Starting phenix.real_space_refine on Sun Feb 18 10:56:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dnh_30783/02_2024/7dnh_30783.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dnh_30783/02_2024/7dnh_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_30783/02_2024/7dnh_30783.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dnh_30783/02_2024/7dnh_30783.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dnh_30783/02_2024/7dnh_30783.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dnh_30783/02_2024/7dnh_30783.pdb" } resolution = 3.64 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 12.73, per 1000 atoms: 0.58 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: 7.79 Conformation dependent library (CDL) restraints added in 4.4 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: 2.53 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: 6.95 Time building geometry restraints manager: 8.50 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: 3.870 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: 0.040 Extract box with map and model: 17.250 Check model and map are aligned: 0.350 Set scattering table: 0.190 Process input model: 57.750 Find NCS groups from input model: 1.790 Set up NCS constraints: 0.110 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.340 ------------------------------------------------------------------------------- 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 % Allowed : 13.55 % Favored : 85.67 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP L 92 HIS 0.010 0.002 HIS H 204 PHE 0.033 0.003 PHE A 454 TYR 0.021 0.003 TYR D 369 ARG 0.010 0.001 ARG D 263 *********************** 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 : 2.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 TYR cc_start: 0.8718 (m-10) cc_final: 0.8464 (m-10) REVERT: B 126 LYS cc_start: 0.8842 (tmtt) cc_final: 0.8222 (tmtt) REVERT: B 172 LYS cc_start: 0.8408 (tppt) cc_final: 0.7902 (tppt) REVERT: B 210 PHE cc_start: 0.8811 (m-80) cc_final: 0.8502 (m-80) REVERT: B 217 LYS cc_start: 0.8303 (mttm) cc_final: 0.7594 (mttt) REVERT: B 315 ARG cc_start: 0.8442 (tpt90) cc_final: 0.8145 (pmt-80) REVERT: B 451 LYS cc_start: 0.8591 (tppp) cc_final: 0.8103 (mmtt) REVERT: A 25 ASP cc_start: 0.8618 (m-30) cc_final: 0.8304 (m-30) REVERT: A 99 LEU cc_start: 0.9087 (mt) cc_final: 0.8705 (mp) REVERT: A 106 LEU cc_start: 0.9286 (tp) cc_final: 0.8962 (tp) REVERT: A 126 LYS cc_start: 0.8886 (tmtt) cc_final: 0.8573 (tptp) REVERT: A 135 ARG cc_start: 0.7951 (mtt180) cc_final: 0.7103 (ptm160) REVERT: A 153 LYS cc_start: 0.8629 (ptmm) cc_final: 0.8317 (pttm) REVERT: A 217 LYS cc_start: 0.9356 (mttm) cc_final: 0.9063 (mtmt) REVERT: A 291 PHE cc_start: 0.8092 (m-80) cc_final: 0.7660 (m-10) REVERT: A 342 MET cc_start: 0.8397 (mtm) cc_final: 0.7828 (ptm) REVERT: A 418 ARG cc_start: 0.4550 (ptt-90) cc_final: 0.3350 (ptt-90) REVERT: C 71 TYR cc_start: 0.8496 (m-80) cc_final: 0.8050 (m-80) REVERT: C 110 ARG cc_start: 0.8430 (mmm-85) cc_final: 0.8007 (mmm-85) REVERT: C 153 LYS cc_start: 0.9310 (ttpp) cc_final: 0.8934 (tttt) REVERT: C 235 LEU cc_start: 0.9525 (mm) cc_final: 0.9251 (mm) REVERT: C 269 GLU cc_start: 0.7926 (mt-10) cc_final: 0.6782 (tt0) REVERT: C 387 MET cc_start: 0.8758 (ttt) cc_final: 0.8355 (tpp) REVERT: C 398 LEU cc_start: 0.9005 (mt) cc_final: 0.8183 (mt) REVERT: C 446 TRP cc_start: 0.8635 (t60) cc_final: 0.8417 (t-100) REVERT: C 453 LYS cc_start: 0.9098 (mmtp) cc_final: 0.8877 (mmtm) REVERT: C 455 SER cc_start: 0.9227 (t) cc_final: 0.8916 (t) REVERT: D 26 GLU cc_start: 0.7814 (tp30) cc_final: 0.7604 (tp30) REVERT: D 50 PHE cc_start: 0.8736 (p90) cc_final: 0.8146 (p90) REVERT: D 71 TYR cc_start: 0.9102 (m-80) cc_final: 0.8885 (m-80) REVERT: D 134 ASN cc_start: 0.8275 (t0) cc_final: 0.7829 (t0) REVERT: D 152 TYR cc_start: 0.7137 (m-10) cc_final: 0.6873 (m-10) REVERT: D 240 GLU cc_start: 0.9053 (tm-30) cc_final: 0.8811 (tm-30) REVERT: D 309 LYS cc_start: 0.9303 (mtmt) cc_final: 0.8741 (ttpp) REVERT: D 399 GLU cc_start: 0.8908 (tm-30) cc_final: 0.8488 (tm-30) REVERT: D 447 GLU cc_start: 0.8758 (tm-30) cc_final: 0.8551 (tm-30) REVERT: D 470 GLN cc_start: 0.9105 (tm-30) cc_final: 0.8899 (tm-30) REVERT: E 65 LYS cc_start: 0.9279 (tttt) cc_final: 0.9074 (tttm) REVERT: E 83 LYS cc_start: 0.8869 (mmtt) cc_final: 0.8649 (mtpp) REVERT: E 84 PHE cc_start: 0.7803 (m-10) cc_final: 0.6987 (t80) REVERT: E 99 LEU cc_start: 0.9461 (mm) cc_final: 0.9150 (mm) REVERT: E 123 TYR cc_start: 0.8947 (m-80) cc_final: 0.8243 (m-80) REVERT: E 146 GLU cc_start: 0.7167 (mm-30) cc_final: 0.6471 (mm-30) REVERT: E 152 TYR cc_start: 0.8198 (m-80) cc_final: 0.7862 (m-10) REVERT: E 154 GLN cc_start: 0.8075 (mp10) cc_final: 0.7756 (mp10) REVERT: E 163 LYS cc_start: 0.9159 (mmtm) cc_final: 0.8954 (mmtp) REVERT: E 217 LYS cc_start: 0.8569 (mttt) cc_final: 0.7962 (ptpp) REVERT: E 244 ASP cc_start: 0.7349 (t70) cc_final: 0.7101 (t70) REVERT: E 303 GLU cc_start: 0.7582 (mp0) cc_final: 0.7134 (mp0) REVERT: E 306 LEU cc_start: 0.9294 (mt) cc_final: 0.9047 (mt) REVERT: E 311 TYR cc_start: 0.8260 (m-80) cc_final: 0.7533 (m-10) REVERT: E 321 ASN cc_start: 0.8977 (t0) cc_final: 0.8533 (t0) REVERT: E 329 LEU cc_start: 0.8931 (mt) cc_final: 0.8622 (mt) REVERT: E 342 MET cc_start: 0.9060 (mmm) cc_final: 0.8672 (mmm) REVERT: E 402 GLN cc_start: 0.8198 (mp10) cc_final: 0.7990 (mp10) REVERT: E 418 ARG cc_start: 0.7902 (tmm160) cc_final: 0.6339 (mtt-85) REVERT: E 451 LYS cc_start: 0.8846 (mptt) cc_final: 0.8586 (mptt) REVERT: L 23 CYS cc_start: 0.4481 (t) cc_final: 0.4133 (t) REVERT: L 142 LYS cc_start: 0.4187 (tttt) cc_final: 0.3778 (tttm) REVERT: L 175 MET cc_start: 0.7868 (ttt) cc_final: 0.7438 (tpt) REVERT: H 104 TYR cc_start: 0.4351 (m-80) cc_final: 0.3545 (m-80) outliers start: 19 outliers final: 15 residues processed: 666 average time/residue: 0.3435 time to fit residues: 346.6206 Evaluate side-chains 483 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 468 time to evaluate : 2.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 396 ASN Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain C residue 158 CYS Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 459 ASP Chi-restraints excluded: chain H residue 20 ILE 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: 1.9990 chunk 115 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 chunk 140 optimal weight: 0.4980 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: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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** ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 ASN C 139 GLN ** C 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 320 ASN D 47 ASN 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 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: 0.7835 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22371 Z= 0.197 Angle : 0.676 9.467 30428 Z= 0.342 Chirality : 0.046 0.305 3287 Planarity : 0.006 0.084 3972 Dihedral : 5.917 37.738 3013 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 3.11 % Allowed : 20.76 % Favored : 76.13 % 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: -3.79 (0.13), residues: 2748 helix: -3.36 (0.24), residues: 207 sheet: -1.85 (0.17), residues: 709 loop : -2.87 (0.12), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP L 92 HIS 0.006 0.001 HIS H 204 PHE 0.021 0.001 PHE E 291 TYR 0.016 0.001 TYR H 150 ARG 0.008 0.001 ARG E 251 *********************** 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 624 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 548 time to evaluate : 2.587 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: B 49 TYR cc_start: 0.8751 (m-10) cc_final: 0.8455 (m-10) REVERT: B 127 PHE cc_start: 0.8823 (t80) cc_final: 0.8606 (t80) REVERT: B 134 ASN cc_start: 0.7471 (t0) cc_final: 0.7112 (t0) REVERT: B 172 LYS cc_start: 0.8158 (tppt) cc_final: 0.7747 (tppt) REVERT: B 217 LYS cc_start: 0.8245 (mttm) cc_final: 0.8009 (mttp) REVERT: B 315 ARG cc_start: 0.8434 (tpt90) cc_final: 0.8037 (pmt-80) REVERT: