Starting phenix.real_space_refine (version: 1.21rc1) on Wed Apr 26 02:46:24 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dnh_30783/04_2023/7dnh_30783.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dnh_30783/04_2023/7dnh_30783.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dnh_30783/04_2023/7dnh_30783.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dnh_30783/04_2023/7dnh_30783.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dnh_30783/04_2023/7dnh_30783.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dnh_30783/04_2023/7dnh_30783.pdb" } resolution = 3.64 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= 0.002 sd= 1.261 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 13857 2.51 5 N 3628 2.21 5 O 4183 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 8": "OE1" <-> "OE2" Residue "B TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 80": "OD1" <-> "OD2" Residue "B GLU 107": "OE1" <-> "OE2" Residue "B ARG 110": "NH1" <-> "NH2" Residue "B ASP 129": "OD1" <-> "OD2" Residue "B ASP 151": "OD1" <-> "OD2" Residue "B GLU 196": "OE1" <-> "OE2" Residue "B ASP 233": "OD1" <-> "OD2" Residue "B ARG 251": "NH1" <-> "NH2" Residue "B GLU 253": "OE1" <-> "OE2" Residue "B ARG 263": "NH1" <-> "NH2" Residue "B GLU 269": "OE1" <-> "OE2" Residue "B ASP 273": "OD1" <-> "OD2" Residue "B ASP 335": "OD1" <-> "OD2" Residue "B GLU 347": "OE1" <-> "OE2" Residue "B TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 357": "OD1" <-> "OD2" Residue "B GLU 368": "OE1" <-> "OE2" Residue "B TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 370": "OD1" <-> "OD2" Residue "B PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 385": "OE1" <-> "OE2" Residue "B ASP 394": "OD1" <-> "OD2" Residue "B ASP 415": "OD1" <-> "OD2" Residue "B ASP 457": "OD1" <-> "OD2" Residue "B ASP 459": "OD1" <-> "OD2" Residue "B ARG 465": "NH1" <-> "NH2" Residue "A ASP 25": "OD1" <-> "OD2" Residue "A GLU 26": "OE1" <-> "OE2" Residue "A TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 80": "OD1" <-> "OD2" Residue "A PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 95": "OD1" <-> "OD2" Residue "A TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 129": "OD1" <-> "OD2" Residue "A GLU 146": "OE1" <-> "OE2" Residue "A ASP 151": "OD1" <-> "OD2" Residue "A ASP 184": "OD1" <-> "OD2" Residue "A GLU 189": "OE1" <-> "OE2" Residue "A GLU 196": "OE1" <-> "OE2" Residue "A ASP 209": "OD1" <-> "OD2" Residue "A ASP 223": "OD1" <-> "OD2" Residue "A GLU 253": "OE1" <-> "OE2" Residue "A ASP 335": "OD1" <-> "OD2" Residue "A ASP 357": "OD1" <-> "OD2" Residue "A ARG 364": "NH1" <-> "NH2" Residue "A GLU 367": "OE1" <-> "OE2" Residue "A ASP 370": "OD1" <-> "OD2" Residue "A GLU 399": "OE1" <-> "OE2" Residue "A ASP 400": "OD1" <-> "OD2" Residue "A ARG 418": "NH1" <-> "NH2" Residue "A GLU 452": "OE1" <-> "OE2" Residue "A ARG 465": "NH1" <-> "NH2" Residue "C TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 72": "NH1" <-> "NH2" Residue "C ASP 80": "OD1" <-> "OD2" Residue "C ASP 95": "OD1" <-> "OD2" Residue "C ASP 129": "OD1" <-> "OD2" Residue "C GLU 131": "OE1" <-> "OE2" Residue "C ASP 143": "OD1" <-> "OD2" Residue "C GLU 146": "OE1" <-> "OE2" Residue "C ASP 151": "OD1" <-> "OD2" Residue "C GLU 168": "OE1" <-> "OE2" Residue "C ASP 184": "OD1" <-> "OD2" Residue "C PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 223": "OD1" <-> "OD2" Residue "C GLU 253": "OE1" <-> "OE2" Residue "C PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 335": "OD1" <-> "OD2" Residue "C GLU 347": "OE1" <-> "OE2" Residue "C GLU 361": "OE1" <-> "OE2" Residue "C ARG 364": "NH1" <-> "NH2" Residue "C GLU 367": "OE1" <-> "OE2" Residue "C ASP 370": "OD1" <-> "OD2" Residue "C ASP 438": "OD1" <-> "OD2" Residue "C GLU 452": "OE1" <-> "OE2" Residue "C ASP 457": "OD1" <-> "OD2" Residue "D TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 88": "OD1" <-> "OD2" Residue "D TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 146": "OE1" <-> "OE2" Residue "D ASP 209": "OD1" <-> "OD2" Residue "D PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 219": "OD1" <-> "OD2" Residue "D ASP 244": "OD1" <-> "OD2" Residue "D GLU 253": "OE1" <-> "OE2" Residue "D GLU 269": "OE1" <-> "OE2" Residue "D ASP 335": "OD1" <-> "OD2" Residue "D GLU 351": "OE1" <-> "OE2" Residue "D PHE 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 361": "OE1" <-> "OE2" Residue "D GLU 367": "OE1" <-> "OE2" Residue "D GLU 368": "OE1" <-> "OE2" Residue "D TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 399": "OE1" <-> "OE2" Residue "D ASP 400": "OD1" <-> "OD2" Residue "D PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 418": "NH1" <-> "NH2" Residue "D GLU 437": "OE1" <-> "OE2" Residue "D GLU 447": "OE1" <-> "OE2" Residue "D ASP 457": "OD1" <-> "OD2" Residue "E GLU 8": "OE1" <-> "OE2" Residue "E PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 80": "OD1" <-> "OD2" Residue "E PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 95": "OD1" <-> "OD2" Residue "E TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 143": "OD1" <-> "OD2" Residue "E ARG 145": "NH1" <-> "NH2" Residue "E GLU 146": "OE1" <-> "OE2" Residue "E GLU 189": "OE1" <-> "OE2" Residue "E ASP 202": "OD1" <-> "OD2" Residue "E PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 244": "OD1" <-> "OD2" Residue "E GLU 253": "OE1" <-> "OE2" Residue "E ASP 273": "OD1" <-> "OD2" Residue "E GLU 361": "OE1" <-> "OE2" Residue "E ASP 370": "OD1" <-> "OD2" Residue "E PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 385": "OE1" <-> "OE2" Residue "E TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 400": "OD1" <-> "OD2" Residue "E PHE 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 437": "OE1" <-> "OE2" Residue "E ASP 438": "OD1" <-> "OD2" Residue "E GLU 452": "OE1" <-> "OE2" Residue "L ASP 1": "OD1" <-> "OD2" Residue "L GLU 17": "OE1" <-> "OE2" Residue "L GLU 27": "OE1" <-> "OE2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 105": "OE1" <-> "OE2" Residue "L PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 143": "OD1" <-> "OD2" Residue "L ASP 165": "OD1" <-> "OD2" Residue "L TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 185": "OE1" <-> "OE2" Residue "L TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 55": "OD1" <-> "OD2" Residue "H PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 73": "OD1" <-> "OD2" Residue "H TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 90": "OD1" <-> "OD2" Residue "H PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 212": "OD1" <-> "OD2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 21788 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 3743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3743 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 33, 'TRANS': 438} Chain: "A" Number of atoms: 3671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3671 Classifications: {'peptide': 463} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 430} Chain: "C" Number of atoms: 3743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3743 Classifications: {'peptide': 472} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 438} Chain: "D" Number of