Starting phenix.real_space_refine (version: 1.21rc1) on Wed Apr 26 03:18:33 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dnl_30787/04_2023/7dnl_30787.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dnl_30787/04_2023/7dnl_30787.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dnl_30787/04_2023/7dnl_30787.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dnl_30787/04_2023/7dnl_30787.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dnl_30787/04_2023/7dnl_30787.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dnl_30787/04_2023/7dnl_30787.pdb" } resolution = 4.19 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 1.018 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 119 5.16 5 C 13900 2.51 5 N 3632 2.21 5 O 4196 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L ASP 1": "OD1" <-> "OD2" Residue "L TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 61": "OE1" <-> "OE2" Residue "L ASP 66": "OD1" <-> "OD2" Residue "L ASP 76": "OD1" <-> "OD2" Residue "L GLU 87": "OE1" <-> "OE2" Residue "L ASP 88": "OD1" <-> "OD2" Residue "L TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 171": "OD1" <-> "OD2" Residue "L GLU 191": "OE1" <-> "OE2" Residue "L TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 201": "OE1" <-> "OE2" Residue "L PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 219": "OE1" <-> "OE2" Residue "H PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 57": "OD1" <-> "OD2" Residue "H ASP 88": "OD1" <-> "OD2" Residue "H TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 105": "OD1" <-> "OD2" Residue "H ASP 108": "OD1" <-> "OD2" Residue "H ASP 136": "OD1" <-> "OD2" Residue "H PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 213": "OD1" <-> "OD2" Residue "B GLU 8": "OE1" <-> "OE2" Residue "B TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 107": "OE1" <-> "OE2" Residue "B ARG 110": "NH1" <-> "NH2" Residue "B GLU 196": "OE1" <-> "OE2" Residue "B PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 367": "OE1" <-> "OE2" Residue "B TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 415": "OD1" <-> "OD2" Residue "B TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 438": "OD1" <-> "OD2" Residue "B ARG 465": "NH1" <-> "NH2" Residue "A GLU 26": "OE1" <-> "OE2" Residue "A TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 95": "OD1" <-> "OD2" Residue "A GLU 131": "OE1" <-> "OE2" Residue "A ASP 151": "OD1" <-> "OD2" Residue "A GLU 189": "OE1" <-> "OE2" Residue "A ASP 202": "OD1" <-> "OD2" Residue "A PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 219": "OD1" <-> "OD2" Residue "A PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 351": "OE1" <-> "OE2" Residue "A TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 361": "OE1" <-> "OE2" Residue "A ARG 364": "NH1" <-> "NH2" Residue "A GLU 367": "OE1" <-> "OE2" Residue "A PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 399": "OE1" <-> "OE2" Residue "A ASP 415": "OD1" <-> "OD2" Residue "A ARG 418": "NH1" <-> "NH2" Residue "A PHE 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 447": "OE1" <-> "OE2" Residue "A ARG 465": "NH1" <-> "NH2" Residue "C GLU 26": "OE1" <-> "OE2" Residue "C TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 72": "NH1" <-> "NH2" Residue "C ASP 95": "OD1" <-> "OD2" Residue "C GLU 131": "OE1" <-> "OE2" Residue "C ASP 151": "OD1" <-> "OD2" Residue "C GLU 189": "OE1" <-> "OE2" Residue "C ASP 199": "OD1" <-> "OD2" Residue "C ASP 202": "OD1" <-> "OD2" Residue "C ASP 219": "OD1" <-> "OD2" Residue "C ASP 223": "OD1" <-> "OD2" Residue "C GLU 253": "OE1" <-> "OE2" Residue "C ASP 273": "OD1" <-> "OD2" Residue "C PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 361": "OE1" <-> "OE2" Residue "C ARG 364": "NH1" <-> "NH2" Residue "C GLU 368": "OE1" <-> "OE2" Residue "C TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 400": "OD1" <-> "OD2" Residue "C ASP 415": "OD1" <-> "OD2" Residue "C TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 25": "OD1" <-> "OD2" Residue "D GLU 26": "OE1" <-> "OE2" Residue "D TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 80": "OD1" <-> "OD2" Residue "D PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 131": "OE1" <-> "OE2" Residue "D GLU 168": "OE1" <-> "OE2" Residue "D ASP 202": "OD1" <-> "OD2" Residue "D PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 219": "OD1" <-> "OD2" Residue "D ASP 335": "OD1" <-> "OD2" 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 GLU 385": "OE1" <-> "OE2" Residue "D ASP 394": "OD1" <-> "OD2" Residue "D ASP 400": "OD1" <-> "OD2" Residue "D TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 418": "NH1" <-> "NH2" Residue "D GLU 437": "OE1" <-> "OE2" Residue "E GLU 8": "OE1" <-> "OE2" Residue "E ASP 25": "OD1" <-> "OD2" Residue "E GLU 26": "OE1" <-> "OE2" Residue "E TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 131": "OE1" <-> "OE2" Residue "E ARG 145": "NH1" <-> "NH2" Residue "E ASP 151": "OD1" <-> "OD2" Residue "E GLU 196": "OE1" <-> "OE2" Residue "E ASP 202": "OD1" <-> "OD2" Residue "E PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 233": "OD1" <-> "OD2" Residue "E ASP 244": "OD1" <-> "OD2" Residue "E GLU 269": "OE1" <-> "OE2" Residue "E ASP 335": "OD1" <-> "OD2" Residue "E GLU 347": "OE1" <-> "OE2" 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 GLU 452": "OE1" <-> "OE2" Residue "E ASP 457": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 21847 Number of models: 1 Model: "" Number of chains: 7 Chain: "L" Number of atoms: 1719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1719 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 209} Chain: "H" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1625 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 203} 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: 3743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3743 Classifications: {'peptide': 472} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 32, 'TRANS': 437} Time building chain proxies: 11.72, per 1000 atoms: 0.54 Number of scatterers: 21847 At special positions: 0 Unit cell: (187.207, 178.239, 137.883, 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 119 16.00 O 4196 8.00 N 3632 7.00 C 13900 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 94 " distance=2.03 Simple disulfide: pdb=" SG CYS L 140 " - pdb=" SG CYS L 200 " distance=2.03 Simple disulfide: pdb=" SG CYS L 220 " - pdb=" SG CYS H 134 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS H 146 " - pdb=" SG CYS H 201 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.98 Conformation dependent library (CDL) restraints added in 3.5 seconds 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5158 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 50 sheets defined 12.5% alpha, 28.