Starting phenix.real_space_refine on Sun Feb 18 11:19:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dnl_30787/02_2024/7dnl_30787.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dnl_30787/02_2024/7dnl_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_30787/02_2024/7dnl_30787.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dnl_30787/02_2024/7dnl_30787.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dnl_30787/02_2024/7dnl_30787.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dnl_30787/02_2024/7dnl_30787.pdb" } resolution = 4.19 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 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: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 11.66, per 1000 atoms: 0.53 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: 8.38 Conformation dependent library (CDL) restraints added in 4.2 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: 2.55 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: 6.99 Time building geometry restraints manager: 9.11 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: 4.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 17.000 Check model and map are aligned: 0.320 Set scattering table: 0.200 Process input model: 57.460 Find NCS groups from input model: 1.500 Set up NCS constraints: 0.080 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.540 ------------------------------------------------------------------------------- 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 % Allowed : 8.64 % Favored : 90.79 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 55 HIS 0.008 0.002 HIS B 365 PHE 0.028 0.002 PHE E 256 TYR 0.024 0.002 TYR B 417 ARG 0.007 0.001 ARG H 99 *********************** 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 : 2.682 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: H 82 LEU cc_start: 0.8517 (tp) cc_final: 0.8248 (mm) REVERT: B 20 LYS cc_start: 0.9412 (pttp) cc_final: 0.9110 (ptpp) REVERT: B 36 TYR cc_start: 0.9256 (t80) cc_final: 0.8914 (t80) REVERT: B 70 GLN cc_start: 0.9038 (mt0) cc_final: 0.8662 (mp10) REVERT: B 80 ASP cc_start: 0.9449 (t70) cc_final: 0.9014 (t0) REVERT: B 83 LYS cc_start: 0.9306 (mmtm) cc_final: 0.9075 (mmtm) REVERT: B 128 ASP cc_start: 0.9177 (m-30) cc_final: 0.8714 (m-30) REVERT: B 150 MET cc_start: 0.9318 (pmm) cc_final: 0.8841 (pmm) REVERT: B 163 LYS cc_start: 0.9438 (tppp) cc_final: 0.9206 (tppp) REVERT: B 242 TYR cc_start: 0.9160 (m-80) cc_final: 0.8925 (m-10) REVERT: B 248 PHE cc_start: 0.8382 (t80) cc_final: 0.7625 (t80) REVERT: B 255 MET cc_start: 0.8370 (tmm) cc_final: 0.7899 (tmm) REVERT: B 260 PHE cc_start: 