atoms: 3603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3603 Classifications: {'peptide': 454} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 424} Chain: "E" Number of atoms: 3745 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 472, 3743 Classifications: {'peptide': 472} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 32, 'TRANS': 437} Conformer: "B" Number of residues, atoms: 472, 3743 Classifications: {'peptide': 472} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 32, 'TRANS': 437} bond proxies already assigned to first conformer: 3843 Chain: "L" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1658 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 6, 'TRANS': 204} Chain: "H" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1625 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 200} Time building chain proxies: 12.51, per 1000 atoms: 0.57 Number of scatterers: 21788 At special positions: 0 Unit cell: (172.634, 179.36, 158.061, 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 120 16.00 O 4183 8.00 N 3628 7.00 C 13857 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 145 " - pdb=" SG CYS H 200 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.30 Conformation dependent library (CDL) restraints added in 3.4 seconds 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5140 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 50 sheets defined 11.1% alpha, 29.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'B' and resid 233 through 238 Processing helix chain 'B' and resid 272 through 276 removed outlier: 3.802A pdb=" N LEU B 275 " --> pdb=" O PRO B 272 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N TYR B 276 " --> pdb=" O ASP B 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 272 through 276' Processing helix chain 'B' and resid 280 through 285 removed outlier: 3.763A pdb=" N ALA B 284 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL B 285 " --> pdb=" O ASN B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 357 No H-bonds generated for 'chain 'B' and resid 355 through 357' Processing helix chain 'B' and resid 383 through 394 removed outlier: 3.558A pdb=" N MET B 387 " --> pdb=" O THR B 383 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR B 388 " --> pdb=" O ALA B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 402 removed outlier: 4.432A pdb=" N LEU B 398 " --> pdb=" O ASP B 394 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ASP B 400 " --> pdb=" O ASN B 396 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TRP B 401 " --> pdb=" O ILE B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.803A pdb=" N ASN B 441 " --> pdb=" O ASP B 438 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS B 442 " --> pdb=" O PRO B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 472 removed outlier: 4.091A pdb=" N GLN B 470 " --> pdb=" O LYS B 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 225 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.517A pdb=" N MET A 237 " --> pdb=" O ASP A 233 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA A 238 " --> pdb=" O TYR A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 276 removed outlier: 3.590A pdb=" N LEU A 275 " --> pdb=" O PRO A 272 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N TYR A 276 " --> pdb=" O ASP A 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 272 through 276' Processing helix chain 'A' and resid 324 through 328 removed outlier: 3.631A pdb=" N ASN A 327 " --> pdb=" O CYS A 324 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLN A 328 " --> pdb=" O TRP A 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 324 through 328' Processing helix chain 'A' and resid 355 through 357 No H-bonds generated for 'chain 'A' and resid 355 through 357' Processing helix chain 'A' and resid 383 through 394 removed outlier: 3.856A pdb=" N THR A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N TYR A 389 " --> pdb=" O GLU A 385 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR A 392 " --> pdb=" O THR A 388 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET A 393 " --> pdb=" O TYR A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 400 removed outlier: 3.555A pdb=" N ASP A 400 " --> pdb=" O ASN A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 443 removed outlier: 4.497A pdb=" N LYS A 442 " --> pdb=" O PRO A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 460 removed outlier: 4.138A pdb=" N GLN A 460 " --> pdb=" O ASP A 457 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 457 through 460' Processing helix chain 'A' and resid 461 through 472 removed outlier: 3.859A pdb=" N LEU A 469 " --> pdb=" O ARG A 465 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN A 470 " --> pdb=" O LYS A 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 84 removed outlier: 3.535A pdb=" N LYS C 83 " --> pdb=" O ASP C 80 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE C 84 " --> pdb=" O PRO C 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 80 through 84' Processing helix chain 'C' and resid 272 through 276 removed outlier: 3.880A pdb=" N LEU C 275 " --> pdb=" O PRO C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 394 Processing helix chain 'C' and resid 407 through 411 removed outlier: 3.666A pdb=" N ALA C 411 " --> pdb=" O PRO C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 442 removed outlier: 4.047A pdb=" N LYS C 442 " --> pdb=" O PRO C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 460 removed outlier: 4.176A pdb=" N GLN C 460 " --> pdb=" O ASP C 457 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 457 through 460' Processing helix chain 'C' and resid 461 through 472 removed outlier: 3.820A pdb=" N ARG C 465 " --> pdb=" O PHE C 461 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS C 466 " --> pdb=" O PRO C 462 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU C 469 " --> pdb=" O ARG C 465 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLN C 470 " --> pdb=" O LYS C 466 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER C 471 " --> pdb=" O PHE C 467 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY C 472 " --> pdb=" O LEU C 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 84 Processing helix chain 'D' and resid 324 through 328 removed outlier: 4.069A pdb=" N ASN D 327 " --> pdb=" O CYS D 324 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN D 328 " --> pdb=" O TRP D 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 324 through 328' Processing helix chain 'D' and resid 383 through 394 removed outlier: 3.766A pdb=" N TYR D 389 " --> pdb=" O GLU D 385 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N MET D 393 " --> pdb=" O TYR D 389 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASP D 394 " --> pdb=" O ILE D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 401 removed outlier: 3.611A pdb=" N ASP D 400 " --> pdb=" O ASN D 396 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N TRP D 401 " --> pdb=" O ILE D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 457 through 461 removed outlier: 3.811A pdb=" N GLN D 460 " --> pdb=" O ASP D 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 