B 359 PHE cc_start: 0.8207 (OUTLIER) cc_final: 0.7737 (m-80) REVERT: B 452 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7831 (tt0) REVERT: A 25 ASP cc_start: 0.8572 (m-30) cc_final: 0.8261 (m-30) REVERT: A 41 ARG cc_start: 0.8843 (mtp180) cc_final: 0.7035 (pmt-80) REVERT: A 126 LYS cc_start: 0.8702 (tmtt) cc_final: 0.8187 (tptp) REVERT: A 135 ARG cc_start: 0.7868 (mtt180) cc_final: 0.7087 (ptm160) REVERT: A 145 ARG cc_start: 0.8912 (mtm180) cc_final: 0.8687 (mtm110) REVERT: A 153 LYS cc_start: 0.8690 (ptmm) cc_final: 0.8416 (pttm) REVERT: A 217 LYS cc_start: 0.9399 (mttm) cc_final: 0.9127 (mtmt) REVERT: A 247 PHE cc_start: 0.8661 (m-10) cc_final: 0.8252 (m-80) REVERT: A 342 MET cc_start: 0.8284 (mtm) cc_final: 0.7488 (ptp) REVERT: A 360 LYS cc_start: 0.8501 (ttpt) cc_final: 0.8224 (ttmm) REVERT: A 418 ARG cc_start: 0.4302 (ptt-90) cc_final: 0.1890 (mpp80) REVERT: A 454 PHE cc_start: 0.8970 (OUTLIER) cc_final: 0.8128 (m-10) REVERT: C 4 TRP cc_start: 0.7000 (m100) cc_final: 0.6725 (m-90) REVERT: C 151 ASP cc_start: 0.7401 (t0) cc_final: 0.7195 (t70) REVERT: C 255 MET cc_start: 0.8501 (ppp) cc_final: 0.8151 (ppp) REVERT: C 269 GLU cc_start: 0.7904 (mt-10) cc_final: 0.6741 (tt0) REVERT: C 381 THR cc_start: 0.9055 (OUTLIER) cc_final: 0.8738 (p) REVERT: C 387 MET cc_start: 0.8790 (ttt) cc_final: 0.8338 (tpp) REVERT: D 50 PHE cc_start: 0.8703 (p90) cc_final: 0.8188 (p90) REVERT: D 71 TYR cc_start: 0.8929 (m-80) cc_final: 0.8419 (m-80) REVERT: D 134 ASN cc_start: 0.8281 (t0) cc_final: 0.7893 (t0) REVERT: D 269 GLU cc_start: 0.8189 (tp30) cc_final: 0.7956 (tp30) REVERT: D 302 SER cc_start: 0.8984 (p) cc_final: 0.8562 (p) REVERT: D 309 LYS cc_start: 0.9089 (mtmt) cc_final: 0.8837 (ttmm) REVERT: D 447 GLU cc_start: 0.8715 (tm-30) cc_final: 0.8419 (tm-30) REVERT: D 470 GLN cc_start: 0.9099 (tm-30) cc_final: 0.8826 (tm-30) REVERT: E 65 LYS cc_start: 0.9272 (tttt) cc_final: 0.9010 (tttp) REVERT: E 84 PHE cc_start: 0.7530 (m-10) cc_final: 0.6980 (t80) REVERT: E 123 TYR cc_start: 0.8830 (m-80) cc_final: 0.8095 (m-80) REVERT: E 146 GLU cc_start: 0.6808 (mm-30) cc_final: 0.6325 (mm-30) REVERT: E 153 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.7884 (pttm) REVERT: E 163 LYS cc_start: 0.9096 (mmtm) cc_final: 0.8871 (mmtp) REVERT: E 196 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7822 (mm-30) REVERT: E 217 LYS cc_start: 0.8526 (mttt) cc_final: 0.7933 (ptpt) REVERT: E 252 ARG cc_start: 0.7904 (mtp-110) cc_final: 0.7668 (ttm110) REVERT: E 303 GLU cc_start: 0.7141 (mp0) cc_final: 0.6883 (mp0) REVERT: E 306 LEU cc_start: 0.9323 (mt) cc_final: 0.8951 (mt) REVERT: E 311 TYR cc_start: 0.8102 (m-80) cc_final: 0.7506 (m-10) REVERT: E 321 ASN cc_start: 0.8919 (t0) cc_final: 0.8430 (t0) REVERT: E 418 ARG cc_start: 0.7820 (tmm160) cc_final: 0.6368 (mtt-85) REVERT: L 139 PHE cc_start: 0.3452 (p90) cc_final: 0.3099 (p90) REVERT: L 175 MET cc_start: 0.7264 (ttt) cc_final: 0.6844 (tpt) REVERT: L 181 LEU cc_start: 0.5287 (OUTLIER) cc_final: 0.4466 (tt) REVERT: H 60 TYR cc_start: 0.6435 (m-80) cc_final: 0.5596 (m-80) REVERT: H 104 TYR cc_start: 0.4315 (m-80) cc_final: 0.3855 (m-80) outliers start: 76 outliers final: 52 residues processed: 589 average time/residue: 0.3288 time to fit residues: 302.5611 Evaluate side-chains 517 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 460 time to evaluate : 2.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 441 ASN Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 454 PHE Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 320 ASN Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 442 LYS Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 378 CYS Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 459 ASP Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 153 LYS Chi-restraints excluded: chain E residue 202 ASP Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 374 VAL Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 61 ASN Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 190 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 138 optimal weight: 0.0670 chunk 77 optimal weight: 2.9990 chunk 207 optimal weight: 10.0000 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: 5.9990 chunk 247 optimal weight: 0.0770 chunk 84 optimal weight: 0.1980 chunk 199 optimal weight: 20.0000 overall best weight: 1.8680 ------------------------------------------------------------------------------- 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 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 GLN D 320 ASN D 391 HIS ** 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 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2228 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= 0.171 Angle : 0.634 11.145 30428 Z= 0.315 Chirality : 0.045 0.154 3287 Planarity : 0.005 0.072 3972 Dihedral : 5.308 36.130 3003 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 4.42 % Allowed : 21.13 % Favored : 74.45 % 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: -3.35 (0.14), residues: 2748 helix: -2.73 (0.28), residues: 203 sheet: -1.58 (0.18), residues: 726 loop : -2.59 (0.13), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP L 92 HIS 0.005 0.001 HIS H 204 PHE 0.024 0.001 PHE H 151 TYR 0.018 0.001 TYR H 150 ARG 0.005 0.000 ARG E 251 *********************** 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 646 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 538 time to evaluate : 2.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 TYR cc_start: 0.8788 (m-10) cc_final: 0.8501 (m-10) REVERT: B 126 LYS cc_start: 0.8833 (tmtt) cc_final: 0.8488 (tptp) REVERT: B 172 LYS cc_start: 0.8098 (tppt) cc_final: 0.7739 (tppt) REVERT: B 217 LYS cc_start: 0.8317 (mttm) cc_final: 0.8109 (mttp) REVERT: B 219 ASP cc_start: 0.8956 (p0) cc_final: 0.8739 (p0) REVERT: A 25 ASP cc_start: 0.8514 (m-30) cc_final: 0.8224 (m-30) REVERT: A 41 ARG cc_start: 0.8811 (mtp180) cc_final: 0.7134 (pmt-80) REVERT: A 126 LYS cc_start: 0.8660 (tmtt) cc_final: 0.8187 (tptp) REVERT: A 135 ARG cc_start: 0.7679 (mtt180) cc_final: 0.7002 (ptm160) REVERT: A 145 ARG cc_start: 0.8782 (mtm180) cc_final: 0.8442 (mtm180) REVERT: A 146 GLU cc_start: 0.6196 (mm-30) cc_final: 0.5369 (mm-30) REVERT: A 153 LYS cc_start: 0.8649 (ptmm) cc_final: 0.8374 (pttm) REVERT: A 217 LYS cc_start: 0.9413 (mttm) cc_final: 0.8902 (ptmt) REVERT: A 242 TYR cc_start: 0.8845 (m-80) cc_final: 0.8454 (m-80) REVERT: A 247 PHE cc_start: 0.8766 (m-10) cc_final: 0.8480 (m-80) REVERT: A 418 ARG cc_start: 0.4226 (ptt-90) cc_final: 0.1663 (mpp80) REVERT: A 454 PHE cc_start: 0.8914 (OUTLIER) cc_final: 0.8117 (m-10) REVERT: C 4 TRP cc_start: 0.6956 (m100) cc_final: 0.6693 (m-90) REVERT: C 255 MET cc_start: 0.8676 (ppp) cc_final: 0.8364 (ppp) REVERT: C 303 GLU cc_start: 0.7990 (tt0) cc_final: 0.7743 (tt0) REVERT: C 361 GLU cc_start: 0.7538 (mp0) cc_final: 0.7227 (mp0) REVERT: C 387 MET cc_start: 0.8816 (ttt) cc_final: 0.8277 (tpp) REVERT: D 71 TYR cc_start: 0.8924 (m-80) cc_final: 0.8393 (m-80) REVERT: D 127 PHE cc_start: 0.8540 (t80) cc_final: 0.8057 (t80) REVERT: D 134 ASN cc_start: 0.8370 (t0) cc_final: 0.7830 (t0) REVERT: D 146 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.7950 (mp0) REVERT: D 154 GLN cc_start: 0.8659 (pt0) cc_final: 0.8152 (pt0) REVERT: D 269 GLU cc_start: 0.8299 (tp30) cc_final: 0.8065 (tp30) REVERT: D 287 GLN cc_start: 0.6424 (OUTLIER) cc_final: 0.6184 (mm-40) REVERT: D 302 SER cc_start: 0.8800 (p) cc_final: 0.8573 (p) REVERT: D 309 LYS cc_start: 0.9148 (mtmt) cc_final: 0.8766 (ttpp) REVERT: D 320 ASN cc_start: 0.9365 (t0) cc_final: 0.9117 (t0) REVERT: D 351 GLU cc_start: 0.7698 (tp30) cc_final: 0.7169 (tt0) REVERT: D 370 ASP cc_start: 0.8486 (t0) cc_final: 0.8178 (t0) REVERT: D 372 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.8354 (mp10) REVERT: D 423 GLN cc_start: 0.8268 (mm-40) cc_final: 0.7506 (tt0) REVERT: D 447 GLU cc_start: 0.8613 (tm-30) cc_final: 0.8375 (tm-30) REVERT: D 460 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.7928 (mp10) REVERT: D 470 GLN cc_start: 0.9063 (tm-30) cc_final: 0.8796 (tm-30) REVERT: E 65 LYS cc_start: 0.9297 (tttt) cc_final: 0.8990 (tttp) REVERT: E 84 PHE cc_start: 0.7377 (m-10) cc_final: 0.6925 (t80) REVERT: E 123 TYR cc_start: 0.8869 (m-80) cc_final: 0.8099 (m-80) REVERT: E 136 TYR cc_start: 0.7376 (OUTLIER) cc_final: 0.4765 (m-80) REVERT: E 146 GLU cc_start: 0.6697 (mm-30) cc_final: 0.6216 (mm-30) REVERT: E 196 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7768 (mm-30) REVERT: E 244 ASP cc_start: 0.6824 (t70) cc_final: 0.6585 (t0) REVERT: E 306 LEU cc_start: 0.9309 (mt) cc_final: 0.8932 (mt) REVERT: E 311 TYR cc_start: 0.8059 (m-80) cc_final: 0.7499 (m-10) REVERT: E 321 ASN cc_start: 0.8951 (t0) cc_final: 0.8436 (t0) REVERT: E 393 MET cc_start: 0.9171 (tmm) cc_final: 0.8939 (tmm) REVERT: E 418 ARG cc_start: 0.7867 (tmm160) cc_final: 0.6333 (mtt-85) REVERT: L 104 LEU cc_start: 0.7165 (tp) cc_final: 0.6906 (tt) REVERT: L 175 MET cc_start: 0.7285 (ttt) cc_final: 0.6740 (tpt) REVERT: L 181 LEU cc_start: 0.5091 (OUTLIER) cc_final: 0.4389 (tt) REVERT: H 60 TYR cc_start: 0.6598 (m-80) cc_final: 0.5811 (m-80) REVERT: H 104 TYR cc_start: 0.4578 (m-80) cc_final: 0.4034 (m-80) REVERT: H 150 TYR cc_start: 0.4188 (p90) cc_final: 0.3971 (p90) outliers start: 108 outliers final: 77 residues processed: 598 average time/residue: 0.3155 time to fit residues: 295.5211 Evaluate side-chains 561 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 477 time to evaluate : 2.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 305 GLN Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 441 ASN Chi-restraints excluded: chain A residue 454 PHE Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 254 GLN Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 442 LYS Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 248 PHE Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 287 GLN Chi-restraints excluded: chain D residue 291 PHE Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 319 HIS Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 372 GLN Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 378 CYS Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 460 GLN Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 136 TYR Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 324 CYS Chi-restraints excluded: chain E residue 374 VAL Chi-restraints excluded: chain E residue 412 SER Chi-restraints excluded: chain E residue 459 ASP Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 61 ASN Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 102 ASP Chi-restraints excluded: chain H residue 140 MET Chi-restraints excluded: chain H residue 169 HIS Chi-restraints excluded: chain H residue 190 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 246 optimal weight: 7.9990 chunk 187 optimal weight: 8.9990 chunk 129 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 118 optimal weight: 10.0000 chunk 167 optimal weight: 5.9990 chunk 250 optimal weight: 30.0000 chunk 264 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 237 optimal weight: 30.0000 chunk 71 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 177 ASN B 423 GLN ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 ASN ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 376 GLN D 391 HIS ** E 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 GLN ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 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: 0.7886 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 22371 Z= 0.311 Angle : 0.673 10.525 30428 Z= 0.338 Chirality : 0.045 0.253 3287 Planarity : 0.005 0.073 3972 Dihedral : 5.392 33.944 2999 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 6.06 % Allowed : 21.58 % Favored : 72.36 % 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: -3.19 (0.14), residues: 2748 helix: -2.05 (0.32), residues: 198 sheet: -1.54 (0.18), residues: 741 loop : -2.53 (0.13), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP L 92 HIS 0.004 0.001 HIS B 365 PHE 0.022 0.002 PHE C 210 TYR 0.020 0.001 TYR C 234 ARG 0.009 0.000 ARG E 5 *********************** 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 614 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 466 time to evaluate : 2.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 TYR cc_start: 0.8863 (m-10) cc_final: 0.8528 (m-10) REVERT: B 126 LYS cc_start: 0.8800 (tmtt) cc_final: 0.8511 (tptp) REVERT: B 172 LYS cc_start: 0.8114 (tppt) cc_final: 0.7768 (tppt) REVERT: B 217 LYS cc_start: 0.8432 (mttm) cc_final: 0.8228 (mttp) REVERT: B 219 ASP cc_start: 0.8955 (p0) cc_final: 0.8718 (p0) REVERT: B 459 ASP cc_start: 0.9117 (OUTLIER) cc_final: 0.8766 (p0) REVERT: A 25 ASP cc_start: 0.8543 (m-30) cc_final: 0.8242 (m-30) REVERT: A 135 ARG cc_start: 0.7620 (mtt180) cc_final: 0.7015 (ptm160) REVERT: A 145 ARG cc_start: 0.8850 (mtm180) cc_final: 0.8640 (mtm180) REVERT: A 148 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8373 (mm) REVERT: A 153 LYS cc_start: 0.8653 (ptmm) cc_final: 0.8351 (pttm) REVERT: A 217 LYS cc_start: 0.9398 (mttm) cc_final: 0.8885 (ptmt) REVERT: A 242 TYR cc_start: 0.8851 (m-80) cc_final: 0.7739 (m-80) REVERT: A 244 ASP cc_start: 0.8817 (m-30) cc_final: 0.8573 (m-30) REVERT: A 247 PHE cc_start: 0.8793 (m-10) cc_final: 0.8561 (m-80) REVERT: A 418 ARG cc_start: 0.4290 (ptt-90) cc_final: 0.3200 (ptt-90) REVERT: A 454 PHE cc_start: 0.8940 (OUTLIER) cc_final: 0.8136 (m-10) REVERT: C 154 GLN cc_start: 0.7411 (mp10) cc_final: 0.7189 (mp10) REVERT: C 235 LEU cc_start: 0.9563 (mm) cc_final: 0.9242 (mm) REVERT: C 255 MET cc_start: 0.8799 (ppp) cc_final: 0.8501 (ppp) REVERT: C 361 GLU cc_start: 0.7583 (mp0) cc_final: 0.7253 (mp0) REVERT: C 381 THR cc_start: 0.8985 (OUTLIER) cc_final: 0.8737 (p) REVERT: C 387 MET cc_start: 0.8935 (ttt) cc_final: 0.8410 (tpp) REVERT: D 71 TYR cc_start: 0.9086 (m-80) cc_final: 0.8549 (m-80) REVERT: D 146 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7868 (mp0) REVERT: D 154 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.8141 (pt0) REVERT: D 208 MET cc_start: 0.7632 (pmm) cc_final: 0.6864 (pmm) REVERT: D 269 GLU cc_start: 0.8293 (tp30) cc_final: 0.7971 (tp30) REVERT: D 309 LYS cc_start: 0.9186 (mtmt) cc_final: 0.8869 (ttpp) REVERT: D 370 ASP cc_start: 0.8462 (t0) cc_final: 0.8112 (t0) REVERT: D 372 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.8275 (mp10) REVERT: D 423 GLN cc_start: 0.8291 (mm-40) cc_final: 0.7484 (tt0) REVERT: D 470 GLN cc_start: 0.9124 (tm-30) cc_final: 0.8838 (tm-30) REVERT: E 65 LYS cc_start: 0.9230 (tttt) cc_final: 0.8903 (tttp) REVERT: E 84 PHE cc_start: 0.7641 (m-10) cc_final: 0.7058 (t80) REVERT: E 92 TYR cc_start: 0.8875 (OUTLIER) cc_final: 0.7374 (p90) REVERT: E 123 TYR cc_start: 0.8981 (m-80) cc_final: 0.8074 (m-80) REVERT: E 152 TYR cc_start: 0.8024 (m-80) cc_final: 0.7694 (m-10) REVERT: E 196 GLU cc_start: 0.8455 (mm-30) cc_final: 0.7695 (mm-30) REVERT: E 252 ARG cc_start: 0.8137 (mtp-110) cc_final: 0.7687 (ttm-80) REVERT: E 311 TYR cc_start: 0.8160 (m-80) cc_final: 0.7562 (m-10) REVERT: E 321 ASN cc_start: 0.8961 (t0) cc_final: 0.8521 (t0) REVERT: E 418 ARG cc_start: 0.7917 (tmm160) cc_final: 0.6266 (mtt-85) REVERT: L 98 PHE cc_start: 0.8222 (m-10) cc_final: 0.7825 (m-80) REVERT: L 104 LEU cc_start: 0.7166 (tp) cc_final: 0.6866 (tt) REVERT: L 175 MET cc_start: 0.7468 (ttt) cc_final: 0.6907 (tpt) REVERT: L 181 LEU cc_start: 0.5036 (OUTLIER) cc_final: 0.4363 (tt) REVERT: H 104 TYR cc_start: 0.4711 (m-80) cc_final: 0.4050 (m-80) outliers start: 148 outliers final: 104 residues processed: 552 average time/residue: 0.3172 time to fit residues: 274.6858 Evaluate side-chains 551 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 438 time to evaluate : 2.