0.9208 (m-80) cc_final: 0.8890 (m-80) REVERT: B 323 ILE cc_start: 0.9510 (mp) cc_final: 0.9221 (mp) REVERT: B 324 CYS cc_start: 0.9153 (OUTLIER) cc_final: 0.8384 (t) REVERT: B 345 CYS cc_start: 0.8690 (p) cc_final: 0.8469 (p) REVERT: B 387 MET cc_start: 0.9583 (mtp) cc_final: 0.9373 (mtt) REVERT: B 449 ASN cc_start: 0.9102 (t0) cc_final: 0.8237 (t0) REVERT: B 452 GLU cc_start: 0.9224 (pm20) cc_final: 0.8975 (pm20) REVERT: A 121 HIS cc_start: 0.9112 (t-90) cc_final: 0.8876 (t70) REVERT: A 127 PHE cc_start: 0.9197 (t80) cc_final: 0.8993 (t80) REVERT: A 128 ASP cc_start: 0.9172 (m-30) cc_final: 0.8671 (m-30) REVERT: A 131 GLU cc_start: 0.6762 (mp0) cc_final: 0.6513 (mp0) REVERT: A 159 LEU cc_start: 0.9469 (mm) cc_final: 0.9157 (mm) REVERT: A 233 ASP cc_start: 0.9144 (t0) cc_final: 0.8698 (t70) REVERT: A 236 LYS cc_start: 0.9340 (tttp) cc_final: 0.9125 (ttmm) REVERT: A 237 MET cc_start: 0.8846 (mtp) cc_final: 0.8501 (mtp) REVERT: A 246 LEU cc_start: 0.9750 (mp) cc_final: 0.9541 (mp) REVERT: A 259 HIS cc_start: 0.9225 (m-70) cc_final: 0.8714 (m-70) REVERT: A 267 LEU cc_start: 0.9132 (tp) cc_final: 0.8899 (mp) REVERT: A 282 ASN cc_start: 0.9375 (m110) cc_final: 0.8692 (t0) REVERT: A 309 LYS cc_start: 0.9449 (mttp) cc_final: 0.9054 (mmmm) REVERT: A 311 TYR cc_start: 0.9178 (m-80) cc_final: 0.8657 (m-80) REVERT: A 320 ASN cc_start: 0.8480 (t0) cc_final: 0.8135 (t0) REVERT: A 359 PHE cc_start: 0.9069 (m-80) cc_final: 0.8431 (m-10) REVERT: A 418 ARG cc_start: 0.4403 (mtm-85) cc_final: 0.2535 (mpp80) REVERT: C 83 LYS cc_start: 0.9421 (mmtp) cc_final: 0.9064 (mtpt) REVERT: C 107 GLU cc_start: 0.8384 (tm-30) cc_final: 0.7957 (tp30) REVERT: C 150 MET cc_start: 0.8910 (mmm) cc_final: 0.8689 (mmm) REVERT: C 154 GLN cc_start: 0.9347 (mm110) cc_final: 0.8621 (mt0) REVERT: C 159 LEU cc_start: 0.9438 (mm) cc_final: 0.9116 (mm) REVERT: C 163 LYS cc_start: 0.9181 (ttmt) cc_final: 0.8685 (ttpt) REVERT: C 170 TRP cc_start: 0.9372 (m100) cc_final: 0.8916 (m100) REVERT: C 192 ASN cc_start: 0.8848 (m110) cc_final: 0.8377 (t0) REVERT: C 196 GLU cc_start: 0.8480 (pp20) cc_final: 0.8186 (pp20) REVERT: C 197 ASP cc_start: 0.8279 (p0) cc_final: 0.7788 (p0) REVERT: C 200 MET cc_start: 0.9313 (mmm) cc_final: 0.9007 (mmm) REVERT: C 208 MET cc_start: 0.8434 (ptp) cc_final: 0.6691 (mpp) REVERT: C 209 ASP cc_start: 0.9040 (m-30) cc_final: 0.8637 (m-30) REVERT: C 230 LYS cc_start: 0.9275 (mppt) cc_final: 0.8838 (mppt) REVERT: C 236 LYS cc_start: 0.9492 (tttt) cc_final: 0.8948 (tppt) REVERT: C 246 LEU cc_start: 0.9508 (tp) cc_final: 0.9073 (tp) REVERT: C 248 PHE cc_start: 0.7810 (t80) cc_final: 0.7443 (t80) REVERT: C 255 MET