469 removed outlier: 3.989A pdb=" N LEU D 469 " --> pdb=" O ARG D 465 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 84 removed outlier: 3.596A pdb=" N LYS E 83 " --> pdb=" O ASP E 80 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE E 84 " --> pdb=" O PRO E 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 80 through 84' Processing helix chain 'E' and resid 209 through 214 removed outlier: 3.792A pdb=" N LEU E 213 " --> pdb=" O ASP E 209 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLN E 214 " --> pdb=" O PHE E 210 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 209 through 214' Processing helix chain 'E' and resid 221 through 225 Processing helix chain 'E' and resid 233 through 238 removed outlier: 3.530A pdb=" N MET E 237 " --> pdb=" O ASP E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 276 removed outlier: 3.949A pdb=" N LEU E 275 " --> pdb=" O PRO E 272 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR E 276 " --> pdb=" O ASP E 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 272 through 276' Processing helix chain 'E' and resid 324 through 326 No H-bonds generated for 'chain 'E' and resid 324 through 326' Processing helix chain 'E' and resid 355 through 357 No H-bonds generated for 'chain 'E' and resid 355 through 357' Processing helix chain 'E' and resid 383 through 394 removed outlier: 3.508A pdb=" N TYR E 389 " --> pdb=" O GLU E 385 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR E 392 " --> pdb=" O THR E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 394 through 401 removed outlier: 4.580A pdb=" N LEU E 398 " --> pdb=" O ASP E 394 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASP E 400 " --> pdb=" O ASN E 396 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TRP E 401 " --> pdb=" O ILE E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 442 Processing helix chain 'E' and resid 461 through 472 removed outlier: 3.874A pdb=" N LEU E 469 " --> pdb=" O ARG E 465 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 128 removed outlier: 3.789A pdb=" N LEU L 125 " --> pdb=" O SER L 121 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR L 126 " --> pdb=" O SER L 122 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER L 127 " --> pdb=" O GLU L 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 189 removed outlier: 3.661A pdb=" N GLU L 187 " --> pdb=" O LYS L 183 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ARG L 188 " --> pdb=" O ASP L 184 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N HIS L 189 " --> pdb=" O GLU L 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 183 through 189' Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.663A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.581A pdb=" N ASP H 90 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 161 through 163 No H-bonds generated for 'chain 'H' and resid 161 through 163' Processing sheet with id=AA1, first strand: chain 'B' and resid 311 through 312 removed outlier: 6.760A pdb=" N VAL B 374 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU B 106 " --> pdb=" O GLN B 372 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N GLN B 372 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ILE B 108 " --> pdb=" O ASP B 370 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ASP B 370 " --> pdb=" O ILE B 108 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 44 through 46 removed outlier: 3.636A pdb=" N ALA B 44 " --> pdb=" O GLU B 367 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG B 364 " --> pdb=" O MET B 342 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 52 through 53 removed outlier: 6.930A pdb=" N ILE B 52 " --> pdb=" O LEU B 62 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 291 through 296 removed outlier: 4.140A pdb=" N HIS B 259 " --> pdb=" O THR B 294 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N SER B 296 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N VAL B 257 " --> pdb=" O SER B 296 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N PHE B 248 " --> pdb=" O ILE B 160 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE B 160 " --> pdb=" O PHE B 248 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N CYS B 158 " --> pdb=" O LEU B 250 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN B 154 " --> pdb=" O GLN B 254 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU B 157 " --> pdb=" O VAL B 334 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG B 72 " --> pdb=" O VAL B 333 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL B 448 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N ARG B 75 " --> pdb=" O VAL B 448 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 291 through 296 removed outlier: 4.140A pdb=" N HIS B 259 " --> pdb=" O THR B 294 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N SER B 296 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N VAL B 257 " --> pdb=" O SER B 296 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 119 through 124 removed outlier: 5.120A pdb=" N GLY B 120 " --> pdb=" O MET B 150 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N MET B 150 " --> pdb=" O GLY B 120 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N LEU B 148 " --> pdb=" O PRO B 122 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 188 through 191 Processing sheet with id=AA8, first strand: chain 'B' and resid 266 through 267 removed outlier: 7.653A pdb=" N LYS B 266 " --> pdb=" O GLU C 361 " (cutoff:3.500A) removed outlier: 9.523A pdb=" N VAL C 363 " --> pdb=" O LYS B 266 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N GLU C 368 " --> pdb=" O ARG C 110 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ARG C 110 " --> pdb=" O GLU C 368 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ASP C 370 " --> pdb=" O ILE C 108 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ILE C 108 " --> pdb=" O ASP C 370 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N GLN C 372 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LEU C 106 " --> pdb=" O GLN C 372 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL C 374 " --> pdb=" O VAL C 104 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU C 106 " --> pdb=" O TYR C 311 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 97 through 100 Processing sheet with id=AB1, first strand: chain 'C' and resid 29 through 38 removed outlier: 7.896A pdb=" N SER C 29 " --> pdb=" O THR C 381 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N THR C 381 " --> pdb=" O SER C 29 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N THR C 31 " --> pdb=" O LYS C 379 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N LYS C 379 " --> pdb=" O THR C 31 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ILE C 33 " --> pdb=" O LEU C 377 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA C 44 " --> pdb=" O GLU C 367 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU C 42 " --> pdb=" O TYR C 369 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 300 through 301 removed outlier: 3.559A pdb=" N GLN A 154 " --> pdb=" O GLN A 254 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 97 through 107 removed