Starting phenix.real_space_refine (version: dev) on Wed Dec 14 03:02:52 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d6x_27225/12_2022/8d6x_27225.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d6x_27225/12_2022/8d6x_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_27225/12_2022/8d6x_27225.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d6x_27225/12_2022/8d6x_27225.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d6x_27225/12_2022/8d6x_27225.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d6x_27225/12_2022/8d6x_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 Convert atoms to be neutral 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: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 27.80, 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: 22.88 Conformation dependent library (CDL) restraints added in 8.2 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: 3.15 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: 32.17 Time building geometry restraints manager: 25.22 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 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. 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: 5.330 Check model and map are aligned: 0.750 Convert atoms to be neutral: 0.440 Process input model: 145.950 Find NCS groups from input model: 4.560 Set up NCS constraints: 0.520 Set refine NCS operators: 0.000 Set scattering table: 0.030 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:2.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 160.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4183 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 : 17.80 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 : 6.202 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: 0.7668 time to fit residues: 464.0408 Evaluate side-chains 275 residues out of total 7024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 275 time to evaluate : 6.132 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.1077 ------------------------------------------------------------------------------- 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: 0.4458 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 11.699 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 : 31.96 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 : 6.206 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: 0.6988 time to fit residues: 371.9441 Evaluate side-chains 271 residues out of total 7024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 252 time to evaluate : 6.119 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.5163 time to fit residues: 26.3115 ------------------------------------------------------------------------------- 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: 7.9990 chunk 864 optimal weight: 4.9990 chunk 712 optimal weight: 9.9990 chunk 793 optimal weight: 20.0000 chunk 272 optimal weight: 10.0000 chunk 642 optimal weight: 20.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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 ** 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** ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 98 GLN ** 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** ** 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** ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4440 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.081 69412 Z= 0.251 Angle : 0.595 7.817 93930 Z= 0.322 Chirality : 0.044 0.205 10704 Planarity : 0.005 0.061 12361 Dihedral : 4.506 32.208 9913 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 27.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer Outliers : 1.03 % 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: 0.51 (0.09), residues: 8825 helix: 1.39 (0.08), residues: 3508 sheet: -0.50 (0.12), residues: 1969 loop : -0.10 (0.11), residues: 3348 *********************** 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 340 residues out of total 7024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 268 time to evaluate : 6.130 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 outliers start: 72 outliers final: 29 residues processed: 329 average time/residue: 0.7188 time to fit residues: 403.2155 Evaluate side-chains 265 residues out of total 7024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 236 time to evaluate : 6.107 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.5684 time to fit residues: 38.0676 ------------------------------------------------------------------------------- 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: 40.0000 chunk 601 optimal weight: 8.9990 chunk 415 optimal weight: 5.9990 chunk 88 optimal weight: 9.9990 chunk 382 optimal weight: 20.0000 chunk 537 optimal weight: 20.0000 chunk 803 optimal weight: 6.9990 chunk 850 optimal weight: 6.9990 chunk 419 optimal weight: 8.9990 chunk 761 optimal weight: 6.9990 chunk 229 optimal weight: 0.6980 overall best weight: 5.5388 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 11 GLN ** 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** G 165 ASN ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 129 HIS ** J 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 216 ASN ** 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** Y 415 GLN ** Z 381 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 ** 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: 0.4448 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 0.061 69412 Z= 0.227 Angle : 0.581 10.328 93930 Z= 0.311 Chirality : 0.044 0.242 10704 Planarity : 0.005 0.062 12361 Dihedral : 4.481 39.990 9913 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 28.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer Outliers : 1.18 % 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: 0.52 (0.09), residues: 8825 helix: 1.46 (0.08), residues: 3520 sheet: -0.54 (0.12), residues: 1965 loop : -0.15 (0.12), 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 336 residues out of total 7024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 253 time to evaluate : 6.041 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 outliers start: 83 outliers final: 33 residues processed: 330 average time/residue: 0.6871 time to fit residues: 389.3710 Evaluate side-chains 270 residues out of total 7024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 237 time to evaluate : 6.033 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.5004 time to fit residues: 39.3985 ------------------------------------------------------------------------------- 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: 3.9990 chunk 482 optimal weight: 20.0000 chunk 12 optimal weight: 50.0000 chunk 633 optimal weight: 3.9990 chunk 350 optimal weight: 9.9990 chunk 725 optimal weight: 20.0000 chunk 587 optimal weight: 20.0000 chunk 1 optimal weight: 9.9990 chunk 434 optimal weight: 20.0000 chunk 763 optimal weight: 10.0000 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 ** J 98 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 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** X 415 GLN ** Z 381 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** ** b 381 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4564 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.079 69412 Z= 0.294 Angle : 0.665 13.337 93930 Z= 0.357 Chirality : 0.046 0.256 10704 Planarity : 0.006 0.061 12361 Dihedral : 4.798 45.696 9913 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 35.