal weight: 30.0000 chunk 621 optimal weight: 9.9990 chunk 481 optimal weight: 8.9990 chunk 716 optimal weight: 20.0000 chunk 475 optimal weight: 20.0000 chunk 848 optimal weight: 0.6980 chunk 530 optimal weight: 9.9990 chunk 517 optimal weight: 20.0000 chunk 391 optimal weight: 5.9990 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 152 HIS G 231 GLN ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 415 GLN ** X 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 172 GLN ** O 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 105 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4682 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 69412 Z= 0.225 Angle : 0.610 12.402 93930 Z= 0.322 Chirality : 0.044 0.230 10704 Planarity : 0.005 0.048 12361 Dihedral : 4.702 57.442 9913 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 31.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer Outliers : 0.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.09), residues: 8825 helix: 1.16 (0.09), residues: 3556 sheet: -0.63 (0.12), residues: 1882 loop : -0.37 (0.11), residues: 3387 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17650 Ramachandran restraints generated. 8825 Oldfield, 0 Emsley, 8825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17650 Ramachandran restraints generated. 8825 Oldfield, 0 Emsley, 8825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 7024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 234 time to evaluate : 6.381 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 outliers start: 59 outliers final: 26 residues processed: 287 average time/residue: 0.7252 time to fit residues: 357.9074 Evaluate side-chains 244 residues out of total 7024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 218 time to evaluate : 6.274 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.5564 time to fit residues: 34.8862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 880 random chunks: chunk 524 optimal weight: 0.0270 chunk 338 optimal weight: 30.0000 chunk 506 optimal weight: 40.0000 chunk 255 optimal weight: 40.0000 chunk 166 optimal weight: 0.0010 chunk 164 optimal weight: 1.9990 chunk 539 optimal weight: 5.9990 chunk 577 optimal weight: 10.0000 chunk 419 optimal weight: 5.9990 chunk 79 optimal weight: 30.0000 chunk 666 optimal weight: 20.0000 overall best weight: 2.8050 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 514 ASN ** l 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 GLN ** H 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 381 ASN ** R 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 381 ASN ** T 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 381 ASN ** a 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4595 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 69412 Z= 0.177 Angle : 0.590 16.328 93930 Z= 0.306 Chirality : 0.044 0.199 10704 Planarity : 0.004 0.056 12361 Dihedral : 4.540 58.031 9913 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 25.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.09), residues: 8825 helix: 1.37 (0.09), residues: 3552 sheet: -0.54 (0.12), residues: 1889 loop : -0.26 (0.11), residues: 3384 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17650 Ramachandran restraints generated. 8825 Oldfield, 0 Emsley, 8825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17650 Ramachandran restraints generated. 8825 Oldfield, 0 Emsley, 8825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 7024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 238 time to evaluate : 6.336 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 outliers start: 21 outliers final: 7 residues processed: 258 average time/residue: 0.7817 time to fit residues: 342.8535 Evaluate side-chains 224 residues out of total 7024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 217 time to evaluate : 6.312 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.5541 time to fit residues: 15.5399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 880 random chunks: chunk 771 optimal weight: 10.0000 chunk 812 optimal weight: 2.9990 chunk 741 optimal weight: 8.9990 chunk 790 optimal weight: 40.0000 chunk 475 optimal weight: 20.0000 chunk 344 optimal weight: 5.9990 chunk 620 optimal weight: 0.2980 chunk 242 optimal weight: 30.0000 chunk 714 optimal weight: 6.9990 chunk 747 optimal weight: 5.9990 chunk 787 optimal weight: 6.9990 overall best weight: 4.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 514 ASN ** k 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 174 ASN l 231 GLN ** H 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 381 ASN ** R 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 381 ASN ** S 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 381 ASN ** e 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4642 moved from start: 0.4563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 69412 Z= 0.202 Angle : 0.611 15.093 93930 Z= 0.318 Chirality : 0.044 0.227 10704 Planarity : 0.004 0.073 12361 Dihedral : 4.568 58.592 9913 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 28.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.09), residues: 8825 helix: 1.35 (0.09), residues: 3565 sheet: -0.50 (0.12), residues: 1873 loop : -0.31 (0.11), residues: 3387 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17650 Ramachandran restraints generated. 8825 Oldfield, 0 Emsley, 8825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17650 Ramachandran restraints generated. 8825 Oldfield, 0 Emsley, 8825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 7024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 222 time to evaluate : 6.344 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 outliers start: 25 outliers final: 14 residues processed: 244 average time/residue: 0.7501 time to fit residues: 315.5044 Evaluate side-chains 229 residues out of total 7024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 215 time to evaluate : 6.366 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.6128 time to fit residues: 24.1021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 880 random chunks: chunk 519 optimal weight: 7.9990 chunk 835 optimal weight: 20.0000 chunk 510 optimal weight: 0.6980 chunk 396 optimal weight: 6.9990 chunk 581 optimal weight: 10.0000 chunk 876 optimal weight: 10.0000 chunk 806 optimal weight: 6.9990 chunk 698 optimal weight: 7.9990 chunk 72 optimal weight: 50.0000 chunk 539 optimal weight: 5.9990 chunk 428 optimal weight: 5.9990 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 514 ASN ** k 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 381 ASN ** a 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 381 ASN ** e 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4689 moved from start: 0.4988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.067 69412 Z= 0.227 Angle : 0.641 13.525 93930 Z= 0.336 Chirality : 0.045 0.326 10704 Planarity : 0.005 0.064 12361 Dihedral : 4.720 61.303 9913 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 31.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.09), residues: 8825 helix: 1.19 (0.09), residues: 3566 sheet: -0.58 (0.12), residues: 1851 loop : -0.34 (0.11), residues: 3408 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17650 Ramachandran restraints generated. 8825 Oldfield, 0 Emsley, 8825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17650 Ramachandran restraints generated. 8825 Oldfield, 0 Emsley, 8825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 7024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 221 time to evaluate : 6.421 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 outliers start: 13 outliers final: 4 residues processed: 232 average time/residue: 0.7450 time to fit residues: 296.0718 Evaluate side-chains 219 residues out of total 7024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 215 time to evaluate : 6.389 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.8003 time to fit residues: 14.5788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 880 random chunks: chunk 554 optimal weight: 0.4980 chunk 743 optimal weight: 5.9990 chunk 213 optimal weight: 50.0000 chunk 643 optimal weight: 7.9990 chunk 103 optimal weight: 30.0000 chunk 194 optimal weight: 20.0000 chunk 699 optimal weight: 8.9990 chunk 292 optimal weight: 2.9990 chunk 718 optimal weight: 9.9990 chunk 88 optimal weight: 7.9990 chunk 128 optimal weight: 6.9990 overall best weight: 4.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 98 GLN ** H 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.112024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.108149 restraints weight = 514350.114| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 1.88 r_work: 0.3629 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5543 moved from start: 0.5160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 69412 Z= 0.214 Angle : 0.631 13.021 93930 Z= 0.329 Chirality : 0.044 0.228 10704 Planarity : 0.004 0.061 12361 Dihedral : 4.695 62.454 9913 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 31.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.09), residues: 8825 helix: 1.22 (0.09), residues: 3565 sheet: -0.62 (0.12), residues: 2015 loop : -0.44 (0.12), residues: 3245 =============================================================================== Job complete usr+sys time: 9455.55 seconds wall clock time: 172 minutes 30.67 seconds (10350.67 seconds total)