outlier: 6.713A pdb=" N VAL A 374 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LEU A 106 " --> pdb=" O GLN A 372 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLN A 372 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ILE A 33 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N LYS A 379 " --> pdb=" O THR A 31 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N THR A 31 " --> pdb=" O LYS A 379 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N THR A 381 " --> pdb=" O SER A 29 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N SER A 29 " --> pdb=" O THR A 381 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 43 through 46 Processing sheet with id=AB5, first strand: chain 'A' and resid 52 through 53 removed outlier: 6.879A pdb=" N ILE A 52 " --> pdb=" O LEU A 62 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 74 through 75 Processing sheet with id=AB7, first strand: chain 'A' and resid 119 through 124 removed outlier: 4.857A pdb=" N GLY A 120 " --> pdb=" O MET A 150 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N MET A 150 " --> pdb=" O GLY A 120 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N LEU A 148 " --> pdb=" O PRO A 122 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 188 through 194 removed outlier: 3.511A pdb=" N PHE A 191 " --> pdb=" O HIS A 169 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N HIS A 169 " --> pdb=" O PHE A 191 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY A 167 " --> pdb=" O SER A 193 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 257 through 262 removed outlier: 6.938A pdb=" N THR A 294 " --> pdb=" O ARG A 258 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N PHE A 260 " --> pdb=" O PHE A 292 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N PHE A 292 " --> pdb=" O PHE A 260 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 346 through 347 removed outlier: 4.050A pdb=" N LYS E 266 " --> pdb=" O PHE A 359 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 52 through 53 removed outlier: 7.221A pdb=" N ILE C 52 " --> pdb=" O LEU C 62 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 446 through 447 removed outlier: 3.817A pdb=" N ARG C 75 " --> pdb=" O TRP C 446 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU C 329 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU C 157 " --> pdb=" O VAL C 334 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N CYS C 158 " --> pdb=" O LEU C 250 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU C 250 " --> pdb=" O CYS C 158 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 189 through 194 removed outlier: 3.516A pdb=" N PHE C 191 " --> pdb=" O HIS C 169 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N HIS C 169 " --> pdb=" O PHE C 191 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 257 through 262 removed outlier: 7.006A pdb=" N THR C 294 " --> pdb=" O ARG C 258 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N PHE C 260 " --> pdb=" O PHE C 292 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N PHE C 292 " --> pdb=" O PHE C 260 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 266 through 267 removed outlier: 7.280A pdb=" N LYS C 266 " --> pdb=" O GLU D 361 " (cutoff:3.500A) removed outlier: 9.446A pdb=" N VAL D 363 " --> pdb=" O LYS C 266 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU D 377 " --> pdb=" O ILE D 33 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N ILE D 33 " --> pdb=" O LEU D 377 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N LYS D 379 " --> pdb=" O THR D 31 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N THR D 31 " --> pdb=" O LYS D 379 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 266 through 267 removed outlier: 7.280A pdb=" N LYS C 266 " --> pdb=" O GLU D 361 " (cutoff:3.500A) removed outlier: 9.446A pdb=" N VAL D 363 " --> pdb=" O LYS C 266 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 42 through 46 removed outlier: 6.544A pdb=" N ASP D 370 " --> pdb=" O ILE D 108 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ILE D 108 " --> pdb=" O ASP D 370 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLN D 372 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N LEU D 106 " --> pdb=" O GLN D 372 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL D 374 " --> pdb=" O VAL D 104 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU D 106 " --> pdb=" O TYR D 311 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 52 through 53 removed outlier: 7.266A pdb=" N ILE D 52 " --> pdb=" O LEU D 62 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 248 through 254 removed outlier: 4.056A pdb=" N PHE D 248 " --> pdb=" O ILE D 160 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE D 160 " --> pdb=" O PHE D 248 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN D 154 " --> pdb=" O GLN D 254 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TRP D 446 " --> pdb=" O VAL D 73 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 119 through 124 removed outlier: 5.641A pdb=" N GLY D 120 " --> pdb=" O MET D 150 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N MET D 150 " --> pdb=" O GLY D 120 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N LEU D 148 " --> pdb=" O PRO D 122 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 128 through 129 removed outlier: 4.010A pdb=" N ASP D 128 " --> pdb=" O ASN D 262 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASN D 262 " --> pdb=" O ASP D 128 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N VAL D 257 " --> pdb=" O SER D 296 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N SER D 296 " --> pdb=" O VAL D 257 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N HIS D 259 " --> pdb=" O THR D 294 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR D 294 " --> pdb=" O HIS D 259 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 189 through 194 Processing sheet with id=AD5, first strand: chain 'D' and resid 266 through 267 removed outlier: 6.822A pdb=" N LYS D 266 " --> pdb=" O GLU E 361 " (cutoff:3.500A) removed outlier: 8.817A pdb=" N VAL E 363 " --> pdb=" O LYS D 266 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU E 377 " --> pdb=" O ILE E 33 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N ILE E 33 " --> pdb=" O LEU E 377 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N LYS E 379 " --> pdb=" O THR E 31 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N THR E 31 " --> pdb=" O LYS E 379 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N THR E 381 " --> pdb=" O SER E 29 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N SER E 29 " --> pdb=" O THR E 381 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 42 through 46 removed outlier: 3.577A pdb=" N ALA E 44 " --> pdb=" O GLU E 367 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU E 367 " --> pdb=" O ALA E 44 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 106 through 109 removed outlier: 3.573A pdb=" N GLU E 107 " --> pdb=" O GLN E 372 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASP E 370 " --> pdb=" O GLY E 109 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 250 through 254 removed outlier: 