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 308 ASN Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 441 ASN Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 454 PHE Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 56 ASN Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 442 LYS Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 154 GLN Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 248 PHE Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 291 PHE Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 319 HIS Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 372 GLN Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 378 CYS Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 397 ILE Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 82 ASN Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 324 CYS Chi-restraints excluded: chain E residue 374 VAL Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain E residue 412 SER Chi-restraints excluded: chain E residue 459 ASP Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 61 ASN Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 102 ASP Chi-restraints excluded: chain H residue 140 MET Chi-restraints excluded: chain H residue 169 HIS Chi-restraints excluded: chain H residue 190 SER Chi-restraints excluded: chain H residue 198 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 220 optimal weight: 4.9990 chunk 150 optimal weight: 20.0000 chunk 3 optimal weight: 10.0000 chunk 197 optimal weight: 20.0000 chunk 109 optimal weight: 0.1980 chunk 226 optimal weight: 3.9990 chunk 183 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 135 optimal weight: 0.0870 chunk 237 optimal weight: 4.9990 chunk 66 optimal weight: 10.0000 overall best weight: 2.8564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 GLN B 305 GLN B 358 ASN ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 GLN ** C 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 ASN ** E 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 GLN ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 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: 0.7852 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22371 Z= 0.189 Angle : 0.623 8.988 30428 Z= 0.308 Chirality : 0.044 0.264 3287 Planarity : 0.005 0.065 3972 Dihedral : 5.089 33.859 2999 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 5.45 % Allowed : 22.81 % Favored : 71.74 % 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: -2.99 (0.15), residues: 2748 helix: -1.83 (0.33), residues: 206 sheet: -1.48 (0.18), residues: 746 loop : -2.35 (0.13), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP L 92 HIS 0.004 0.001 HIS B 365 PHE 0.019 0.001 PHE L 139 TYR 0.014 0.001 TYR E 354 ARG 0.005 0.000 ARG E 252 *********************** 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 615 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 482 time to evaluate : 2.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 TYR cc_start: 0.8823 (m-10) cc_final: 0.8477 (m-10) REVERT: B 126 LYS cc_start: 0.8722 (tmtt) cc_final: 0.8509 (tptp) REVERT: B 148 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8061 (mm) REVERT: B 172 LYS cc_start: 0.8072 (tppt) cc_final: 0.7731 (tppt) REVERT: B 208 MET cc_start: 0.7727 (ptp) cc_final: 0.7228 (ptp) REVERT: B 459 ASP cc_start: 0.9054 (OUTLIER) cc_final: 0.8570 (p0) REVERT: A 25 ASP cc_start: 0.8537 (m-30) cc_final: 0.8242 (m-30) REVERT: A 135 ARG cc_start: 0.7690 (mtt180) cc_final: 0.7012 (ptm160) REVERT: A 148 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8429 (mm) REVERT: A 153 LYS cc_start: 0.8613 (ptmm) cc_final: 0.8316 (pttm) REVERT: A 217 LYS cc_start: 0.9430 (mttm) cc_final: 0.8904 (ptmt) REVERT: A 242 TYR cc_start: 0.8823 (m-80) cc_final: 0.7826 (m-80) REVERT: A 247 PHE cc_start: 0.8746 (m-10) cc_final: 0.8498 (m-80) REVERT: A 393 MET cc_start: 0.8246 (tpt) cc_final: 0.7883 (tpt) REVERT: A 418 ARG cc_start: 0.4183 (ptt-90) cc_final: 0.2108 (mpp80) REVERT: A 454 PHE cc_start: 0.8931 (OUTLIER) cc_final: 0.8108 (m-10) REVERT: C 235 LEU cc_start: 0.9490 (mm) cc_final: 0.9161 (mm) REVERT: C 255 MET cc_start: 0.8900 (ppp) cc_final: 0.8636 (ppp) REVERT: C 361 GLU cc_start: 0.7380 (mp0) cc_final: 0.7010 (mp0) REVERT: C 380 ILE cc_start: 0.8651 (tp) cc_final: 0.8415 (tt) REVERT: C 381 THR cc_start: 0.8921 (OUTLIER) cc_final: 0.8638 (p) REVERT: C 387 MET cc_start: 0.8936 (ttt) cc_final: 0.8411 (tpp) REVERT: D 71 TYR cc_start: 0.9090 (m-80) cc_final: 0.8607 (m-80) REVERT: D 134 ASN cc_start: 0.8422 (t0) cc_final: 0.7952 (t0) REVERT: D 146 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.8009 (mp0) REVERT: D 154 GLN cc_start: 0.8624 (pt0) cc_final: 0.8097 (pt0) REVERT: D 269 GLU cc_start: 0.8254 (tp30) cc_final: 0.7974 (tp30) REVERT: D 309 LYS cc_start: 0.9211 (mtmt) cc_final: 0.9009 (ttpp) REVERT: D 370 ASP cc_start: 0.8403 (t0) cc_final: 0.8091 (t0) REVERT: D 372 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.8285 (mp10) REVERT: D 423 GLN cc_start: 0.8334 (mm-40) cc_final: 0.7508 (tt0) REVERT: D 470 GLN cc_start: 0.9067 (tm-30) cc_final: 0.8802 (tm-30) REVERT: E 65 LYS cc_start: 0.9244 (tttt) cc_final: 0.8959 (tttp) REVERT: E 84 PHE cc_start: 0.7457 (m-10) cc_final: 0.7033 (t80) REVERT: E 92 TYR cc_start: 0.8788 (OUTLIER) cc_final: 0.7230 (p90) REVERT: E 123 TYR cc_start: 0.8930 (m-80) cc_final: 0.8055 (m-80) REVERT: E 146 GLU cc_start: 0.6656 (mm-30) cc_final: 0.6451 (mm-30) REVERT: E 196 GLU cc_start: 0.8318 (mm-30) cc_final: 0.7854 (mm-30) REVERT: E 252 ARG cc_start: 0.8069 (mtp-110) cc_final: 0.7724 (ttm-80) REVERT: E 311 TYR cc_start: 0.8144 (m-80) cc_final: 0.7498 (m-10) REVERT: E 321 ASN cc_start: 0.8968 (t0) cc_final: 0.8437 (t0) REVERT: E 393 MET cc_start: 0.9206 (tmm) cc_final: 0.8986 (tmm) REVERT: E 399 GLU cc_start: 0.8963 (mt-10) cc_final: 0.8751 (mt-10) REVERT: E 418 ARG cc_start: 0.7872 (tmm160) cc_final: 0.6388 (mtt-85) REVERT: L 104 LEU cc_start: 0.7213 (tp) cc_final: 0.6900 (tt) REVERT: L 175 MET cc_start: 0.7470 (ttt) cc_final: 0.6953 (tpt) REVERT: H 104 TYR cc_start: 0.4667 (m-80) cc_final: 0.4023 (m-80) outliers start: 133 outliers final: 103 residues processed: 559 average time/residue: 0.3078 time to fit residues: 271.5738 Evaluate side-chains 571 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 460 time to evaluate : 2.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 154 GLN Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 396 ASN Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 308 ASN Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 441 ASN Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 454 PHE Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 56 ASN Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 254 GLN Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 442 LYS Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 248 PHE Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 319 HIS Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 372 GLN Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 378 CYS Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 82 ASN Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 324 CYS Chi-restraints excluded: chain E residue 374 VAL Chi-restraints excluded: chain E residue 412 SER Chi-restraints excluded: chain E residue 459 ASP Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain H residue 61 ASN Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 102 ASP Chi-restraints excluded: chain H residue 140 MET Chi-restraints excluded: chain H residue 169 HIS Chi-restraints excluded: chain H residue 190 SER Chi-restraints excluded: chain H residue 198 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 89 optimal weight: 20.0000 chunk 238 optimal weight: 30.0000 chunk 52 optimal weight: 8.9990 chunk 155 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 265 optimal weight: 40.0000 chunk 220 optimal weight: 9.9990 chunk 122 optimal weight: 7.9990 chunk 22 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 chunk 139 optimal weight: 2.