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'L' and resid 127 through 133 removed outlier: 3.644A pdb=" N SER L 133 " --> pdb=" O GLU L 129 " (cutoff:3.500A) Processing helix chain 'L' and resid 189 through 193 Processing helix chain 'H' and resid 88 through 92 removed outlier: 3.685A pdb=" N THR H 92 " --> pdb=" O THR H 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 214 Processing helix chain 'B' and resid 233 through 239 Processing helix chain 'B' and resid 272 through 276 removed outlier: 4.021A pdb=" N TYR B 276 " --> pdb=" O ASP B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 285 removed outlier: 3.606A pdb=" N ALA B 284 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N VAL B 285 " --> pdb=" O ASN B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 326 No H-bonds generated for 'chain 'B' and resid 324 through 326' 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: 3.976A pdb=" N MET B 387 " --> pdb=" O THR B 383 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N THR B 388 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N MET B 393 " --> pdb=" O TYR B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.551A pdb=" N ASN B 441 " --> pdb=" O ASP B 438 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS B 442 " --> pdb=" O PRO B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 460 removed outlier: 4.271A pdb=" N GLN B 460 " --> pdb=" O ASP B 457 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 457 through 460' Processing helix chain 'B' and resid 461 through 472 removed outlier: 3.512A pdb=" N GLY B 472 " --> pdb=" O LEU B 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 27 removed outlier: 3.815A pdb=" N TYR A 27 " --> pdb=" O THR A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 84 Processing helix chain 'A' and resid 88 through 92 removed outlier: 4.499A pdb=" N PHE A 91 " --> pdb=" O ASP A 88 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N TYR A 92 " --> pdb=" O THR A 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 88 through 92' Processing helix chain 'A' and resid 221 through 225 removed outlier: 3.739A pdb=" N CYS A 225 " --> pdb=" O ILE A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 239 Processing helix chain 'A' and resid 272 through 276 removed outlier: 3.522A pdb=" N TYR A 276 " --> pdb=" O ASP A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 328 removed outlier: 3.753A pdb=" N ASN A 327 " --> pdb=" O CYS A 324 " (cutoff:3.500A) removed outlier: 4.080A 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 383 through 394 removed outlier: 4.123A pdb=" N THR A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N TYR A 389 " --> pdb=" O GLU A 385 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE A 390 " --> pdb=" O ILE A 386 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N MET A 393 " --> pdb=" O TYR A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 401 removed outlier: 3.603A pdb=" N TRP A 401 " --> pdb=" O ILE A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 443 removed outlier: 4.417A pdb=" N LYS A 442 " --> pdb=" O PRO A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 472 removed outlier: 3.870A pdb=" N LEU A 469 " --> pdb=" O ARG A 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 84 removed outlier: 3.735A pdb=" N LYS C 83 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 213 Processing helix chain 'C' and resid 221 through 226 removed outlier: 3.676A pdb=" N CYS C 225 " --> pdb=" O PRO C 221 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ASN C 226 " --> pdb=" O ILE C 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 221 through 226' Processing helix chain 'C' and resid 272 through 276 Processing helix chain 'C' and resid 280 through 284 removed outlier: 4.024A pdb=" N ALA C 284 " --> pdb=" O GLY C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 357 No H-bonds generated for 'chain 'C' and resid 355 through 357' Processing helix chain 'C' and resid 383 through 394 removed outlier: 3.635A pdb=" N MET C 387 " --> pdb=" O THR C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 411 Processing helix chain 'C' and resid 438 through 442 removed outlier: 3.510A pdb=" N ASN C 441 " --> pdb=" O ASP C 438 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LYS C 442 " --> pdb=" O PRO C 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 438 through 442' Processing helix chain 'C' and resid 457 through 460 removed outlier: 3.921A 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: 3.591A pdb=" N ARG C 465 " --> pdb=" O PHE C 461 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS C 466 " --> pdb=" O PRO C 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 214 Processing helix chain 'D' and resid 233 through 239 Processing helix chain 'D' and resid 272 through 276 removed outlier: 3.703A pdb=" N LEU D 275 " --> pdb=" O PRO D 272 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR D 276 " --> pdb=" O ASP D 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 272 through 276' Processing helix chain 'D' and resid 280 through 284 removed outlier: 3.801A pdb=" N ALA D 284 " --> pdb=" O GLY D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 394 removed outlier: 3.558A pdb=" N MET D 387 " --> pdb=" O THR D 383 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR D 388 " --> pdb=" O ALA D 384 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR D 389 " --> pdb=" O GLU D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 401 removed outlier: 3.945A pdb=" N GLU D 399 " --> pdb=" O SER D 395 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP D 400 " --> pdb=" O ASN D 396 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TRP D 401 " --> pdb=" O ILE D 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 395 through 401' Processing helix chain 'D' and resid 438 through 443 removed outlier: 3.832A pdb=" N ASN D 441 " --> pdb=" O ASP D 438 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LYS D 442 " --> pdb=" O PRO D 439 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR D 443 " --> pdb=" O LEU D 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 438 through 443' Processing helix chain 'D' and resid 457 through 461 removed outlier: 3.838A pdb=" N GLN D 460 " --> pdb=" O ASP D 457 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE D 461 " --> pdb=" O LEU D 458 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 457 through 461' Processing helix chain 'D' and resid 463 through 472 removed outlier: 3.767A pdb=" N GLY D 472 " --> pdb=" O LEU D 468 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 84 removed outlier: 3.526A pdb=" N LYS E 83 " --> pdb=" O ASP E 80 " (cutoff:3.500A) removed outlier: 3.518A 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 221 through 225 Processing helix chain 'E' and resid 236 through 240 Processing helix chain 'E' and resid 272 through 276 removed outlier: 3.766A pdb=" N TYR E 276 " --> pdb=" O ASP E 273 " (cutoff:3.500A) 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: 3.636A pdb=" N MET E 387 " --> pdb=" O THR E 383 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR E 388 " --> pdb=" O ALA E 384 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR E 389 " --> pdb=" O GLU E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 