3.612A pdb=" N VAL E 334 " --> pdb=" O LEU E 157 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR E 332 " --> pdb=" O LEU E 159 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU E 329 " --> pdb=" O VAL E 76 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VAL E 73 " --> pdb=" O TRP E 446 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N VAL E 448 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ARG E 75 " --> pdb=" O VAL E 448 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 119 through 124 removed outlier: 3.625A pdb=" N TYR E 123 " --> pdb=" O GLU E 146 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N GLU E 146 " --> pdb=" O TYR E 123 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 128 through 129 removed outlier: 4.003A pdb=" N ASP E 128 " --> pdb=" O ASN E 262 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN E 262 " --> pdb=" O ASP E 128 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N HIS E 259 " --> pdb=" O THR E 294 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR E 294 " --> pdb=" O HIS E 259 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE E 261 " --> pdb=" O PHE E 292 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 166 through 167 Processing sheet with id=AE3, first strand: chain 'E' and resid 170 through 172 Processing sheet with id=AE4, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.719A pdb=" N ILE L 75 " --> pdb=" O VAL L 19 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE L 21 " --> pdb=" O LEU L 73 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU L 73 " --> pdb=" O ILE L 21 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'L' and resid 10 through 13 removed outlier: 5.693A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR L 102 " --> pdb=" O TYR L 86 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU L 47 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN L 37 " --> pdb=" O GLN L 45 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 114 through 117 removed outlier: 3.594A pdb=" N ASN L 137 " --> pdb=" O THR L 114 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER L 116 " --> pdb=" O PHE L 135 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE L 135 " --> pdb=" O SER L 116 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 153 through 155 removed outlier: 4.673A pdb=" N TRP L 148 " --> pdb=" O ARG L 155 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ASN L 145 " --> pdb=" O THR L 197 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR L 192 " --> pdb=" O PHE L 209 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS L 207 " --> pdb=" O CYS L 194 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA L 196 " --> pdb=" O ILE L 205 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.543A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL H 18 " --> pdb=" O LEU H 83 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU H 83 " --> pdb=" O VAL H 18 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N CYS H 22 " --> pdb=" O ALA H 79 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA H 79 " --> pdb=" O CYS H 22 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR H 71 " --> pdb=" O TYR H 80 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 9 through 12 removed outlier: 3.515A pdb=" N THR H 116 " --> pdb=" O GLU H 10 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 45 through 51 removed outlier: 5.192A pdb=" N TRP H 47 " --> pdb=" O LYS H 38 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LYS H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N TRP H 36 " --> pdb=" O GLY H 49 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS H 35 " --> pdb=" O ALA H 97 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL H 93 " --> pdb=" O GLN H 39 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 125 through 129 removed outlier: 3.745A pdb=" N SER H 125 " --> pdb=" O LYS H 148 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY H 144 " --> pdb=" O LEU H 129 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N LEU H 146 " --> pdb=" O SER H 184 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N SER H 184 " --> pdb=" O LEU H 146 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N LYS H 148 " --> pdb=" O LEU H 182 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N LEU H 182 " --> pdb=" O LYS H 148 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N SER H 185 " --> pdb=" O HIS H 169 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N HIS H 169 " --> pdb=" O SER H 185 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 125 through 129 removed outlier: 3.745A pdb=" N SER H 125 " --> pdb=" O LYS H 148 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY H 144 " --> pdb=" O LEU H 129 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N LEU H 146 " --> pdb=" O SER H 184 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N SER H 184 " --> pdb=" O LEU H 146 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N LYS H 148 " --> pdb=" O LEU H 182 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N LEU H 182 " --> pdb=" O LYS H 148 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 140 through 142 removed outlier: 3.607A pdb=" N VAL H 188 " --> pdb=" O VAL H 141 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 156 through 159 removed outlier: 3.550A pdb=" N LYS H 213 " --> pdb=" O CYS H 200 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL H 211 " --> pdb=" O VAL H 202 " (cutoff:3.500A) 396 hydrogen bonds defined for protein. 996 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: 6.75 Time building geometry restraints manager: 8.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 6783 1.33 - 1.45: 4573 1.45 - 1.57: 10850 1.57 - 1.69: 0 1.69 - 1.81: 165 Bond restraints: 22371 Sorted by residual: bond pdb=" C GLY L 93 " pdb=" N THR L 94 " ideal model delta sigma weight residual 1.334 1.245 0.090 1.72e-02 3.38e+03 2.73e+01 bond pdb=" C LYS D 434 " pdb=" N GLU D 435 " ideal model delta sigma weight residual 1.331 1.376 -0.044 1.62e-02 3.81e+03 7.50e+00 bond pdb=" C PRO C 408 " pdb=" N PRO C 409 " ideal model delta sigma weight residual 1.334 1.395 -0.062 2.34e-02 1.83e+03 6.91e+00 bond pdb=" C ASP B 80 " pdb=" N PRO B 81 " ideal model delta sigma weight residual 1.334 1.312 0.022 8.40e-03 1.42e+04 6.76e+00 bond pdb=" CA PHE E 260 " pdb=" CB PHE E 260 " ideal model delta sigma weight residual 1.532 1.494 0.038 1.62e-02 3.81e+03 5.63e+00 ... (remaining 22366 not shown) Histogram of bond angle deviations from ideal: 97.49 - 105.14: 608 105.14 - 112.80: 11399 112.80 - 120.46: 9271 120.46 - 128.12: 8953 128.12 - 135.78: 197 Bond angle restraints: 30428 Sorted by residual: angle pdb=" N ALA D 411 " pdb=" CA ALA D 411 " pdb=" C ALA D 411 " ideal model delta sigma weight residual 111.02 119.32 -8.30 1.22e+00 6.72e-01 4.62e+01 angle pdb=" N GLN A 423 " pdb=" CA GLN A 423 " pdb=" C GLN A 423 " ideal model delta sigma weight residual 110.91 117.52 -6.61 1.17e+00 7.31e-01 3.20e+01 angle pdb=" C SER H 177 " pdb=" N ASP H 178 " pdb=" CA ASP H 178 " ideal model delta sigma weight residual 122.61 129.68 -7.07 1.56e+00 4.11e-01 2.05e+01 angle pdb=" C VAL E 63 " pdb=" CA VAL