cc_start: 0.8583 (ppp) cc_final: 0.8017 (tmm) REVERT: C 274 ASP cc_start: 0.9578 (p0) cc_final: 0.9354 (p0) REVERT: C 368 GLU cc_start: 0.9190 (tt0) cc_final: 0.8684 (tt0) REVERT: C 376 GLN cc_start: 0.8730 (tt0) cc_final: 0.8509 (tm-30) REVERT: C 385 GLU cc_start: 0.9428 (pm20) cc_final: 0.9211 (pm20) REVERT: C 387 MET cc_start: 0.9456 (mtm) cc_final: 0.9106 (mtt) REVERT: C 394 ASP cc_start: 0.9174 (t0) cc_final: 0.8765 (t70) REVERT: C 438 ASP cc_start: 0.8852 (m-30) cc_final: 0.8507 (t70) REVERT: C 451 LYS cc_start: 0.9221 (mttt) cc_final: 0.8776 (mttp) REVERT: D 34 TYR cc_start: 0.9343 (m-80) cc_final: 0.8951 (m-10) REVERT: D 63 VAL cc_start: 0.9240 (OUTLIER) cc_final: 0.9037 (m) REVERT: D 71 TYR cc_start: 0.9029 (m-80) cc_final: 0.8685 (m-80) REVERT: D 78 LEU cc_start: 0.9427 (tt) cc_final: 0.9216 (tt) REVERT: D 153 LYS cc_start: 0.9061 (tmmt) cc_final: 0.8617 (ttpt) REVERT: D 189 GLU cc_start: 0.9166 (tp30) cc_final: 0.8506 (mp0) REVERT: D 196 GLU cc_start: 0.8558 (pt0) cc_final: 0.8358 (tt0) REVERT: D 210 PHE cc_start: 0.9257 (m-80) cc_final: 0.8771 (m-80) REVERT: D 231 TYR cc_start: 0.9299 (t80) cc_final: 0.9020 (t80) REVERT: D 255 MET cc_start: 0.8806 (ptm) cc_final: 0.8335 (ppp) REVERT: D 303 GLU cc_start: 0.9352 (tm-30) cc_final: 0.9078 (tm-30) REVERT: D 320 ASN cc_start: 0.8790 (t0) cc_final: 0.8571 (t0) REVERT: D 321 ASN cc_start: 0.9415 (t0) cc_final: 0.9107 (t0) REVERT: D 344 LEU cc_start: 0.9318 (mt) cc_final: 0.8863 (mt) REVERT: D 351 GLU cc_start: 0.9459 (mm-30) cc_final: 0.8911 (mm-30) REVERT: D 360 LYS cc_start: 0.9598 (mttt) cc_final: 0.9345 (tppt) REVERT: D 369 TYR cc_start: 0.8717 (m-80) cc_final: 0.8516 (m-10) REVERT: D 372 GLN cc_start: 0.8174 (mp-120) cc_final: 0.7738 (mp10) REVERT: D 378 CYS cc_start: 0.8984 (m) cc_final: 0.8328 (t) REVERT: D 387 MET cc_start: 0.9425 (ppp) cc_final: 0.9081 (ppp) REVERT: D 390 ILE cc_start: 0.9820 (OUTLIER) cc_final: 0.9619 (mp) REVERT: D 393 MET cc_start: 0.9298 (tpp) cc_final: 0.8977 (tmm) REVERT: D 397 ILE cc_start: 0.9678 (mp) cc_final: 0.9422 (mp) REVERT: D 399 GLU cc_start: 0.9274 (pp20) cc_final: 0.9021 (pp20) REVERT: D 401 TRP cc_start: 0.9483 (m-10) cc_final: 0.9235 (m-10) REVERT: D 417 TYR cc_start: 0.9014 (m-80) cc_final: 0.8746 (m-80) REVERT: D 443 TYR cc_start: 0.9463 (m-80) cc_final: 0.9103 (m-80) REVERT: D 449 ASN cc_start: 0.9220 (t0) cc_final: 0.8730 (t0) REVERT: D 470 GLN cc_start: 0.9007 (tm-30) cc_final: 0.8572 (tt0) REVERT: E 47 ASN cc_start: 0.9309 (t0) cc_final: 0.9106 (t0) REVERT: E 52 ILE cc_start: 0.8793 (mm) cc_final: 0.8593 (pt) REVERT: E 80 ASP cc_start: 0.9386 (t0) cc_final: 0.9170 (t0) REVERT: E 83 LYS