400 Processing helix chain 'E' and resid 438 through 443 Processing helix chain 'E' and resid 461 through 472 removed outlier: 3.667A pdb=" N ARG E 465 " --> pdb=" O PHE E 461 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS E 466 " --> pdb=" O PRO E 462 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.717A pdb=" N SER L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL L 19 " --> pdb=" O ILE L 81 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.627A pdb=" N GLU L 111 " --> pdb=" O LEU L 11 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 59 through 60 removed outlier: 3.536A pdb=" N LEU L 53 " --> pdb=" O TRP L 41 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N TYR L 55 " --> pdb=" O LEU L 39 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU L 39 " --> pdb=" O TYR L 55 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG L 96 " --> pdb=" O THR L 103 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR L 103 " --> pdb=" O ARG L 96 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 135 through 145 removed outlier: 4.908A pdb=" N SER L 137 " --> pdb=" O LEU L 187 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N LEU L 187 " --> pdb=" O SER L 137 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N VAL L 139 " --> pdb=" O LEU L 185 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LEU L 185 " --> pdb=" O VAL L 139 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N PHE L 141 " --> pdb=" O SER L 183 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N SER L 183 " --> pdb=" O PHE L 141 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ASN L 143 " --> pdb=" O MET L 181 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N MET L 181 " --> pdb=" O ASN L 143 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER L 168 " --> pdb=" O SER L 182 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR L 184 " --> pdb=" O LEU L 166 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LEU L 166 " --> pdb=" O THR L 184 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 159 through 160 removed outlier: 3.535A pdb=" N GLU L 201 " --> pdb=" O LYS L 153 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N CYS L 200 " --> pdb=" O LYS L 213 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS L 213 " --> pdb=" O CYS L 200 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA L 202 " --> pdb=" O ILE L 211 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE L 211 " --> pdb=" O ALA L 202 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA7, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.062A pdb=" N LEU H 12 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA H 98 " --> pdb=" O GLY H 37 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLY H 35 " --> pdb=" O ILE H 100 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N VAL H 36 " --> pdb=" O HIS H 52 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N HIS H 52 " --> pdb=" O VAL H 36 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N TRP H 38 " --> pdb=" O LEU H 50 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG H 40 " --> pdb=" O GLU H 48 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU H 48 " --> pdb=" O ARG H 40 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N HIS H 52 " --> pdb=" O ASN H 60 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN H 60 " --> pdb=" O HIS H 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 126 through 130 removed outlier: 3.653A pdb=" N LYS H 149 " --> pdb=" O SER H 126 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY H 145 " --> pdb=" O LEU H 130 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LYS H 149 " --> pdb=" O LEU H 183 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LEU H 183 " --> pdb=" O LYS H 149 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 126 through 130 removed outlier: 3.653A pdb=" N LYS H 149 " --> pdb=" O SER H 126 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY H 145 " --> pdb=" O LEU H 130 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU H 144 " --> pdb=" O VAL H 187 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL H 187 " --> pdb=" O LEU H 144 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 311 through 312 removed outlier: 3.671A pdb=" N LEU B 106 " --> pdb=" O TYR B 311 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LEU B 99 " --> pdb=" O ILE B 380 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ILE B 380 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N TRP B 101 " --> pdb=" O CYS B 378 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N CYS B 378 " --> pdb=" O TRP B 101 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N CYS B 103 " --> pdb=" O GLN B 376 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLN B 376 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU B 377 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N ILE B 33 " --> pdb=" O LEU B 377 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N LYS B 379 " --> pdb=" O THR B 31 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N THR B 31 " --> pdb=" O LYS B 379 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N THR B 381 " --> pdb=" O SER B 29 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N SER B 29 " --> pdb=" O THR B 381 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 44 through 46 removed outlier: 3.922A pdb=" N ALA B 44 " --> pdb=" O GLU B 367 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 52 through 53 removed outlier: 7.323A pdb=" N ILE B 52 " --> pdb=" O LEU B 62 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 248 through 254 removed outlier: 3.949A pdb=" N PHE B 248 " --> pdb=" O ILE B 160 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLN B 154 " --> pdb=" O GLN B 254 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL B 76 " --> pdb=" O LEU B 329 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL B 73 " --> pdb=" O TRP B 446 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N VAL B 448 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ARG B 75 " --> pdb=" O VAL B 448 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 119 through 124 removed outlier: 3.581A pdb=" N LEU B 148 " --> pdb=" O HIS B 121 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N GLU B 146 " --> pdb=" O TYR B 123 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 188 through 194 removed outlier: 3.876A pdb=" N TYR B 231 " --> pdb=" O GLU B 168 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N TRP B 170 " --> pdb=" O CYS B 229 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N CYS B 229 " --> pdb=" O TRP B 170 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N MET B 200 " --> pdb=" O LYS B 230 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 256 through 262 removed outlier: 5.160A pdb=" N VAL B 257 " --> pdb=" O SER B 296 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N SER B 296 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N HIS B 259 " --> pdb=" O THR B 294 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N