E 63 " pdb=" CB VAL E 63 " ideal model delta sigma weight residual 110.16 114.64 -4.48 1.01e+00 9.80e-01 1.97e+01 angle pdb=" N VAL E 3 " pdb=" CA VAL E 3 " pdb=" C VAL E 3 " ideal model delta sigma weight residual 112.96 108.55 4.41 1.00e+00 1.00e+00 1.95e+01 ... (remaining 30423 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 11810 17.95 - 35.90: 1267 35.90 - 53.85: 189 53.85 - 71.81: 46 71.81 - 89.76: 16 Dihedral angle restraints: 13328 sinusoidal: 5302 harmonic: 8026 Sorted by residual: dihedral pdb=" CA PRO E 15 " pdb=" C PRO E 15 " pdb=" N VAL E 16 " pdb=" CA VAL E 16 " ideal model delta harmonic sigma weight residual 180.00 138.41 41.59 0 5.00e+00 4.00e-02 6.92e+01 dihedral pdb=" CA TYR B 136 " pdb=" C TYR B 136 " pdb=" N PRO B 137 " pdb=" CA PRO B 137 " ideal model delta harmonic sigma weight residual 180.00 141.48 38.52 0 5.00e+00 4.00e-02 5.94e+01 dihedral pdb=" CA SER A 422 " pdb=" C SER A 422 " pdb=" N GLN A 423 " pdb=" CA GLN A 423 " ideal model delta harmonic sigma weight residual 180.00 149.00 31.00 0 5.00e+00 4.00e-02 3.84e+01 ... (remaining 13325 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2330 0.059 - 0.119: 741 0.119 - 0.178: 183 0.178 - 0.238: 28 0.238 - 0.297: 5 Chirality restraints: 3287 Sorted by residual: chirality pdb=" CB VAL E 201 " pdb=" CA VAL E 201 " pdb=" CG1 VAL E 201 " pdb=" CG2 VAL E 201 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CB VAL C 22 " pdb=" CA VAL C 22 " pdb=" CG1 VAL C 22 " pdb=" CG2 VAL C 22 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CB VAL D 201 " pdb=" CA VAL D 201 " pdb=" CG1 VAL D 201 " pdb=" CG2 VAL D 201 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 3284 not shown) Planarity restraints: 3972 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO E 408 " -0.068 5.00e-02 4.00e+02 1.02e-01 1.68e+01 pdb=" N PRO E 409 " 0.177 5.00e-02 4.00e+02 pdb=" CA PRO E 409 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO E 409 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 406 " -0.051 5.00e-02 4.00e+02 7.67e-02 9.42e+00 pdb=" N PRO B 407 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO B 407 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 407 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 16 " -0.015 2.00e-02 2.50e+03 2.94e-02 8.67e+00 pdb=" C VAL E 16 " 0.051 2.00e-02 2.50e+03 pdb=" O VAL E 16 " -0.019 2.00e-02 2.50e+03 pdb=" N PRO E 17 " -0.017 2.00e-02 2.50e+03 ... (remaining 3969 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 89 2.41 - 3.03: 12205 3.03 - 3.66: 32144 3.66 - 4.28: 43326 4.28 - 4.90: 72200 Nonbonded interactions: 159964 Sorted by model distance: nonbonded pdb=" O PRO D 409 " pdb=" OG SER D 410 " model vdw 1.791 2.440 nonbonded pdb=" O PRO E 409 " pdb=" OG SER E 410 " model vdw 2.038 2.440 nonbonded pdb=" OG1 THR A 346 " pdb=" O LYS A 360 " model vdw 2.249 2.440 nonbonded pdb=" OG SER E 23 " pdb=" OD1 ASP E 25 " model vdw 2.281 2.440 nonbonded pdb=" O ILE B 425 " pdb=" OG1 THR B 426 " model vdw 2.282 2.440 ... (remaining 159959 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 20 through 157 or resid 159 through 473)) selection = (chain 'B' and (resid 20 through 157 or resid 159 through 473)) selection = (chain 'C' and (resid 20 through 157 or resid 159 through 473)) selection = (chain 'D' and (resid 20 through 157 or resid 159 through 473)) selection = (chain 'E' and (resid 20 through 157 or resid 159 through 473)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.41 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 17.790 Check model and map are aligned: 0.310 Set scattering table: 0.170 Process input model: 54.300 Find NCS groups from input model: 1.440 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 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 : 0.008 0.090 22371 Z= 0.541 Angle : 1.085 10.781 30428 Z= 0.608 Chirality : 0.062 0.297 3287 Planarity : 0.008 0.102 3972 Dihedral : 15.006 89.758 8176 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.61 % Favored : 90.21 % Rotamer Outliers : 0.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.46 % Cis-general : 0.04 % Twisted Proline : 0.55 % Twisted General : 0.12 % 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: -4.48 (0.12), residues: 2748 helix: -4.28 (0.17), residues: 179 sheet: -2.45 (0.16), residues: 744 loop : -3.27 (0.11), residues: 1825 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 651 time to evaluate : 2.514 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 outliers start: 19 outliers final: 15 residues processed: 666 average time/residue: 0.3562 time to fit residues: 358.7323 Evaluate side-chains 473 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 458 time to evaluate : 2.572 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1903 time to fit residues: 8.9983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 231 optimal weight: 2.9990 chunk 207 optimal weight: 9.9990 chunk 115 optimal weight: 10.0000 chunk 70 optimal weight: 6.9990 chunk 140 optimal weight: 2.9990 chunk 110 optimal weight: 0.4980 chunk 214 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 159 optimal weight: 9.9990 chunk 248 optimal weight: 7.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 ASN B 112 GLN B 134 ASN ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 ASN B 423 GLN ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 GLN ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 320 ASN ** D 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 GLN D 177 ASN D 320 ASN D 328 GLN D 391 HIS E 47 ASN E 56 ASN ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 178 ASN E 179 ASN E 216 ASN ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 376 GLN E 441 ASN E 460 GLN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN L 79 GLN ** H 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 201 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 22371 Z= 0.231 Angle : 0.696 9.278 30428 Z= 0.355 Chirality : 0.046 0.262 3287 Planarity : 0.006 0.084 3972 Dihedral : 5.862 37.851 2992 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer Outliers : 3.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.46 % Cis-general : 0.04 % Twisted Proline : 0.55 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.84 (0.13), residues: 2748 helix: -3.40 (0.24), residues: 207 sheet: -1.94 (0.17), residues: 718 loop : -2.87 (0.12), residues: 1823 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 524 time to evaluate : 2.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 77 outliers final: 51 residues processed: 560 average time/residue: 0.3281 time to fit residues: 289.7121 Evaluate side-chains 493 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 442 time to evaluate : 2.369 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 0 residues processed: 51 average time/residue: 0.2064 time to fit residues: 22.7605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 138 optimal weight: 10.0000 chunk 77 optimal weight: 0.0980 chunk 207 optimal weight: 7.9990 chunk 169 optimal weight: 10.0000 chunk 68 optimal weight: 9.9990 chunk 249 optimal weight: 50.0000 chunk 269 optimal weight: 50.0000 chunk 221 optimal weight: 6.9990 chunk 247 optimal weight: 30.0000 chunk 84 optimal weight: 8.9990 chunk 199 optimal weight: 10.0000 overall best weight: 6.