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer Outliers : 1.44 % 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: 0.10 (0.09), residues: 8825 helix: 1.03 (0.08), residues: 3530 sheet: -0.70 (0.12), residues: 1948 loop : -0.33 (0.11), residues: 3347 *********************** 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 349 residues out of total 7024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 248 time to evaluate : 6.249 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 outliers start: 101 outliers final: 40 residues processed: 341 average time/residue: 0.6605 time to fit residues: 384.8438 Evaluate side-chains 269 residues out of total 7024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 229 time to evaluate : 6.048 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.5449 time to fit residues: 47.2542 ------------------------------------------------------------------------------- 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: 9.9990 chunk 766 optimal weight: 20.0000 chunk 168 optimal weight: 6.9990 chunk 499 optimal weight: 8.9990 chunk 209 optimal weight: 50.0000 chunk 851 optimal weight: 9.9990 chunk 706 optimal weight: 20.0000 chunk 394 optimal weight: 8.9990 chunk 70 optimal weight: 50.0000 chunk 281 optimal weight: 40.0000 chunk 446 optimal weight: 8.9990 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 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** G 231 GLN ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 98 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 98 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 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 ** W 381 ASN ** 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 381 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 396 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** ** d 172 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4612 moved from start: 0.4376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.076 69412 Z= 0.311 Angle : 0.672 12.722 93930 Z= 0.360 Chirality : 0.046 0.366 10704 Planarity : 0.006 0.060 12361 Dihedral : 4.963 56.573 9913 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 37.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer Outliers : 1.42 % 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: -0.10 (0.09), residues: 8825 helix: 0.89 (0.08), residues: 3510 sheet: -0.72 (0.12), residues: 1883 loop : -0.53 (0.11), residues: 3432 *********************** 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 334 residues out of total 7024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 234 time to evaluate : 6.052 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 outliers start: 100 outliers final: 53 residues processed: 327 average time/residue: 0.6567 time to fit residues: 369.6933 Evaluate side-chains 277 residues out of total 7024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 224 time to evaluate : 6.055 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 0 residues processed: 53 average time/residue: 0.5404 time to fit residues: 60.3372 ------------------------------------------------------------------------------- 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: 0.9990 chunk 485 optimal weight: 20.0000 chunk 621 optimal weight: 20.0000 chunk 481 optimal weight: 20.0000 chunk 716 optimal weight: 10.0000 chunk 475 optimal weight: 5.9990 chunk 848 optimal weight: 7.9990 chunk 530 optimal weight: 0.9980 chunk 517 optimal weight: 20.0000 chunk 391 optimal weight: 5.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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 ** l 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 152 HIS ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 98 GLN ** 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** ** R 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 381 ASN ** Z 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 381 ASN ** a 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4493 moved from start: 0.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 69412 Z= 0.204 Angle : 0.600 11.677 93930 Z= 0.315 Chirality : 0.044 0.188 10704 Planarity : 0.004 0.047 12361 Dihedral : 4.723 59.188 9913 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 29.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer Outliers : 0.73 % 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: 1.15 (0.09), residues: 3556 sheet: -0.62 (0.12), residues: 1873 loop : -0.36 (0.11), residues: 3396 *********************** 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: 51 poor density : 242 time to evaluate : 7.853 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 outliers start: 51 outliers final: 21 residues processed: 288 average time/residue: 0.7105 time to fit residues: 347.2380 Evaluate side-chains 239 residues out of total 7024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 218 time to evaluate : 6.045 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.5596 time to fit residues: 29.1346 ------------------------------------------------------------------------------- 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: 0.0040 chunk 338 optimal weight: 20.0000 chunk 506 optimal weight: 40.0000 chunk 255 optimal weight: 7.9990 chunk 166 optimal weight: 5.9990 chunk 164 optimal weight: 8.9990 chunk 539 optimal weight: 0.8980 chunk 577 optimal weight: 7.9990 chunk 419 optimal weight: 5.9990 chunk 79 optimal weight: 30.0000 chunk 666 optimal weight: 5.9990 overall best weight: 3.7798 ------------------------------------------------------------------------------- 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 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 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 331 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** H 11 GLN ** J 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 73 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 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** ** X 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** O 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4490 moved from start: 0.4511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 69412 Z= 0.198 Angle : 0.604 13.983 93930 Z= 0.315 Chirality : 0.044 0.186 10704 Planarity : 0.004 0.066 12361 Dihedral : 4.649 60.012 9913 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 28.