cc_start: 0.9350 (mmmt) cc_final: 0.9118 (mmmt) REVERT: E 121 HIS cc_start: 0.9045 (t-90) cc_final: 0.8272 (t-170) REVERT: E 125 ASN cc_start: 0.9462 (t0) cc_final: 0.9061 (p0) REVERT: E 135 ARG cc_start: 0.8669 (mmt90) cc_final: 0.7963 (mtp85) REVERT: E 150 MET cc_start: 0.8695 (mtm) cc_final: 0.8426 (mtm) REVERT: E 156 GLN cc_start: 0.8330 (mt0) cc_final: 0.8036 (mt0) REVERT: E 172 LYS cc_start: 0.8335 (tptm) cc_final: 0.8074 (tppt) REVERT: E 194 ILE cc_start: 0.9750 (mt) cc_final: 0.9370 (tp) REVERT: E 229 CYS cc_start: 0.9054 (m) cc_final: 0.8226 (p) REVERT: E 234 TYR cc_start: 0.9352 (m-80) cc_final: 0.8958 (m-10) REVERT: E 251 ARG cc_start: 0.9428 (ptt90) cc_final: 0.8751 (ptt90) REVERT: E 259 HIS cc_start: 0.9225 (m-70) cc_final: 0.8820 (m-70) REVERT: E 311 TYR cc_start: 0.9166 (m-80) cc_final: 0.8713 (m-80) REVERT: E 314 GLN cc_start: 0.9315 (mt0) cc_final: 0.8604 (pm20) REVERT: E 344 LEU cc_start: 0.8185 (tp) cc_final: 0.7876 (tp) REVERT: E 354 TYR cc_start: 0.8560 (t80) cc_final: 0.8299 (t80) REVERT: E 367 GLU cc_start: 0.8642 (tt0) cc_final: 0.8175 (tt0) REVERT: E 387 MET cc_start: 0.9161 (tmm) cc_final: 0.8678 (tpp) REVERT: E 399 GLU cc_start: 0.9432 (tm-30) cc_final: 0.9222 (tm-30) REVERT: E 400 ASP cc_start: 0.9110 (p0) cc_final: 0.8844 (p0) outliers start: 14 outliers final: 3 residues processed: 778 average time/residue: 0.3218 time to fit residues: 384.7790 Evaluate side-chains 569 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 563 time to evaluate : 2.515 ------------------------------------------------------------------------------- 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: 10.0000 chunk 208 optimal weight: 0.0050 chunk 115 optimal weight: 0.1980 chunk 71 optimal weight: 20.0000 chunk 140 optimal weight: 5.9990 chunk 111 optimal weight: 8.9990 chunk 215 optimal weight: 20.0000 chunk 83 optimal weight: 6.9990 chunk 131 optimal weight: 0.8980 chunk 160 optimal weight: 0.9990 chunk 249 optimal weight: 7.9990 overall best weight: 1.6198 ------------------------------------------------------------------------------- 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 327 ASN ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 287 GLN D 327 ASN D 449 ASN ** D 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 GLN E 125 ASN E 154 GLN E 179 ASN E 192 ASN ** E 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 376 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 22431 Z= 0.182 Angle : 0.638 8.305 30515 Z= 0.325 Chirality : 0.045 0.166 3307 Planarity : 0.006 0.081 3973 Dihedral : 5.750 60.911 2998 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.61 % Favored : 93.36 % Rotamer: Outliers : 0.16 % Allowed : 5.30 % Favored : 94.54 % 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: -3.46 (0.14), residues: 2755 helix: -2.36 (0.28), residues: 189 sheet: -1.62 (0.18), residues: 715 loop : -2.74 (0.12), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 110 HIS 0.007 0.001 HIS C 259 PHE 0.027 0.001 PHE E 454 TYR 0.023 0.001 TYR A 369 ARG 0.007 0.000 ARG B 135 *********************** 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: 4 poor density : 715 time to evaluate : 2.715 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: H 36 VAL cc_start: 0.6084 (m) cc_final: 0.5523 (t) REVERT: B 20 LYS cc_start: 0.9347 (pttp) cc_final: 0.9033 (ptpp) REVERT: B 36 TYR cc_start: 0.9287 (t80) cc_final: 0.9006 (t80) REVERT: B 80 ASP cc_start: 0.9526 (t70) cc_final: 0.9074 (t70) REVERT: B 82 ASN cc_start: 0.9232 (m-40) cc_final: 0.9031 (m-40) REVERT: B 84 PHE cc_start: 0.8361 (t80) cc_final: 0.8117 (t80) REVERT: B 163 LYS cc_start: 0.9420 (tppp) cc_final: 0.9199 (tppp) REVERT: B 255 MET cc_start: 0.8355 (tmm) cc_final: 0.8080 (tmm) REVERT: B 347 GLU cc_start: 0.9119 (pp20) cc_final: 0.8634 (pp20) REVERT: B 357 ASP cc_start: 0.9112 (p0) cc_final: 0.8895 (m-30) REVERT: B 370 ASP cc_start: 0.9165 (t0) cc_final: 0.8627 (t0) REVERT: B 371 LEU cc_start: 0.9689 (mt) cc_final: 0.9460 (mt) REVERT: B 372 GLN cc_start: 0.9333 (mt0) cc_final: 0.8938 (mm110) REVERT: B 378 CYS cc_start: 0.8474 (m) cc_final: 0.8212 (m) REVERT: B 387 MET cc_start: 0.9651 (mtp) cc_final: 0.9032 (mtt) REVERT: B 452 GLU cc_start: 0.9257 (pm20) cc_final: 0.9005 (pm20) REVERT: A 41 ARG cc_start: 0.8960 (mtp180) cc_final: 0.7002 (pmt170) REVERT: A 67 SER cc_start: 0.9076 (p) cc_final: 0.8859 (m) REVERT: A 106 LEU cc_start: 0.9587 (tp) cc_final: 0.9284 (tp) REVERT: A 127 PHE cc_start: 0.9179 (t80) cc_final: 0.8423 (t80) REVERT: A 128 ASP cc_start: 0.9086 (m-30) cc_final: 0.8220 (m-30) REVERT: A 166 THR cc_start: 0.9227 (p) cc_final: 0.8584 (p) REVERT: A 208 MET cc_start: 0.8097 (pmm) cc_final: 0.6823 (pmm) REVERT: A 237 MET cc_start: 0.8656 (mtp) cc_final: 0.8448 (mmm) REVERT: A 246 LEU cc_start: 0.9735 (mp) cc_final: 0.9450 (mp) REVERT: A 250 LEU cc_start: 0.9512 (mm) cc_final: 0.9249 (mm) REVERT: A 282 ASN cc_start: 0.9395 (m110) cc_final: 0.8663 (t0) REVERT: A 309 LYS cc_start: 0.9479 (mttp) cc_final: 0.9028 (mmmm) REVERT: A 311 TYR cc_start: 0.9130 (m-80) cc_final: 0.8705 (m-80) REVERT: A 317 GLN cc_start: 0.9333 (pp30) cc_final: 0.9111 (pm20) REVERT: A 320 ASN cc_start: 0.8309 (t0) cc_final: 0.7940 (t0) REVERT: A 330 PHE cc_start: 0.9449 (m-80) cc_final: 0.8676 (m-10) REVERT: A 