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 GLN ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 396 ASN ** 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 391 HIS E 70 GLN ** E 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 GLN ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 1 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 22371 Z= 0.401 Angle : 0.718 8.487 30428 Z= 0.363 Chirality : 0.046 0.214 3287 Planarity : 0.005 0.065 3972 Dihedral : 5.501 41.534 2999 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.15 % Favored : 89.85 % Rotamer: Outliers : 6.88 % Allowed : 23.18 % Favored : 69.94 % 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: -3.05 (0.15), residues: 2748 helix: -1.71 (0.33), residues: 206 sheet: -1.49 (0.18), residues: 737 loop : -2.43 (0.13), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP L 92 HIS 0.005 0.001 HIS C 169 PHE 0.025 0.002 PHE L 98 TYR 0.018 0.002 TYR B 152 ARG 0.007 0.001 ARG B 98 *********************** 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 608 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 440 time to evaluate : 2.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 TYR cc_start: 0.8904 (m-10) cc_final: 0.8633 (m-10) REVERT: B 126 LYS cc_start: 0.8788 (tmtt) cc_final: 0.8512 (tptp) REVERT: B 148 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8129 (mm) REVERT: B 172 LYS cc_start: 0.8149 (tppt) cc_final: 0.7821 (tppt) REVERT: B 208 MET cc_start: 0.7951 (ptp) cc_final: 0.7603 (ptp) REVERT: B 320 ASN cc_start: 0.9244 (OUTLIER) cc_final: 0.8645 (p0) REVERT: B 459 ASP cc_start: 0.9118 (OUTLIER) cc_final: 0.8618 (p0) REVERT: A 25 ASP cc_start: 0.8561 (m-30) cc_final: 0.8275 (m-30) REVERT: A 135 ARG cc_start: 0.7692 (mtt180) cc_final: 0.7087 (ptm160) REVERT: A 148 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8298 (mm) REVERT: A 153 LYS cc_start: 0.8674 (ptmm) cc_final: 0.8398 (pttm) REVERT: A 217 LYS cc_start: 0.9426 (mttm) cc_final: 0.8912 (ptmt) REVERT: A 242 TYR cc_start: 0.8827 (m-80) cc_final: 0.7636 (m-80) REVERT: A 244 ASP cc_start: 0.8898 (m-30) cc_final: 0.8613 (m-30) REVERT: A 291 PHE cc_start: 0.8031 (m-80) cc_final: 0.7717 (m-10) REVERT: A 393 MET cc_start: 0.8230 (tpt) cc_final: 0.7763 (tpt) REVERT: A 418 ARG cc_start: 0.4522 (ptt-90) cc_final: 0.3537 (ptt-90) REVERT: A 454 PHE cc_start: 0.8995 (OUTLIER) cc_final: 0.8181 (m-10) REVERT: C 254 GLN cc_start: 0.9115 (pt0) cc_final: 0.8785 (pm20) REVERT: C 255 MET cc_start: 0.8941 (ppp) cc_final: 0.8681 (ppp) REVERT: C 303 GLU cc_start: 0.8110 (tt0) cc_final: 0.7878 (tt0) REVERT: C 361 GLU cc_start: 0.7385 (mp0) cc_final: 0.7016 (mp0) REVERT: C 381 THR cc_start: 0.9066 (OUTLIER) cc_final: 0.8788 (p) REVERT: C 382 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.8830 (tt) REVERT: C 387 MET cc_start: 0.8971 (ttt) cc_final: 0.8427 (tpp) REVERT: D 71 TYR cc_start: 0.9168 (m-80) cc_final: 0.8657 (m-80) REVERT: D 134 ASN cc_start: 0.8457 (t0) cc_final: 0.7895 (t0) REVERT: D 146 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7541 (mp0) REVERT: D 237 MET cc_start: 0.8817 (mtm) cc_final: 0.8497 (mtt) REVERT: D 309 LYS cc_start: 0.9198 (mtmt) cc_final: 0.8867 (ttpp) REVERT: D 372 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.8261 (mp10) REVERT: D 470 GLN cc_start: 0.9145 (tm-30) cc_final: 0.8887 (tm-30) REVERT: E 65 LYS cc_start: 0.9198 (tttt) cc_final: 0.8888 (tttp) REVERT: E 84 PHE cc_start: 0.7675 (m-10) cc_final: 0.6974 (t80) REVERT: E 92 TYR cc_start: 0.8874 (OUTLIER) cc_final: 0.7542 (p90) REVERT: E 123 TYR cc_start: 0.9048 (m-80) cc_final: 0.8254 (m-80) REVERT: E 146 GLU cc_start: 0.6700 (mm-30) cc_final: 0.6484 (mm-30) REVERT: E 152 TYR cc_start: 0.8061 (m-80) cc_final: 0.7795 (m-80) REVERT: E 252 ARG cc_start: 0.8219 (mtp-110) cc_final: 0.7791 (ttm-80) REVERT: E 311 TYR cc_start: 0.8312 (m-80) cc_final: 0.7575 (m-10) REVERT: E 321 ASN cc_start: 0.8957 (t0) cc_final: 0.8545 (t0) REVERT: E 393 MET cc_start: 0.9226 (tmm) cc_final: 0.8987 (tmm) REVERT: L 104 LEU cc_start: 0.7227 (tp) cc_final: 0.6920 (tt) REVERT: L 175 MET cc_start: 0.7552 (ttt) cc_final: 0.7098 (tpt) outliers start: 168 outliers final: 125 residues processed: 542 average time/residue: 0.3037 time to fit residues: 265.5613 Evaluate side-chains 557 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 422 time to evaluate : 2.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 262 ASN Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 320 ASN Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 396 ASN Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 308 ASN Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 441 ASN Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 454 PHE Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 56 ASN Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 442 LYS Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 248 PHE Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 287 GLN Chi-restraints excluded: chain D residue 291 PHE Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 319 HIS Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 372 GLN Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 378 CYS Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 397 ILE Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 459 ASP Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 82 ASN Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 324 CYS Chi-restraints excluded: chain E residue 374 VAL Chi-restraints excluded: chain E residue 412 SER Chi-restraints excluded: chain E residue 415 ASP Chi-restraints excluded: chain E residue 459 ASP Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 61 ASN Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 102 ASP Chi-restraints excluded: chain H residue 140 MET Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 169 HIS Chi-restraints excluded: chain H residue 190 SER Chi-restraints excluded: chain H residue 198 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 255 optimal weight: 30.0000 chunk 29 optimal weight: 5.9990 chunk 151 optimal weight: 20.0000 chunk 193 optimal weight: 0.0170 chunk 149 optimal weight: 0.9980 chunk 223 optimal weight: 8.9990 chunk 148 optimal weight: 1.9990 chunk 264 optimal weight: 0.6980 chunk 165 optimal weight: 10.0000 chunk 161 optimal weight: 7.9990 chunk 121 optimal weight: 0.4980 overall best weight: 0.8420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 GLN ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 460 GLN E 70 GLN E 112 GLN ** E 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 GLN ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 45 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 22371 Z= 0.158 Angle : 0.631 11.166 30428 Z= 0.308 Chirality : 0.044 0.249 3287 Planarity : 0.005 0.060 3972 Dihedral : 4.933 38.290 2999 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 4.87 % Allowed : 25.10 % Favored : 70.02 % 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: -2.74 (0.15), residues: 2748 helix: -1.48 (0.34), residues: 206 sheet: -1.35 (0.18), residues: 747 loop : -2.18 (0.14), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP L 92 HIS 0.004 0.000 HIS H 82 PHE 0.028 0.001 PHE L 98 TYR 0.012 0.001 TYR E 417 ARG 0.004 0.000 ARG E 251 *********************** 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 614 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 495 time to evaluate : 2.728 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: B 49 TYR cc_start: 0.8769 (m-10) cc_final: 0.8499 (m-10) REVERT: B 75 ARG cc_start: 0.8608 (ttt180) cc_final: 0.8187 (ttt-90) REVERT: B 126 LYS cc_start: 0.8584 (tmtt) cc_final: 0.8339 (tptp) REVERT: B 129 ASP cc_start: 0.7254 (t0) cc_final: 0.7008 (t0) REVERT: B 131 GLU cc_start: 0.6843 (mt-10) cc_final: 0.6151 (mp0) REVERT: B 148 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.8022 (mm) REVERT: B 172 LYS cc_start: 0.8087 (tppt) cc_final: 0.7739 (tppt) REVERT: B 246 LEU cc_start: 0.9382 (mt) cc_final: 0.9166 (mt) REVERT: B 422 SER cc_start: 0.8484 (t) cc_final: 0.8104 (m) REVERT: B 459 ASP cc_start: 0.9028 (p0) cc_final: 0.8462 (p0) REVERT: A 25 ASP cc_start: 0.8575 (m-30) cc_final: 0.8286 (m-30) REVERT: A 135 ARG cc_start: 0.7677 (mtt180) cc_final: 0.6966 (ptm160) REVERT: A 148 