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 GLN ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 ASN ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 GLN ** C 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 376 GLN D 391 HIS D 470 GLN ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 138 ASN ** H 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.081 22371 Z= 0.361 Angle : 0.724 9.405 30428 Z= 0.368 Chirality : 0.047 0.193 3287 Planarity : 0.006 0.071 3972 Dihedral : 5.724 35.675 2992 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer Outliers : 3.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.46 % Cis-general : 0.04 % Twisted Proline : 0.55 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.57 (0.14), residues: 2748 helix: -2.41 (0.31), residues: 196 sheet: -1.80 (0.17), residues: 734 loop : -2.78 (0.13), residues: 1818 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 460 time to evaluate : 2.798 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 outliers start: 89 outliers final: 53 residues processed: 518 average time/residue: 0.3089 time to fit residues: 255.8320 Evaluate side-chains 463 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 410 time to evaluate : 2.563 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 0 residues processed: 53 average time/residue: 0.1990 time to fit residues: 23.3256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 246 optimal weight: 30.0000 chunk 187 optimal weight: 6.9990 chunk 129 optimal weight: 8.9990 chunk 27 optimal weight: 20.0000 chunk 118 optimal weight: 5.9990 chunk 167 optimal weight: 7.9990 chunk 250 optimal weight: 9.9990 chunk 264 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 chunk 237 optimal weight: 20.0000 chunk 71 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 ASN ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 320 ASN ** D 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 ASN D 391 HIS E 70 GLN ** E 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 GLN ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.073 22371 Z= 0.369 Angle : 0.726 8.667 30428 Z= 0.369 Chirality : 0.047 0.247 3287 Planarity : 0.005 0.065 3972 Dihedral : 5.687 35.905 2992 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer Outliers : 4.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.46 % Cis-general : 0.04 % Twisted Proline : 0.55 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.37 (0.14), residues: 2748 helix: -1.98 (0.32), residues: 194 sheet: -1.70 (0.18), residues: 723 loop : -2.65 (0.13), residues: 1831 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 447 time to evaluate : 2.970 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 98 outliers final: 68 residues processed: 503 average time/residue: 0.3103 time to fit residues: 250.4304 Evaluate side-chains 472 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 404 time to evaluate : 2.289 Switching outliers to nearest non-outliers outliers start: 68 outliers final: 0 residues processed: 68 average time/residue: 0.2280 time to fit residues: 32.0263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 220 optimal weight: 20.0000 chunk 150 optimal weight: 20.0000 chunk 3 optimal weight: 3.9990 chunk 197 optimal weight: 1.9990 chunk 109 optimal weight: 0.4980 chunk 226 optimal weight: 7.9990 chunk 183 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 135 optimal weight: 3.9990 chunk 237 optimal weight: 0.5980 chunk 66 optimal weight: 8.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 396 ASN ** C 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 GLN D 47 ASN D 376 GLN E 70 GLN ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 GLN ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN L 89 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 22371 Z= 0.178 Angle : 0.651 8.951 30428 Z= 0.324 Chirality : 0.045 0.176 3287 Planarity : 0.005 0.062 3972 Dihedral : 5.122 34.607 2992 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer Outliers : 2.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.46 % Cis-general : 0.04 % Twisted Proline : 0.55 % 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: -3.10 (0.14), residues: 2748 helix: -1.69 (0.34), residues: 193 sheet: -1.61 (0.18), residues: 729 loop : -2.43 (0.13), residues: 1826 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 494 time to evaluate : 2.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 23 residues processed: 529 average time/residue: 0.3119 time to fit residues: 262.2462 Evaluate side-chains 467 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 444 time to evaluate : 2.341 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.2048 time to fit residues: 11.9695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 89 optimal weight: 8.9990 chunk 238 optimal weight: 30.0000 chunk 52 optimal weight: 9.9990 chunk 155 optimal weight: 8.9990 chunk 65 optimal weight: 0.9980 chunk 265 optimal weight: 0.7980 chunk 220 optimal weight: 10.0000 chunk 122 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 87 optimal weight: 0.1980 chunk 139 optimal weight: 9.9990 overall best weight: 3.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 320 ASN D 376 GLN ** E 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 GLN ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 22371 Z= 0.238 Angle : 0.674 9.517 30428 Z= 0.333 Chirality : 0.045 0.225 3287 Planarity : 0.005 0.084 3972 Dihedral : 5.067 33.367 2992 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer Outliers : 2.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.46 % Cis-general : 0.04 % Twisted Proline : 0.55 % 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: -3.00 (0.15), residues: 2748 helix: -1.51 (0.34), residues: 195 sheet: -1.60 (0.18), residues: 748 loop : -2.34 (0.13), residues: 1805 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 450 time to evaluate : 2.671 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 71 outliers final: 45 residues processed: 484 average time/residue: 0.3202 time to fit residues: 249.0902 Evaluate side-chains 465 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 420 time to evaluate : 2.682 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 0.2123 time to fit residues: 22.0961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 255 optimal weight: 20.0000 chunk 29 optimal weight: 4.9990 chunk 151 optimal weight: 20.0000 chunk 193 optimal weight: 7.9990 chunk 149 optimal weight: 0.9990 chunk 223 optimal weight: 9.9990 chunk 148 optimal weight: 5.9990 chunk 264 optimal weight: 30.0000 chunk 165 optimal weight: 20.0000 chunk 161 optimal weight: 8.9990 chunk 121 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 GLN ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 GLN ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 166 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.059 22371 Z= 0.298 Angle : 0.695 8.703 30428 Z= 0.347 Chirality : 0.046 0.275 3287 Planarity : 0.005 0.076 3972 Dihedral : 5.171 32.836 2992 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.46 % Favored : 90.54 % Rotamer Outliers : 1.