THR B 294 " --> pdb=" O HIS B 259 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 344 through 347 removed outlier: 3.723A pdb=" N LYS A 266 " --> pdb=" O PHE B 359 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 97 through 103 Processing sheet with id=AC1, first strand: chain 'A' and resid 97 through 103 removed outlier: 3.622A pdb=" N LEU A 377 " --> pdb=" O ILE A 33 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ILE A 33 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 8.659A pdb=" N LYS A 379 " --> pdb=" O THR A 31 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N THR A 31 " --> pdb=" O LYS A 379 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N THR A 381 " --> pdb=" O SER A 29 " (cutoff:3.500A) removed outlier: 8.778A pdb=" N SER A 29 " --> pdb=" O THR A 381 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 42 through 46 removed outlier: 3.777A pdb=" N TYR A 369 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG A 364 " --> pdb=" O MET A 342 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N MET A 342 " --> pdb=" O ARG A 364 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 42 through 46 removed outlier: 3.777A pdb=" N TYR A 369 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N LYS E 266 " --> pdb=" O PHE A 359 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 52 through 53 Processing sheet with id=AC5, first strand: chain 'A' and resid 250 through 254 removed outlier: 3.615A pdb=" N LEU A 250 " --> pdb=" O CYS A 158 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN A 154 " --> pdb=" O GLN A 254 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A 157 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL A 334 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A 333 " --> pdb=" O ARG A 72 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N TRP A 446 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG A 75 " --> pdb=" O TRP A 446 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL A 448 " --> pdb=" O ARG A 75 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 119 through 124 removed outlier: 3.760A pdb=" N TYR A 123 " --> pdb=" O GLU A 146 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N GLU A 146 " --> pdb=" O TYR A 123 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 188 through 194 removed outlier: 3.690A pdb=" N HIS A 169 " --> pdb=" O PHE A 191 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU A 168 " --> pdb=" O TYR A 231 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TYR A 231 " --> pdb=" O GLU A 168 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 257 through 262 removed outlier: 4.267A pdb=" N HIS A 259 " --> pdb=" O THR A 294 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR A 294 " --> pdb=" O HIS A 259 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 323 through 324 removed outlier: 4.745A pdb=" N TRP C 101 " --> pdb=" O CYS C 324 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU C 99 " --> pdb=" O ILE C 380 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ILE C 380 " --> pdb=" O LEU C 99 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N TRP C 101 " --> pdb=" O CYS C 378 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N CYS C 378 " --> pdb=" O TRP C 101 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N CYS C 103 " --> pdb=" O GLN C 376 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N GLN C 376 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL C 374 " --> pdb=" O GLY C 105 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU C 107 " --> pdb=" O GLN C 372 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLN C 372 " --> pdb=" O GLU C 107 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N LEU C 371 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ALA C 37 " --> pdb=" O LEU C 371 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N PHE C 373 " --> pdb=" O TYR C 35 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N TYR C 35 " --> pdb=" O PHE C 373 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N PHE C 375 " --> pdb=" O ILE C 33 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE C 33 " --> pdb=" O PHE C 375 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N LEU C 377 " --> pdb=" O THR C 31 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS C 379 " --> pdb=" O SER C 29 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER C 455 " --> pdb=" O TYR C 36 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 44 through 46 removed outlier: 3.672A pdb=" N ALA C 44 " --> pdb=" O GLU C 367 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 52 through 53 removed outlier: 7.360A pdb=" N ILE C 52 " --> pdb=" O LEU C 62 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 446 through 448 removed outlier: 6.745A pdb=" N VAL C 73 " --> pdb=" O TRP C 446 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N VAL C 448 " --> pdb=" O VAL C 73 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ARG C 75 " --> pdb=" O VAL C 448 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL C 331 " --> pdb=" O PHE C 74 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL C 334 " --> pdb=" O LEU C 157 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU C 157 " --> pdb=" O VAL C 334 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN C 154 " --> pdb=" O GLN C 254 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN C 254 " --> pdb=" O GLN C 154 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N CYS C 158 " --> pdb=" O LEU C 250 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU C 250 " --> pdb=" O CYS C 158 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE C 248 " --> pdb=" O ILE C 160 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET C 255 " --> pdb=" O VAL D 300 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 188 through 194 removed outlier: 3.575A pdb=" N PHE C 191 " --> pdb=" O HIS C 169 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N HIS C 169 " --> pdb=" O PHE C 191 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N TRP C 170 " --> pdb=" O CYS C 229 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N CYS C 229 " --> pdb=" O TRP C 170 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N MET C 200 " --> pdb=" O LYS C 230 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 257 through 262 removed outlier: 6.863A pdb=" N THR C 294 " --> pdb=" O ARG C 258 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N PHE C 260 " --> pdb=" O PHE C 292 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N PHE C 292 " --> pdb=" O PHE C 260 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 266 through 267 removed outlier: 7.441A pdb=" N LYS C 266 " --> pdb=" O GLU D 361 " (cutoff:3.500A) removed outlier: 9.383A pdb=" N VAL D 363 " --> pdb=" O LYS C 266 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY D 105 " --> pdb=" O VAL D 374 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS D 379 " --> pdb=" O SER D 29 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 42 