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8365 (mm) REVERT: A 153 LYS cc_start: 0.8554 (ptmm) cc_final: 0.8268 (pttt) REVERT: A 217 LYS cc_start: 0.9391 (mttm) cc_final: 0.8873 (ptmt) REVERT: A 242 TYR cc_start: 0.8793 (m-80) cc_final: 0.7923 (m-80) REVERT: A 247 PHE cc_start: 0.8697 (m-10) cc_final: 0.8477 (m-80) REVERT: A 251 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.8242 (ptp90) REVERT: A 418 ARG cc_start: 0.4182 (ptt-90) cc_final: 0.1998 (mpp80) REVERT: A 454 PHE cc_start: 0.8759 (OUTLIER) cc_final: 0.7716 (m-10) REVERT: C 200 MET cc_start: 0.8880 (mmm) cc_final: 0.8479 (mmp) REVERT: C 235 LEU cc_start: 0.9489 (mm) cc_final: 0.9053 (mm) REVERT: C 255 MET cc_start: 0.8942 (ppp) cc_final: 0.8694 (ppp) REVERT: C 266 LYS cc_start: 0.8532 (pttm) cc_final: 0.8168 (pttm) REVERT: C 303 GLU cc_start: 0.7990 (tt0) cc_final: 0.7772 (tt0) REVERT: C 306 LEU cc_start: 0.9415 (mm) cc_final: 0.9203 (mm) REVERT: C 320 ASN cc_start: 0.8083 (OUTLIER) cc_final: 0.7820 (p0) REVERT: C 361 GLU cc_start: 0.7404 (mp0) cc_final: 0.7096 (mp0) REVERT: C 381 THR cc_start: 0.8937 (OUTLIER) cc_final: 0.8707 (p) REVERT: C 382 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.8771 (tt) REVERT: C 387 MET cc_start: 0.8986 (ttt) cc_final: 0.8394 (tpp) REVERT: D 71 TYR cc_start: 0.9070 (m-80) cc_final: 0.8596 (m-80) REVERT: D 134 ASN cc_start: 0.8447 (t0) cc_final: 0.8005 (t0) REVERT: D 146 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7855 (mp0) REVERT: D 154 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.8039 (pt0) REVERT: D 237 MET cc_start: 0.8696 (mtm) cc_final: 0.8417 (mtt) REVERT: D 269 GLU cc_start: 0.7966 (tp30) cc_final: 0.7675 (tp30) REVERT: D 309 LYS cc_start: 0.9241 (mtmt) cc_final: 0.9038 (ttpp) REVERT: D 372 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.8309 (mp10) REVERT: D 393 MET cc_start: 0.8470 (tpt) cc_final: 0.8240 (tpp) REVERT: D 470 GLN cc_start: 0.9107 (tm-30) cc_final: 0.8859 (tm-30) REVERT: E 65 LYS cc_start: 0.9267 (tttt) cc_final: 0.8969 (tttp) REVERT: E 84 PHE cc_start: 0.7396 (m-10) cc_final: 0.6918 (t80) REVERT: E 92 TYR cc_start: 0.8766 (OUTLIER) cc_final: 0.7283 (p90) REVERT: E 123 TYR cc_start: 0.8907 (m-80) cc_final: 0.8067 (m-80) REVERT: E 196 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7843 (mm-30) REVERT: E 311 TYR cc_start: 0.8095 (m-80) cc_final: 0.7535 (m-10) REVERT: E 321 ASN cc_start: 0.8954 (t0) cc_final: 0.8389 (t0) REVERT: E 393 MET cc_start: 0.9175 (tmm) cc_final: 0.8905 (tmm) REVERT: E 418 ARG cc_start: 0.7714 (tmm160) cc_final: 0.6456 (mtt-85) REVERT: L 104 LEU cc_start: 0.7337 (tp) cc_final: 0.7016 (tt) REVERT: L 175 MET cc_start: 0.7572 (ttt) cc_final: 0.7122 (tpt) REVERT: H 81 MET cc_start: 0.7231 (ptt) cc_final: 0.7030 (ptt) REVERT: H 102 ASP cc_start: -0.0037 (OUTLIER) cc_final: -0.0245 (p0) outliers start: 119 outliers final: 86 residues processed: 560 average time/residue: 0.2909 time to fit residues: 258.0384 Evaluate side-chains 560 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 462 time to evaluate : 2.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 154 GLN Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 251 ARG Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 454 PHE Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 291 PHE Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 320 ASN Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 154 GLN Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 248 PHE Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 372 GLN Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 378 CYS Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 82 ASN Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 112 GLN Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 374 VAL Chi-restraints excluded: chain E residue 459 ASP Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 102 ASP Chi-restraints excluded: chain H residue 140 MET Chi-restraints excluded: chain H residue 169 HIS Chi-restraints excluded: chain H residue 190 SER Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 201 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 163 optimal weight: 6.9990 chunk 105 optimal weight: 7.9990 chunk 157 optimal weight: 10.0000 chunk 79 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 167 optimal weight: 6.9990 chunk 179 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 chunk 207 optimal weight: 5.9990 chunk 240 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 GLN ** C 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 GLN ** E 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 GLN ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 166 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 22371 Z= 0.278 Angle : 0.664 11.408 30428 Z= 0.330 Chirality : 0.045 0.208 3287 Planarity : 0.005 0.061 3972 Dihedral : 5.053 42.140 2999 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 5.45 % Allowed : 25.51 % Favored : 69.04 % 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: -2.75 (0.15), residues: 2748 helix: -1.41 (0.34), residues: 204 sheet: -1.38 (0.18), residues: 760 loop : -2.18 (0.14), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP L 92 HIS 0.003 0.001 HIS C 169 PHE 0.022 0.002 PHE L 139 TYR 0.023 0.001 TYR C 242 ARG 0.006 0.000 ARG B 98 *********************** 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 583 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 450 time to evaluate : 2.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 TYR cc_start: 0.8833 (m-10) cc_final: 0.8578 (m-10) REVERT: B 126 LYS cc_start: 0.8615 (tmtt) cc_final: 0.8374 (tptp) REVERT: B 129 ASP cc_start: 0.7362 (t0) cc_final: 0.7111 (t0) REVERT: B 131 GLU cc_start: 0.6955 (mt-10) cc_final: 0.6250 (mp0) REVERT: B 148 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8098 (mm) REVERT: B 172 LYS cc_start: 0.8124 (tppt) cc_final: 0.7778 (tppt) REVERT: B 459 ASP cc_start: 0.9074 (p0) cc_final: 0.8491 (p0) REVERT: A 25 ASP cc_start: 0.8589 (m-30) cc_final: 0.8315 (m-30) REVERT: A 135 ARG cc_start: 0.7652 (mtt180) cc_final: 0.7045 (ptm-80) REVERT: A 148 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8247 (mm) REVERT: A 153 LYS cc_start: 0.8610 (ptmm) cc_final: 0.8300 (pttm) REVERT: A 217 LYS cc_start: 0.9403 (mttm) cc_final: 0.8900 (ptmt) REVERT: A 244 ASP cc_start: 0.8783 (m-30) cc_final: 0.8490 (m-30) REVERT: A 247 PHE cc_start: 0.8736 (m-10) cc_final: 0.8535 (m-80) REVERT: A 251 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.8201 (ptp90) REVERT: A 418 ARG cc_start: 0.4440 (ptt-90) cc_final: 0.2346 (mpp80) REVERT: A 454 PHE cc_start: 0.8820 (OUTLIER) cc_final: 0.7934 (m-10) REVERT: C 255 MET cc_start: 0.8932 (ppp) cc_final: 0.8616 (ppp) REVERT: C 266 LYS cc_start: 0.8563 (pttm) cc_final: 0.8228 (pttm) REVERT: C 303 GLU cc_start: 0.8031 (tt0) cc_final: 0.7819 (tt0) REVERT: C 320 ASN cc_start: 0.8163 (OUTLIER) cc_final: 0.7915 (p0) REVERT: C 361 GLU cc_start: 0.7376 (mp0) cc_final: 0.7000 (mp0) REVERT: C 382 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.8807 (tt) REVERT: C 387 MET cc_start: 0.8978 (ttt) cc_final: 0.8407 (tpp) REVERT: D 71 TYR cc_start: 0.9144 (m-80) cc_final: 0.8663 (m-80) REVERT: D 146 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7795 (mp0) REVERT: D 154 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.8029 (pt0) REVERT: D 237 MET cc_start: 0.8844 (mtm) cc_final: 0.8543 (mtt) REVERT: D 269 GLU cc_start: 0.8022 (tp30) cc_final: 0.7686 (tp30) REVERT: D 309 LYS cc_start: 0.9219 (mtmt) cc_final: 0.8897 (ttpp) REVERT: D 372 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.8320 (mp10) REVERT: D 470 GLN cc_start: 0.9096 (tm-30) cc_final: 0.8846 (tm-30) REVERT: E 65 LYS cc_start: 0.9263 (tttt) cc_final: 0.9009 (tttp) REVERT: E 84 PHE cc_start: 0.7486 (m-10) cc_final: 0.6915 (t80) REVERT: E 92 TYR cc_start: 0.8890 (OUTLIER) cc_final: 0.7455 (p90) REVERT: E 123 TYR cc_start: 0.8991 (m-80) cc_final: 0.8175 (m-80) REVERT: E 196 GLU cc_start: 0.8538 (mm-30) cc_final: 0.7886 (mm-30) REVERT: E 311 TYR cc_start: 0.8232 (m-80) cc_final: 0.7559 (m-10) REVERT: E 321 ASN cc_start: 0.8965 (t0) cc_final: 0.8437 (t0) REVERT: E 342 MET cc_start: 0.7685 (tpt) cc_final: 0.7316 (tpt) REVERT: E 393 MET cc_start: 0.9192 (tmm) cc_final: 0.8991 (tmm) REVERT: L 104 LEU cc_start: 0.7217 (tp) cc_final: 0.6882 (tt) REVERT: L 175 MET cc_start: 0.7474 (ttt) cc_final: 0.7048 (tpt) REVERT: H 102 ASP cc_start: -0.0736 (OUTLIER) cc_final: -0.1441 (p0) outliers start: 133 outliers final: 106 residues processed: 530 average time/residue: 0.2983 time to fit residues: 251.9511 Evaluate side-chains 560 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 443 time to evaluate : 2.