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer Outliers : 0.48 % 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: 0.30 (0.09), residues: 8825 helix: 1.26 (0.09), residues: 3563 sheet: -0.60 (0.12), residues: 1865 loop : -0.33 (0.11), residues: 3397 *********************** 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 265 residues out of total 7024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 231 time to evaluate : 6.180 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: 34 outliers final: 21 residues processed: 257 average time/residue: 0.7080 time to fit residues: 310.4511 Evaluate side-chains 241 residues out of total 7024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 220 time to evaluate : 6.067 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.5750 time to fit residues: 29.5114 ------------------------------------------------------------------------------- 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: 9.9990 chunk 812 optimal weight: 20.0000 chunk 741 optimal weight: 20.0000 chunk 790 optimal weight: 10.0000 chunk 475 optimal weight: 20.0000 chunk 344 optimal weight: 6.9990 chunk 620 optimal weight: 9.9990 chunk 242 optimal weight: 30.0000 chunk 714 optimal weight: 10.0000 chunk 747 optimal weight: 9.9990 chunk 787 optimal weight: 10.0000 overall best weight: 9.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 HIS ** 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 108 HIS C 348 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 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 11 GLN ** l 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 174 ASN l 216 ASN l 231 GLN n 98 GLN ** H 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 381 ASN ** 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** ** X 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 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** ** 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** ** O 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4691 moved from start: 0.5457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.075 69412 Z= 0.349 Angle : 0.760 15.843 93930 Z= 0.405 Chirality : 0.048 0.230 10704 Planarity : 0.007 0.087 12361 Dihedral : 5.303 66.201 9913 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 45.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer Outliers : 0.51 % 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: -0.47 (0.09), residues: 8825 helix: 0.56 (0.08), residues: 3532 sheet: -0.99 (0.12), residues: 1886 loop : -0.66 (0.11), residues: 3407 *********************** 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 259 residues out of total 7024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 223 time to evaluate : 6.128 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 outliers start: 36 outliers final: 14 residues processed: 255 average time/residue: 0.7089 time to fit residues: 307.5231 Evaluate side-chains 230 residues out of total 7024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 216 time to evaluate : 6.111 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.7463 time to fit residues: 24.6630 ------------------------------------------------------------------------------- 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: 6.9990 chunk 835 optimal weight: 9.9990 chunk 510 optimal weight: 2.9990 chunk 396 optimal weight: 6.9990 chunk 581 optimal weight: 5.9990 chunk 876 optimal weight: 1.9990 chunk 806 optimal weight: 10.0000 chunk 698 optimal weight: 6.9990 chunk 72 optimal weight: 50.0000 chunk 539 optimal weight: 5.9990 chunk 428 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 108 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 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 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 73 ASN ** H 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 98 GLN ** 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 98 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 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 381 ASN ** e 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4565 moved from start: 0.5427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 69412 Z= 0.226 Angle : 0.652 13.219 93930 Z= 0.341 Chirality : 0.045 0.254 10704 Planarity : 0.005 0.063 12361 Dihedral : 5.009 68.113 9913 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 33.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.15 (0.09), residues: 8825 helix: 0.89 (0.08), residues: 3562 sheet: -0.93 (0.12), residues: 1885 loop : -0.51 (0.11), residues: 3378 ********************** 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 242 residues out of total 7024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 229 time to evaluate : 6.170 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 outliers start: 13 outliers final: 5 residues processed: 240 average time/residue: 0.7080 time to fit residues: 290.4094 Evaluate side-chains 224 residues out of total 7024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 219 time to evaluate : 6.102 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.6845 time to fit residues: 13.7513 ------------------------------------------------------------------------------- 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: 0.1980 chunk 743 optimal weight: 5.9990 chunk 213 optimal weight: 20.0000 chunk 643 optimal weight: 50.0000 chunk 103 optimal weight: 9.9990 chunk 194 optimal weight: 7.9990 chunk 699 optimal weight: 10.0000 chunk 292 optimal weight: 0.2980 chunk 718 optimal weight: 5.9990 chunk 88 optimal weight: 50.0000 chunk 128 optimal weight: 5.9990 overall best weight: 3.6986 ------------------------------------------------------------------------------- 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 108 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** ** 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** F 514 ASN ** k 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 11 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** ** 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 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 390 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** ** Y 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 381 ASN ** a 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.111445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.107746 restraints weight = 516797.119| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 1.84 r_work: 0.3723 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3473 moved from start: 0.5479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 69412 Z= 0.204 Angle : 0.649 15.695 93930 Z= 0.337 Chirality : 0.045 0.240 10704 Planarity : 0.005 0.088 12361 Dihedral : 4.868 68.579 9913 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 30.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer Outliers : 0.23 % 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: 0.03 (0.09), residues: 8825 helix: 1.07 (0.09), residues: 3566 sheet: -0.83 (0.12), residues: 1878 loop : -0.46 (0.11), residues: 3381 =============================================================================== Job complete usr+sys time: 8787.18 seconds wall clock time: 163 minutes 13.03 seconds (9793.03 seconds total)