through 46 removed outlier: 3.735A pdb=" N TYR D 369 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 454 through 455 removed outlier: 3.714A pdb=" N SER D 455 " --> pdb=" O TYR D 36 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N TYR D 36 " --> pdb=" O SER D 455 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY D 105 " --> pdb=" O VAL D 374 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU D 106 " --> pdb=" O TYR D 311 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 311 through 312 removed outlier: 3.650A pdb=" N LEU D 106 " --> pdb=" O TYR D 311 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N TRP D 101 " --> pdb=" O CYS D 324 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 52 through 53 removed outlier: 6.906A pdb=" N ILE D 52 " --> pdb=" O LEU D 62 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 291 through 296 removed outlier: 3.768A pdb=" N THR D 294 " --> pdb=" O HIS D 259 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N HIS D 259 " --> pdb=" O THR D 294 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N SER D 296 " --> pdb=" O VAL D 257 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N VAL D 257 " --> pdb=" O SER D 296 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU D 250 " --> pdb=" O CYS D 158 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN D 254 " --> pdb=" O GLN D 154 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN D 154 " --> pdb=" O GLN D 254 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU D 157 " --> pdb=" O VAL D 334 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU D 329 " --> pdb=" O VAL D 76 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG D 72 " --> pdb=" O VAL D 333 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL D 448 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG D 77 " --> pdb=" O VAL D 448 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 291 through 296 removed outlier: 3.768A pdb=" N THR D 294 " --> pdb=" O HIS D 259 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N HIS D 259 " --> pdb=" O THR D 294 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N SER D 296 " --> pdb=" O VAL D 257 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N VAL D 257 " --> pdb=" O SER D 296 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N MET D 255 " --> pdb=" O VAL E 300 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 189 through 194 removed outlier: 3.553A pdb=" N GLU D 168 " --> pdb=" O TYR D 231 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR D 231 " --> pdb=" O GLU D 168 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 266 through 267 removed outlier: 6.960A pdb=" N LYS D 266 " --> pdb=" O GLU E 361 " (cutoff:3.500A) removed outlier: 9.019A pdb=" N VAL E 363 " --> pdb=" O LYS D 266 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 266 through 267 removed outlier: 6.960A pdb=" N LYS D 266 " --> pdb=" O GLU E 361 " (cutoff:3.500A) removed outlier: 9.019A pdb=" N VAL E 363 " --> pdb=" O LYS D 266 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 97 through 100 removed outlier: 3.590A pdb=" N ARG E 98 " --> pdb=" O ILE E 380 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLN E 372 " --> pdb=" O LEU E 106 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU E 106 " --> pdb=" O GLN E 372 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL E 374 " --> pdb=" O VAL E 104 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 97 through 100 removed outlier: 3.590A pdb=" N ARG E 98 " --> pdb=" O ILE E 380 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU E 377 " --> pdb=" O ILE E 33 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N ILE E 33 " --> pdb=" O LEU E 377 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N LYS E 379 " --> pdb=" O THR E 31 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N THR E 31 " --> pdb=" O LYS E 379 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N THR E 381 " --> pdb=" O SER E 29 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N SER E 29 " --> pdb=" O THR E 381 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 52 through 53 removed outlier: 6.833A pdb=" N ILE E 52 " --> pdb=" O LEU E 62 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 250 through 254 removed outlier: 3.737A pdb=" N LEU E 250 " --> pdb=" O CYS E 158 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLN E 154 " --> pdb=" O GLN E 254 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU E 329 " --> pdb=" O VAL E 76 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL E 76 " --> pdb=" O LEU E 329 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG E 77 " --> pdb=" O VAL E 448 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 118 through 125 removed outlier: 4.851A pdb=" N GLU E 146 " --> pdb=" O TYR E 123 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 128 through 129 removed outlier: 3.911A pdb=" N ASP E 128 " --> pdb=" O ASN E 262 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ASN E 262 " --> pdb=" O ASP E 128 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N HIS E 259 " --> pdb=" O THR E 294 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 169 through 172 Processing sheet with id=AF5, first strand: chain 'E' and resid 200 through 201 removed outlier: 6.803A pdb=" N MET E 200 " --> pdb=" O LYS E 230 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 430 hydrogen bonds defined for protein. 1074 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: 6.38 Time building geometry restraints manager: 9.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7018 1.35 - 1.47: 5766 1.47 - 1.60: 9484 1.60 - 1.72: 0 1.72 - 1.84: 163 Bond restraints: 22431 Sorted by residual: bond pdb=" C PRO C 408 " pdb=" N PRO C 409 " ideal model delta sigma weight residual 1.336 1.401 -0.065 1.08e-02 8.57e+03 3.65e+01 bond pdb=" C PRO B 432 " pdb=" N PRO B 433 " ideal model delta sigma weight residual 1.328 1.386 -0.057 1.26e-02 6.30e+03 2.07e+01 bond pdb=" N ASN B 177 " pdb=" CA ASN B 177 " ideal model delta sigma weight residual 1.460 1.488 -0.028 1.42e-02 4.96e+03 3.83e+00 bond pdb=" C LYS D 434 " pdb=" N GLU D 435 " ideal model delta sigma weight residual 1.331 1.378 -0.048 2.56e-02 1.53e+03 3.47e+00 bond pdb=" C TYR B 12 " pdb=" N LEU B 13 " ideal model delta sigma weight residual 1.331 1.280 0.051 2.83e-02 1.25e+03 3.28e+00 ... (remaining 22426 not shown) Histogram of bond angle deviations from ideal: 98.88 - 105.99: 713 105.99 - 113.10: 11588 113.10 - 120.21: 8130 120.21 - 127.32: 9803 127.32 - 134.43: 281 Bond angle restraints: 30515 Sorted by residual: angle pdb=" C LYS A 436 " pdb=" N GLU A 437 " pdb=" CA GLU A 437 " ideal model delta sigma weight residual 121.54 131.53 -9.99 1.91e+00 2.74e-01 2.73e+01 angle pdb=" N VAL C 104 " pdb=" CA VAL C 104 " pdb=" C VAL C 104 " ideal model delta sigma weight residual 113.71 108.82 4.89 9.50e-01 1.11e+00 2.65e+01 angle pdb=" C PRO D 433 " pdb=" N LYS D 434 " pdb=" CA LYS D 434 " ideal model delta sigma weight residual 120.38 127.77 -7.39 1.46e+00 4.69e-01 