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 251 ARG Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 454 PHE Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 56 ASN Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 252 ARG Chi-restraints excluded: chain C residue 254 GLN Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 320 ASN Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 154 GLN Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 248 PHE Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 287 GLN Chi-restraints excluded: chain D residue 291 PHE Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 372 GLN Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 378 CYS Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 82 ASN Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 112 GLN Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 324 CYS Chi-restraints excluded: chain E residue 374 VAL Chi-restraints excluded: chain E residue 415 ASP Chi-restraints excluded: chain E residue 459 ASP Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 99 LYS Chi-restraints excluded: chain H residue 102 ASP Chi-restraints excluded: chain H residue 140 MET Chi-restraints excluded: chain H residue 169 HIS Chi-restraints excluded: chain H residue 190 SER Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 201 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 253 optimal weight: 50.0000 chunk 230 optimal weight: 0.0370 chunk 246 optimal weight: 20.0000 chunk 252 optimal weight: 8.9990 chunk 148 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 193 optimal weight: 5.9990 chunk 75 optimal weight: 20.0000 chunk 222 optimal weight: 5.9990 chunk 232 optimal weight: 40.0000 chunk 245 optimal weight: 20.0000 overall best weight: 4.4066 ------------------------------------------------------------------------------- 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 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 396 ASN ** 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 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 GLN ** E 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 GLN ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 22371 Z= 0.251 Angle : 0.663 11.034 30428 Z= 0.327 Chirality : 0.045 0.201 3287 Planarity : 0.005 0.062 3972 Dihedral : 5.060 43.603 2999 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 5.49 % Allowed : 25.68 % Favored : 68.84 % 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: -2.72 (0.15), residues: 2748 helix: -1.32 (0.34), residues: 204 sheet: -1.41 (0.18), residues: 770 loop : -2.14 (0.14), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP L 92 HIS 0.004 0.001 HIS H 82 PHE 0.025 0.001 PHE B 210 TYR 0.026 0.001 TYR A 242 ARG 0.008 0.000 ARG B 98 *********************** 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 587 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 453 time to evaluate : 2.601 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: B 49 TYR cc_start: 0.8809 (m-10) cc_final: 0.8566 (m-10) REVERT: B 129 ASP cc_start: 0.7338 (t0) cc_final: 0.7050 (t0) REVERT: B 131 GLU cc_start: 0.6957 (mt-10) cc_final: 0.6208 (mp0) REVERT: B 148 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8088 (mm) REVERT: B 172 LYS cc_start: 0.8138 (tppt) cc_final: 0.7784 (tppt) REVERT: B 320 ASN cc_start: 0.9163 (OUTLIER) cc_final: 0.8524 (p0) REVERT: B 422 SER cc_start: 0.8506 (t) cc_final: 0.8134 (m) REVERT: B 459 ASP cc_start: 0.9058 (p0) cc_final: 0.8508 (p0) REVERT: A 25 ASP cc_start: 0.8574 (m-30) cc_final: 0.8299 (m-30) REVERT: A 135 ARG cc_start: 0.7642 (mtt180) cc_final: 0.7042 (ptm-80) REVERT: A 146 GLU cc_start: 0.6586 (mm-30) cc_final: 0.6363 (mm-30) REVERT: A 148 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8355 (mm) REVERT: A 153 LYS cc_start: 0.8545 (ptmm) cc_final: 0.8241 (pttm) REVERT: A 217 LYS cc_start: 0.9405 (mttm) cc_final: 0.8897 (ptmt) REVERT: A 244 ASP cc_start: 0.8771 (m-30) cc_final: 0.8523 (m-30) REVERT: A 251 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.8200 (ptp90) REVERT: A 393 MET cc_start: 0.8008 (mmm) cc_final: 0.7622 (mmm) REVERT: A 418 ARG cc_start: 0.4449 (ptt-90) cc_final: 0.2329 (mpp80) REVERT: A 454 PHE cc_start: 0.8814 (OUTLIER) cc_final: 0.7930 (m-10) REVERT: C 255 MET cc_start: 0.8982 (ppp) cc_final: 0.8683 (ppp) REVERT: C 266 LYS cc_start: 0.8477 (pttm) cc_final: 0.8132 (pttm) REVERT: C 320 ASN cc_start: 0.8142 (OUTLIER) cc_final: 0.7891 (p0) REVERT: C 361 GLU cc_start: 0.7363 (mp0) cc_final: 0.6992 (mp0) REVERT: C 382 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8849 (tt) REVERT: C 387 MET cc_start: 0.8979 (ttt) cc_final: 0.8397 (tpp) REVERT: D 71 TYR cc_start: 0.9151 (m-80) cc_final: 0.8707 (m-80) REVERT: D 127 PHE cc_start: 0.8580 (t80) cc_final: 0.8148 (t80) REVERT: D 146 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7499 (mp0) REVERT: D 237 MET cc_start: 0.8828 (mtm) cc_final: 0.8536 (mtt) REVERT: D 309 LYS cc_start: 0.9230 (mtmt) cc_final: 0.8910 (ttpp) REVERT: D 372 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.8367 (mp10) REVERT: D 470 GLN cc_start: 0.9093 (tm-30) cc_final: 0.8841 (tm-30) REVERT: E 84 PHE cc_start: 0.7385 (m-10) cc_final: 0.6836 (t80) REVERT: E 92 TYR cc_start: 0.8852 (OUTLIER) cc_final: 0.7503 (p90) REVERT: E 123 TYR cc_start: 0.8985 (m-80) cc_final: 0.8175 (m-80) REVERT: E 157 LEU cc_start: 0.9583 (pt) cc_final: 0.9340 (pp) REVERT: E 196 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8222 (mm-30) REVERT: E 311 TYR cc_start: 0.8182 (m-80) cc_final: 0.7540 (m-10) REVERT: E 321 ASN cc_start: 0.8963 (t0) cc_final: 0.8418 (t0) REVERT: E 342 MET cc_start: 0.7616 (tpt) cc_final: 0.7225 (tpt) REVERT: E 393 MET cc_start: 0.9193 (tmm) cc_final: 0.8981 (tmm) REVERT: L 104 LEU cc_start: 0.7192 (tp) cc_final: 0.6878 (tt) REVERT: L 175 MET cc_start: 0.7519 (ttt) cc_final: 0.7108 (tpt) REVERT: H 102 ASP cc_start: -0.0767 (OUTLIER) cc_final: -0.1363 (p0) outliers start: 134 outliers final: 108 residues processed: 533 average time/residue: 0.3036 time to fit residues: 259.9256 Evaluate side-chains 563 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 444 time to evaluate : 2.