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.46 % Cis-general : 0.04 % Twisted Proline : 0.55 % 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: -2.97 (0.15), residues: 2748 helix: -1.43 (0.34), residues: 195 sheet: -1.57 (0.18), residues: 729 loop : -2.34 (0.13), residues: 1824 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 437 time to evaluate : 2.619 Fit side-chains revert: symmetry clash outliers start: 48 outliers final: 32 residues processed: 461 average time/residue: 0.3175 time to fit residues: 235.7048 Evaluate side-chains 448 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 416 time to evaluate : 2.591 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.2183 time to fit residues: 16.9943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 163 optimal weight: 10.0000 chunk 105 optimal weight: 20.0000 chunk 157 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 51 optimal weight: 0.0030 chunk 167 optimal weight: 6.9990 chunk 179 optimal weight: 8.9990 chunk 130 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 207 optimal weight: 7.9990 chunk 240 optimal weight: 8.9990 overall best weight: 4.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 396 ASN ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 GLN ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 22371 Z= 0.277 Angle : 0.692 9.226 30428 Z= 0.345 Chirality : 0.046 0.285 3287 Planarity : 0.005 0.072 3972 Dihedral : 5.135 32.605 2992 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer Outliers : 1.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.46 % Cis-general : 0.04 % Twisted Proline : 0.55 % 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: -2.92 (0.15), residues: 2748 helix: -1.31 (0.35), residues: 196 sheet: -1.59 (0.18), residues: 742 loop : -2.28 (0.14), residues: 1810 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 438 time to evaluate : 2.440 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 30 residues processed: 458 average time/residue: 0.3000 time to fit residues: 219.8565 Evaluate side-chains 445 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 415 time to evaluate : 2.809 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.2002 time to fit residues: 14.9813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 253 optimal weight: 0.0970 chunk 230 optimal weight: 0.0770 chunk 246 optimal weight: 2.9990 chunk 252 optimal weight: 30.0000 chunk 148 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 193 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 chunk 222 optimal weight: 4.9990 chunk 232 optimal weight: 0.0000 chunk 245 optimal weight: 10.0000 overall best weight: 0.8344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 GLN ** E 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 GLN ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 45 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 22371 Z= 0.170 Angle : 0.682 10.310 30428 Z= 0.331 Chirality : 0.046 0.306 3287 Planarity : 0.005 0.068 3972 Dihedral : 4.811 30.969 2992 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer Outliers : 0.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.46 % Cis-general : 0.04 % Twisted Proline : 0.55 % 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: -2.67 (0.15), residues: 2748 helix: -1.23 (0.36), residues: 189 sheet: -1.44 (0.18), residues: 734 loop : -2.08 (0.14), residues: 1825 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 479 time to evaluate : 2.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 5 residues processed: 490 average time/residue: 0.3117 time to fit residues: 244.5945 Evaluate side-chains 447 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 442 time to evaluate : 2.494 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1937 time to fit residues: 5.2551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 161 optimal weight: 0.0980 chunk 260 optimal weight: 50.0000 chunk 158 optimal weight: 4.9990 chunk 123 optimal weight: 5.9990 chunk 180 optimal weight: 6.9990 chunk 272 optimal weight: 50.0000 chunk 251 optimal weight: 7.9990 chunk 217 optimal weight: 0.0470 chunk 22 optimal weight: 8.9990 chunk 167 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 overall best weight: 3.0284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 GLN C 305 GLN C 341 ASN D 154 GLN ** E 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 GLN ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 22371 Z= 0.207 Angle : 0.688 10.113 30428 Z= 0.334 Chirality : 0.046 0.300 3287 Planarity : 0.005 0.069 3972 Dihedral : 4.785 30.300 2992 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.46 % Cis-general : 0.04 % Twisted Proline : 0.55 % 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: -2.59 (0.15), residues: 2748 helix: -1.17 (0.36), residues: 189 sheet: -1.40 (0.18), residues: 725 loop : -2.02 (0.14), residues: 1834 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 444 time to evaluate : 2.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 15 residues processed: 450 average time/residue: 0.3421 time to fit residues: 245.8676 Evaluate side-chains 448 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 433 time to evaluate : 2.756 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2141 time to fit residues: 9.6864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 172 optimal weight: 20.0000 chunk 231 optimal weight: 0.7980 chunk 66 optimal weight: 8.9990 chunk 200 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 chunk 60 optimal weight: 30.0000 chunk 217 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 223 optimal weight: 8.9990 chunk 27 optimal weight: 8.9990 chunk 40 optimal weight: 0.9980 overall best weight: 5.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.144108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.105698 restraints weight = 67797.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.109283 restraints weight = 28333.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.111533 restraints weight = 16606.769| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3506 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3506 r_free = 0.3506 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3506 r_free = 0.3506 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3506 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.061 22371 Z= 0.295 Angle : 0.725 10.443 30428 Z= 0.358 Chirality : 0.046 0.289 3287 Planarity : 0.005 0.069 3972 Dihedral : 5.048 30.126 2992 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer Outliers : 0.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.46 % Cis-general : 0.04 % Twisted Proline : 0.55 % 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: -2.66 (0.15), residues: 2748 helix: -1.14 (0.36), residues: 190 sheet: -1.44 (0.18), residues: 744 loop : -2.08 (0.14), residues: 1814 =============================================================================== Job complete usr+sys time: 5270.33 seconds wall clock time: 96 minutes 16.81 seconds (5776.81 seconds total)