2.56e+01 angle pdb=" N PRO E 407 " pdb=" CA PRO E 407 " pdb=" C PRO E 407 " ideal model delta sigma weight residual 110.70 116.60 -5.90 1.22e+00 6.72e-01 2.34e+01 angle pdb=" C ALA D 175 " pdb=" N CYS D 176 " pdb=" CA CYS D 176 " ideal model delta sigma weight residual 121.54 130.23 -8.69 1.91e+00 2.74e-01 2.07e+01 ... (remaining 30510 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 11829 17.48 - 34.96: 1258 34.96 - 52.44: 203 52.44 - 69.92: 50 69.92 - 87.40: 24 Dihedral angle restraints: 13364 sinusoidal: 5314 harmonic: 8050 Sorted by residual: dihedral pdb=" CA GLN E 139 " pdb=" C GLN E 139 " pdb=" N PRO E 140 " pdb=" CA PRO E 140 " ideal model delta harmonic sigma weight residual -180.00 -135.78 -44.22 0 5.00e+00 4.00e-02 7.82e+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 180.00 137.97 42.03 0 5.00e+00 4.00e-02 7.07e+01 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 180.00 145.77 34.23 0 5.00e+00 4.00e-02 4.69e+01 ... (remaining 13361 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2462 0.059 - 0.119: 660 0.119 - 0.178: 167 0.178 - 0.237: 16 0.237 - 0.296: 2 Chirality restraints: 3307 Sorted by residual: chirality pdb=" CB ILE H 53 " pdb=" CA ILE H 53 " pdb=" CG1 ILE H 53 " pdb=" CG2 ILE H 53 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" CB VAL E 16 " pdb=" CA VAL E 16 " pdb=" CG1 VAL E 16 " pdb=" CG2 VAL E 16 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CB VAL C 201 " pdb=" CA VAL C 201 " pdb=" CG1 VAL C 201 " pdb=" CG2 VAL C 201 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 3304 not shown) Planarity restraints: 3973 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO E 408 " -0.067 5.00e-02 4.00e+02 1.01e-01 1.64e+01 pdb=" N PRO E 409 " 0.175 5.00e-02 4.00e+02 pdb=" CA PRO E 409 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO E 409 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 112 " 0.049 5.00e-02 4.00e+02 7.46e-02 8.90e+00 pdb=" N PRO B 113 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO B 113 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 113 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 431 " 0.045 5.00e-02 4.00e+02 6.76e-02 7.30e+00 pdb=" N PRO E 432 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO E 432 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 432 " 0.037 5.00e-02 4.00e+02 ... (remaining 3970 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 50 2.38 - 3.01: 11270 3.01 - 3.64: 32674 3.64 - 4.27: 45296 4.27 - 4.90: 73133 Nonbonded interactions: 162423 Sorted by model distance: nonbonded pdb=" O PRO D 409 " pdb=" OG SER D 410 " model vdw 1.747 2.440 nonbonded pdb=" OG1 THR D 426 " pdb=" NE2 GLN D 428 " model vdw 2.009 2.520 nonbonded pdb=" O PRO E 409 " pdb=" OG SER E 410 " model vdw 2.025 2.440 nonbonded pdb=" O PRO C 407 " pdb=" OG SER C 410 " model vdw 2.139 2.440 nonbonded pdb=" OG SER A 455 " pdb=" OD1 ASP A 457 " model vdw 2.282 2.440 ... (remaining 162418 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 473) selection = (chain 'B' and resid 20 through 473) selection = (chain 'C' and resid 20 through 473) selection = chain 'D' selection = (chain 'E' and resid 20 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 18.200 Check model and map are aligned: 0.340 Set scattering table: 0.210 Process input model: 56.030 Find NCS groups from input model: 1.720 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 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 : 0.005 0.065 22431 Z= 0.338 Angle : 1.033 14.664 30515 Z= 0.575 Chirality : 0.058 0.296 3307 Planarity : 0.007 0.101 3973 Dihedral : 14.876 87.397 8191 Min Nonbonded Distance : 1.747 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.30 % Favored : 92.60 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.49 % Cis-general : 0.04 % Twisted Proline : 1.10 % 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: -4.29 (0.13), residues: 2755 helix: -3.72 (0.21), residues: 188 sheet: -2.31 (0.17), residues: 701 loop : -3.18 (0.11), residues: 1866 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 784 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 770 time to evaluate : 2.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 3 residues processed: 778 average time/residue: 0.3388 time to fit residues: 407.1530 Evaluate side-chains 535 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 532 time to evaluate : 2.691 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1890 time to fit residues: 4.7533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 232 optimal weight: 0.0060 chunk 208 optimal weight: 6.9990 chunk 115 optimal weight: 20.0000 chunk 71 optimal weight: 20.0000 chunk 140 optimal weight: 8.9990 chunk 111 optimal weight: 10.0000 chunk 215 optimal weight: 0.0870 chunk 83 optimal weight: 0.4980 chunk 131 optimal weight: 0.8980 chunk 160 optimal weight: 0.9980 chunk 249 optimal weight: 5.9990 overall best weight: 0.4974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 78 ASN ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 GLN B 169 HIS B 216 ASN B 226 ASN B 305 GLN B 423 GLN B 460 GLN A 57 ASN A 192 ASN A 254 GLN ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 ASN C 169 HIS C 216 ASN C 319 HIS C 441 ASN D 47 ASN ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 GLN D 134 ASN D 154 GLN D 169 HIS D 287 GLN D 327 ASN ** D 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 GLN ** E 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 GLN E 156 GLN E 179 ASN E 192 ASN E 259 HIS ** E 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 365 HIS E 376 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 22431 Z= 0.170 Angle : 0.650 8.617 30515 Z= 0.328 Chirality : 0.046 0.167 3307 Planarity : 0.006 0.080 3973 Dihedral : 5.692 61.090 2998 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.88 % Favored : 94.08 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.49 % Cis-general : 0.04 % Twisted Proline : 1.10 % 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: -3.47 (0.14), residues: 2755 helix: -2.58 (0.27), residues: 197 sheet: -1.60 (0.18), residues: 739 loop : -2.74 (0.13), residues: 1819 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 719 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 714 time to evaluate : 2.