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 262 ASN Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 320 ASN Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 251 ARG Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 454 PHE Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 56 ASN Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 252 ARG Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 320 ASN Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 248 PHE Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 287 GLN Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 372 GLN Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 378 CYS Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 82 ASN Chi-restraints excluded: chain E residue 86 PHE Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 112 GLN Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 324 CYS Chi-restraints excluded: chain E residue 374 VAL Chi-restraints excluded: chain E residue 459 ASP Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 102 ASP Chi-restraints excluded: chain H residue 140 MET Chi-restraints excluded: chain H residue 169 HIS Chi-restraints excluded: chain H residue 190 SER Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 201 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 161 optimal weight: 9.9990 chunk 260 optimal weight: 0.2980 chunk 158 optimal weight: 7.9990 chunk 123 optimal weight: 10.0000 chunk 180 optimal weight: 9.9990 chunk 272 optimal weight: 50.0000 chunk 251 optimal weight: 10.0000 chunk 217 optimal weight: 0.0980 chunk 22 optimal weight: 10.0000 chunk 167 optimal weight: 4.9990 chunk 133 optimal weight: 0.0970 overall best weight: 2.6982 ------------------------------------------------------------------------------- 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 169 HIS ** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 341 ASN ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 134 ASN E 112 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: 0.7854 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 22371 Z= 0.196 Angle : 0.657 11.118 30428 Z= 0.320 Chirality : 0.045 0.215 3287 Planarity : 0.005 0.064 3972 Dihedral : 4.928 44.353 2999 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 5.08 % Allowed : 26.45 % Favored : 68.47 % 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: -2.61 (0.15), residues: 2748 helix: -1.21 (0.35), residues: 204 sheet: -1.35 (0.18), residues: 744 loop : -2.06 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP L 92 HIS 0.003 0.001 HIS B 365 PHE 0.020 0.001 PHE L 139 TYR 0.019 0.001 TYR A 242 ARG 0.006 0.000 ARG B 98 ********************** 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 588 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 464 time to evaluate : 2.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 TYR cc_start: 0.8764 (m-10) cc_final: 0.8547 (m-10) REVERT: B 75 ARG cc_start: 0.8650 (ttt180) cc_final: 0.8240 (ttt-90) REVERT: B 126 LYS cc_start: 0.8230 (tptp) cc_final: 0.7556 (tptt) REVERT: B 129 ASP cc_start: 0.7118 (t0) cc_final: 0.6570 (t0) REVERT: B 131 GLU cc_start: 0.7037 (mt-10) cc_final: 0.6174 (mp0) REVERT: B 148 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8064 (mm) REVERT: B 172 LYS cc_start: 0.8129 (tppt) cc_final: 0.7768 (tppt) REVERT: B 422 SER cc_start: 0.8529 (t) cc_final: 0.8128 (m) REVERT: B 459 ASP cc_start: 0.9044 (p0) cc_final: 0.8474 (p0) REVERT: A 25 ASP cc_start: 0.8532 (m-30) cc_final: 0.8310 (m-30) REVERT: A 135 ARG cc_start: 0.7655 (mtt180) cc_final: 0.7024 (ptm-80) REVERT: A 146 GLU cc_start: 0.6600 (mm-30) cc_final: 0.6373 (mm-30) REVERT: A 148 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8354 (mm) REVERT: A 153 LYS cc_start: 0.8518 (ptmm) cc_final: 0.8231 (pttt) REVERT: A 217 LYS cc_start: 0.9396 (mttm) cc_final: 0.8894 (ptmt) REVERT: A 251 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.8226 (ptp90) REVERT: A 347 GLU cc_start: 0.9207 (pm20) cc_final: 0.9001 (pm20) REVERT: A 393 MET cc_start: 0.7961 (mmm) cc_final: 0.7609 (mmm) REVERT: A 418 ARG cc_start: 0.4467 (ptt-90) cc_final: 0.2336 (mpp80) REVERT: A 454 PHE cc_start: 0.8805 (OUTLIER) cc_final: 0.7943 (m-10) REVERT: C 255 MET cc_start: 0.8915 (ppp) cc_final: 0.8643 (ppp) REVERT: C 266 LYS cc_start: 0.8467 (pttm) cc_final: 0.8131 (pttm) REVERT: C 320 ASN cc_start: 0.8131 (OUTLIER) cc_final: 0.7867 (p0) REVERT: C 361 GLU cc_start: 0.7362 (mp0) cc_final: 0.7008 (mp0) REVERT: C 382 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8852 (tt) REVERT: C 387 MET cc_start: 0.8971 (ttt) cc_final: 0.8377 (tpp) REVERT: D 71 TYR cc_start: 0.9116 (m-80) cc_final: 0.8654 (m-80) REVERT: D 127 PHE cc_start: 0.8566 (t80) cc_final: 0.8151 (t80) REVERT: D 146 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7658 (mp0) REVERT: D 208 MET cc_start: 0.7463 (pmm) cc_final: 0.7117 (pmm) REVERT: D 237 MET cc_start: 0.8806 (mtm) cc_final: 0.8514 (mtt) REVERT: D 269 GLU cc_start: 0.7985 (tp30) cc_final: 0.7667 (tp30) REVERT: D 372 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.8365 (mp10) REVERT: D 470 GLN cc_start: 0.9076 (tm-30) cc_final: 0.8860 (tm-30) REVERT: E 8 GLU cc_start: 0.7930 (tp30) cc_final: 0.7684 (mm-30) REVERT: E 84 PHE cc_start: 0.7407 (m-10) cc_final: 0.6911 (t80) REVERT: E 92 TYR cc_start: 0.8820 (OUTLIER) cc_final: 0.7457 (p90) REVERT: E 123 TYR cc_start: 0.8941 (m-80) cc_final: 0.8151 (m-80) REVERT: E 157 LEU cc_start: 0.9568 (pt) cc_final: 0.9339 (pp) REVERT: E 196 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8250 (mm-30) REVERT: E 311 TYR cc_start: 0.8137 (m-80) cc_final: 0.7559 (m-10) REVERT: E 321 ASN cc_start: 0.8938 (t0) cc_final: 0.8370 (t0) REVERT: E 342 MET cc_start: 0.7592 (tpt) cc_final: 0.7259 (tpt) REVERT: L 104 LEU cc_start: 0.7289 (tp) cc_final: 0.6943 (tt) REVERT: L 175 MET cc_start: 0.7520 (ttt) cc_final: 0.7163 (tpt) REVERT: H 102 ASP cc_start: -0.0160 (OUTLIER) cc_final: -0.0676 (p0) outliers start: 124 outliers final: 106 residues processed: 540 average time/residue: 0.3013 time to fit residues: 259.7823 Evaluate side-chains 564 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 448 time to evaluate : 2.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 262 ASN Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 251 ARG Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 454 PHE Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 56 ASN Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 254 GLN Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 320 ASN Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 248 PHE Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 372 GLN Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 378 CYS Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 82 ASN Chi-restraints excluded: chain E residue 86 PHE Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 112 GLN Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 207 CYS Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 302 SER Chi-restraints excluded: chain E residue 324 CYS Chi-restraints excluded: chain E residue 374 VAL Chi-restraints excluded: chain E residue 415 ASP Chi-restraints excluded: chain E residue 459 ASP Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 102 ASP Chi-restraints excluded: chain H residue 140 MET Chi-restraints excluded: chain H residue 190 SER Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 201 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 172 optimal weight: 9.9990 chunk 231 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 200 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 60 optimal weight: 30.0000 chunk 217 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 223 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 254 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** A 391 HIS ** A 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 341 ASN ** E 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.142517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.103825 restraints weight = 66964.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.107379 restraints weight = 28239.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.109645 restraints weight = 16557.188| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3442 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3442 r_free = 0.3442 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3442 r_free = 0.3442 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3442 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 22371 Z= 0.252 Angle : 0.675 10.843 30428 Z= 0.331 Chirality : 0.045 0.201 3287 Planarity : 0.005 0.064 3972 Dihedral : 4.938 45.180 2999 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 5.53 % Allowed : 26.04 % Favored : 68.43 % 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 (0.35), residues: 204 sheet: -1.35 (0.18), residues: 756 loop : -2.06 (0.14), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP L 92 HIS 0.005 0.001 HIS H 169 PHE 0.020 0.001 PHE L 139 TYR 0.021 0.001 TYR E 389 ARG 0.006 0.000 ARG B 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5607.69 seconds wall clock time: 102 minutes 3.92 seconds (6123.92 seconds total)