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 716 average time/residue: 0.3191 time to fit residues: 364.8180 Evaluate side-chains 525 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 524 time to evaluate : 2.477 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1795 time to fit residues: 3.7277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 138 optimal weight: 10.0000 chunk 77 optimal weight: 0.9990 chunk 207 optimal weight: 30.0000 chunk 170 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 chunk 250 optimal weight: 10.0000 chunk 270 optimal weight: 20.0000 chunk 222 optimal weight: 0.2980 chunk 248 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 chunk 200 optimal weight: 6.9990 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 GLN B 327 ASN ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 376 GLN A 319 HIS A 341 ASN ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 372 GLN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 HIS C 321 ASN C 365 HIS ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN ** D 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 GLN E 192 ASN E 305 GLN ** E 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 22431 Z= 0.244 Angle : 0.633 10.096 30515 Z= 0.323 Chirality : 0.044 0.157 3307 Planarity : 0.005 0.075 3973 Dihedral : 5.447 57.842 2998 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.49 % Cis-general : 0.04 % Twisted Proline : 1.10 % 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: -3.13 (0.14), residues: 2755 helix: -1.91 (0.31), residues: 204 sheet: -1.37 (0.18), residues: 710 loop : -2.55 (0.13), residues: 1841 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 640 time to evaluate : 2.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 640 average time/residue: 0.3148 time to fit residues: 317.4797 Evaluate side-chains 492 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 491 time to evaluate : 2.627 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1979 time to fit residues: 4.0219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 247 optimal weight: 9.9990 chunk 188 optimal weight: 20.0000 chunk 129 optimal weight: 6.9990 chunk 27 optimal weight: 30.0000 chunk 119 optimal weight: 3.9990 chunk 167 optimal weight: 8.9990 chunk 251 optimal weight: 9.9990 chunk 265 optimal weight: 0.9990 chunk 131 optimal weight: 10.0000 chunk 237 optimal weight: 0.9990 chunk 71 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 ASN B 372 GLN A 139 GLN A 192 ASN ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 GLN A 319 HIS ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 ASN ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 460 GLN ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 254 GLN ** D 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 460 GLN ** E 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 GLN E 192 ASN E 259 HIS ** E 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 22431 Z= 0.272 Angle : 0.632 9.205 30515 Z= 0.321 Chirality : 0.044 0.155 3307 Planarity : 0.005 0.071 3973 Dihedral : 5.387 64.739 2998 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.49 % Cis-general : 0.04 % Twisted Proline : 1.10 % 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: -2.95 (0.15), residues: 2755 helix: -1.71 (0.32), residues: 203 sheet: -1.29 (0.19), residues: 703 loop : -2.41 (0.13), residues: 1849 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 641 time to evaluate : 2.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 641 average time/residue: 0.3213 time to fit residues: 328.8526 Evaluate side-chains 494 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 494 time to evaluate : 3.012 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.0349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 221 optimal weight: 4.9990 chunk 150 optimal weight: 30.0000 chunk 3 optimal weight: 30.0000 chunk 197 optimal weight: 6.9990 chunk 109 optimal weight: 10.0000 chunk 226 optimal weight: 3.9990 chunk 183 optimal weight: 9.9990 chunk 0 optimal weight: 60.0000 chunk 135 optimal weight: 5.9990 chunk 238 optimal weight: 10.0000 chunk 67 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN B 327 ASN B 372 GLN A 112 GLN ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 HIS ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 ASN ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 391 HIS ** D 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 192 ASN ** E 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 372 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.078 22431 Z= 0.339 Angle : 0.677 11.252 30515 Z= 0.348 Chirality : 0.046 0.164 3307 Planarity : 0.005 0.071 3973 Dihedral : 5.593 64.398 2998 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 17.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.49 % Cis-general : 0.04 % Twisted Proline : 1.10 % 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: -2.86 (0.15), residues: 2755 helix: -1.44 (0.34), residues: 205 sheet: -1.21 (0.19), residues: 713 loop : -2.38 (0.13), residues: 1837 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 622 time to evaluate : 2.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 623 average time/residue: 0.3096 time to fit residues: 307.4544 Evaluate side-chains 468 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 468 time to evaluate : 2.740 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 89 optimal weight: 6.9990 chunk 239 optimal weight: 5.9990 chunk 52 optimal weight: 8.9990 chunk 156 optimal weight: 7.9990 chunk 65 optimal weight: 9.9990 chunk 266 optimal weight: 5.9990 chunk 220 optimal weight: 8.9990 chunk 123 optimal weight: 5.9990 chunk 22 optimal weight: 50.0000 chunk 88 optimal weight: 10.0000 chunk 139 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 ASN B 372 GLN B 376 GLN B 460 GLN A 156 GLN ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 ASN ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 192 ASN ** E 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 365 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.079 22431 Z= 0.348 Angle : 0.684 11.060 30515 Z= 0.349 Chirality : 0.046 0.192 3307 Planarity : 0.006 0.084 3973 Dihedral : 5.641 63.847 2998 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 19.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.49 % Cis-general : 0.04 % Twisted Proline : 1.10 % 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: -2.82 (0.15), residues: 2755 helix: -1.37 (0.34), residues: 206 sheet: -1.16 (0.19), residues: 714 loop : -2.37 (0.13), residues: 1835 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 606 time to evaluate : 2.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 606 average time/residue: 0.3130 time to fit residues: 300.3133 Evaluate side-chains 464 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 464 time to evaluate : 2.657 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.6113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 256 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 chunk 151 optimal weight: 6.9990 chunk 194 optimal weight: 7.9990 chunk 150 optimal weight: 10.0000 chunk 223 optimal weight: 0.0270 chunk 148 optimal weight: 1.9990 chunk 265 optimal weight: 6.9990 chunk 165 optimal weight: 4.9990 chunk 161 optimal weight: 7.9990 chunk 122 optimal weight: 4.9990 overall best weight: 3.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 GLN B 214 GLN ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 ASN ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 GLN ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 GLN C 169 HIS ** C 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 GLN E 259 HIS E 305 GLN ** E 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 22431 Z= 0.212 Angle : 0.639 10.033 30515 Z= 0.321 Chirality : 0.045 0.175 3307 Planarity : 0.005 0.071 3973 Dihedral : 5.390 60.437 2998 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.49 % Cis-general : 0.04 % Twisted Proline : 1.10 % 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: 2755 helix: -1.20 (0.35), residues: 199 sheet: -0.97 (0.19), residues: 699 loop : -2.25 (0.13), residues: 1857 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 632 time to evaluate : 2.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 632 average time/residue: 0.3244 time to fit residues: 329.0144 Evaluate side-chains 480 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 480 time to evaluate : 2.790 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 163 optimal weight: 5.9990 chunk 105 optimal weight: 9.9990 chunk 158 optimal weight: 0.0270 chunk 79 optimal weight: 8.9990 chunk 52 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 168 optimal weight: 9.9990 chunk 180 optimal weight: 7.9990 chunk 131 optimal weight: 0.0050 chunk 24 optimal weight: 50.0000 chunk 208 optimal weight: 7.9990 overall best weight: 2.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 ASN ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 ASN C 341 ASN ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 ASN ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 470 GLN ** E 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 259 HIS ** E 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.3951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 22431 Z= 0.208 Angle : 0.639 9.273 30515 Z= 0.319 Chirality : 0.045 0.216 3307 Planarity : 0.005 0.070 3973 Dihedral : 5.249 57.983 2998 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.49 % Cis-general : 0.04 % Twisted Proline : 1.10 % 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: -2.49 (0.15), residues: 2755 helix: -1.23 (0.35), residues: 196 sheet: -0.87 (0.20), residues: 684 loop : -2.14 (0.14), residues: 1875 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 634 time to evaluate : 2.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 634 average time/residue: 0.3309 time to fit residues: 336.4201 Evaluate side-chains 475 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 475 time to evaluate : 2.592 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 241 optimal weight: 9.9990 chunk 253 optimal weight: 6.9990 chunk 231 optimal weight: 10.0000 chunk 246 optimal weight: 9.9990 chunk 148 optimal weight: 5.9990 chunk 107 optimal weight: 20.0000 chunk 193 optimal weight: 20.0000 chunk 75 optimal weight: 3.9990 chunk 223 optimal weight: 4.9990 chunk 233 optimal weight: 20.0000 chunk 162 optimal weight: 20.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 GLN ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 GLN ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 ASN B 372 GLN ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 GLN ** C 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 305 GLN ** E 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.105 22431 Z= 0.355 Angle : 0.711 10.781 30515 Z= 0.363 Chirality : 0.046 0.181 3307 Planarity : 0.006 0.128 3973 Dihedral : 5.618 57.467 2998 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 20.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.73 % Favored : 90.27 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.49 % Cis-general : 0.04 % Twisted Proline : 1.10 % 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: -2.58 (0.15), residues: 2755 helix: -1.12 (0.35), residues: 199 sheet: -0.97 (0.19), residues: 692 loop : -2.21 (0.14), residues: 1864 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 582 time to evaluate : 2.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 582 average time/residue: 0.3086 time to fit residues: 286.5145 Evaluate side-chains 449 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 449 time to evaluate : 2.673 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 261 optimal weight: 9.9990 chunk 159 optimal weight: 3.9990 chunk 123 optimal weight: 8.9990 chunk 181 optimal weight: 10.0000 chunk 273 optimal weight: 4.9990 chunk 252 optimal weight: 9.9990 chunk 218 optimal weight: 7.9990 chunk 22 optimal weight: 30.0000 chunk 168 optimal weight: 0.9990 chunk 133 optimal weight: 9.9990 chunk 173 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 GLN ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 ASN B 372 GLN ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 ASN ** C 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 259 HIS ** E 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 22431 Z= 0.263 Angle : 0.673 12.117 30515 Z= 0.340 Chirality : 0.046 0.192 3307 Planarity : 0.005 0.092 3973 Dihedral : 5.500 62.950 2998 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 17.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.49 % 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: -2.49 (0.15), residues: 2755 helix: -1.04 (0.36), residues: 196 sheet: -0.92 (0.19), residues: 699 loop : -2.15 (0.14), residues: 1860 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 601 time to evaluate : 2.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 602 average time/residue: 0.3127 time to fit residues: 299.3136 Evaluate side-chains 463 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 463 time to evaluate : 2.479 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 232 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 201 optimal weight: 9.9990 chunk 32 optimal weight: 30.0000 chunk 60 optimal weight: 2.9990 chunk 218 optimal weight: 6.9990 chunk 91 optimal weight: 9.9990 chunk 224 optimal weight: 0.0170 chunk 27 optimal weight: 7.9990 chunk 40 optimal weight: 20.0000 chunk 191 optimal weight: 6.9990 overall best weight: 4.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 GLN ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 ASN B 372 GLN ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 ASN ** C 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.139056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.095514 restraints weight = 55828.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.098673 restraints weight = 28731.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.100711 restraints weight = 18298.652| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.065 22431 Z= 0.281 Angle : 0.680 12.400 30515 Z= 0.343 Chirality : 0.046 0.177 3307 Planarity : 0.006 0.112 3973 Dihedral : 5.524 62.514 2998 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 18.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.49 % 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: -2.49 (0.15), residues: 2755 helix: -1.07 (0.36), residues: 198 sheet: -0.89 (0.19), residues: 678 loop : -2.14 (0.14), residues: 1879 =============================================================================== Job complete usr+sys time: 5827.39 seconds wall clock time: 105 minutes 48.64 seconds (6348.64 seconds total)