359 PHE cc_start: 0.9276 (m-80) cc_final: 0.8553 (m-10) REVERT: A 387 MET cc_start: 0.9345 (ptp) cc_final: 0.9107 (ptp) REVERT: A 447 GLU cc_start: 0.8345 (tm-30) cc_final: 0.8112 (tm-30) REVERT: C 107 GLU cc_start: 0.8241 (tm-30) cc_final: 0.7762 (tp30) REVERT: C 121 HIS cc_start: 0.9077 (t70) cc_final: 0.8725 (t70) REVERT: C 150 MET cc_start: 0.8856 (mmm) cc_final: 0.8561 (mmm) REVERT: C 154 GLN cc_start: 0.9294 (mm110) cc_final: 0.8635 (mt0) REVERT: C 159 LEU cc_start: 0.9347 (mm) cc_final: 0.9137 (mm) REVERT: C 160 ILE cc_start: 0.9260 (mp) cc_final: 0.9053 (mp) REVERT: C 192 ASN cc_start: 0.8791 (m110) cc_final: 0.8554 (t0) REVERT: C 196 GLU cc_start: 0.8577 (pp20) cc_final: 0.8190 (pp20) REVERT: C 208 MET cc_start: 0.8851 (ptp) cc_final: 0.7146 (mpp) REVERT: C 229 CYS cc_start: 0.8332 (p) cc_final: 0.8062 (p) REVERT: C 236 LYS cc_start: 0.9518 (tttt) cc_final: 0.8938 (tppt) REVERT: C 248 PHE cc_start: 0.7300 (t80) cc_final: 0.6891 (t80) REVERT: C 253 GLU cc_start: 0.9482 (mm-30) cc_final: 0.9264 (mm-30) REVERT: C 274 ASP cc_start: 0.9574 (p0) cc_final: 0.9228 (p0) REVERT: C 309 LYS cc_start: 0.9662 (ptpt) cc_final: 0.9409 (ptpt) REVERT: C 347 GLU cc_start: 0.9148 (pm20) cc_final: 0.8558 (pp20) REVERT: C 367 GLU cc_start: 0.7192 (tp30) cc_final: 0.6751 (tp30) REVERT: C 368 GLU cc_start: 0.8641 (tt0) cc_final: 0.8389 (tt0) REVERT: C 376 GLN cc_start: 0.8491 (tt0) cc_final: 0.8221 (tm-30) REVERT: C 377 LEU cc_start: 0.8642 (tp) cc_final: 0.8300 (tp) REVERT: C 378 CYS cc_start: 0.7035 (m) cc_final: 0.4598 (m) REVERT: C 387 MET cc_start: 0.9546 (mtm) cc_final: 0.9142 (mtt) REVERT: C 394 ASP cc_start: 0.9204 (t0) cc_final: 0.8500 (t70) REVERT: C 402 GLN cc_start: 0.9375 (mt0) cc_final: 0.9021 (mp10) REVERT: C 451 LYS cc_start: 0.9235 (mttt) cc_final: 0.8800 (mttm) REVERT: D 34 TYR cc_start: 0.9356 (m-80) cc_final: 0.8994 (m-10) REVERT: D 49 TYR cc_start: 0.9051 (m-10) cc_final: 0.8824 (m-10) REVERT: D 65 LYS cc_start: 0.9389 (ttpt) cc_final: 0.8913 (tttp) REVERT: D 71 TYR cc_start: 0.8948 (m-80) cc_final: 0.8395 (m-80) REVERT: D 78 LEU cc_start: 0.9324 (tt) cc_final: 0.8976 (tt) REVERT: D 101 TRP cc_start: 0.8158 (m100) cc_final: 0.7888 (m100) REVERT: D 107 GLU cc_start: 0.8426 (tp30) cc_final: 0.8211 (tp30) REVERT: D 126 LYS cc_start: 0.9297 (tmmt) cc_final: 0.8997 (tmtt) REVERT: D 134 ASN cc_start: 0.7239 (t0) cc_final: 0.6957 (t0) REVERT: D 139 GLN cc_start: 0.8806 (tp40) cc_final: 0.7938 (tm-30) REVERT: D 150 MET cc_start: 0.8949 (pmm) cc_final: 0.8718 (pmm) REVERT: D 154 GLN cc_start: 0.8955 (OUTLIER) cc_final: 0.8470 (pp30) REVERT: D 168 GLU cc_start: 0.9273 (pm20) cc_final: 0.8920 (pm20) REVERT: D 196 GLU cc_start: 0.8585 (pt0) cc_final: 0.8360 (tt0) REVERT: D 210 PHE cc_start: 0.9339 (m-80) cc_final: 0.8994 (m-80) REVERT: D 217 LYS cc_start: 0.9516 (ptpp) cc_final: 0.8791 (pttt) REVERT: D 222 ILE cc_start: 0.9113 (mp) cc_final: 0.8890 (pt) REVERT: D 229 CYS cc_start: 0.8032 (p) cc_final: 0.7589 (p) REVERT: D 231 TYR cc_start: 0.9226 (t80) cc_final: 0.8604 (t80) REVERT: D 234 TYR cc_start: 0.9244 (m-80) cc_final: 0.8944 (m-80) REVERT: D 255 MET cc_start: 0.8777 (ptm) cc_final: 0.8245 (ppp) REVERT: D 303 GLU cc_start: 0.9238 (tm-30) cc_final: 0.9027 (tm-30) REVERT: D 306 LEU cc_start: 0.9562 (mm) cc_final: 0.9099 (mm) REVERT: D 312 TRP cc_start: 0.9076 (m100) cc_final: 0.8785 (m100) REVERT: D 320 ASN cc_start: 0.8850 (t0) cc_final: 0.8641 (t0) REVERT: D 321 ASN cc_start: 0.9394 (t0) cc_final: 0.9002 (t0) REVERT: D 360 LYS cc_start: 0.9614 (mttt) cc_final: 0.9341 (tppt) REVERT: D 369 TYR cc_start: 0.9038 (m-80) cc_final: 0.8546 (m-10) REVERT: D 371 LEU cc_start: 0.9404 (mp) cc_final: 0.9175 (mp) REVERT: D 372 GLN cc_start: 0.7922 (mp-120) cc_final: 0.6719 (mp10) REVERT: D 378 CYS cc_start: 0.8822 (m) cc_final: 0.8113 (t) REVERT: D 399 GLU cc_start: 0.9213 (pp20) cc_final: 0.8974 (pp20) REVERT: D 417 TYR cc_start: 0.8871 (m-80) cc_final: 0.8627 (m-80) REVERT: D 443 TYR cc_start: 0.9480 (m-80) cc_final: 0.9106 (m-80) REVERT: D 444 THR cc_start: 0.8685 (p) cc_final: 0.7960 (p) REVERT: E 97 GLN cc_start: 0.9225 (mt0) cc_final: 0.8964 (mp10) REVERT: E 125 ASN cc_start: 0.9482 (t0) cc_final: 0.9072 (p0) REVERT: E 150 MET cc_start: 0.8334 (mtm) cc_final: 0.7960 (mtm) REVERT: E 172 LYS cc_start: 0.8398 (tptm) cc_final: 0.8010 (tppt) REVERT: E 200 MET cc_start: 0.9240 (mmm) cc_final: 0.8613 (tpp) REVERT: E 229 CYS cc_start: 0.9115 (m) cc_final: 0.8456 (p) REVERT: E 234 TYR cc_start: 0.9308 (m-80) cc_final: 0.9072 (m-10) REVERT: E 246 LEU cc_start: 0.9599 (mm) cc_final: 0.9334 (mm) REVERT: E 251 ARG cc_start: 0.9258 (ptt90) cc_final: 0.8958 (ptt90) REVERT: E 259 HIS cc_start: 0.9075 (m-70) cc_final: 0.8641 (m-70) REVERT: E 295 PRO cc_start: 0.8725 (Cg_endo) cc_final: 0.8508 (Cg_exo) REVERT: E 311 TYR cc_start: 0.9085 (m-80) cc_final: 0.8746 (m-80) REVERT: E 314 GLN cc_start: 0.9327 (mt0) cc_final: 0.8591 (pm20) REVERT: E 338 ARG cc_start: 0.9452 (mtt-85) cc_final: 0.8662 (mtp85) REVERT: E 354 TYR cc_start: 0.8499 (t80) cc_final: 0.8219 (t80) REVERT: E 369 TYR cc_start: 0.8915 (m-80) cc_final: 0.8663 (m-80) REVERT: E 387 MET cc_start: 0.8962 (tmm) cc_final: 0.8464 (tpp) REVERT: E 398 LEU cc_start: 0.9579 (tp) cc_final: 0.9375 (tp) REVERT: E 399 GLU cc_start: 0.9508 (tm-30) cc_final: 0.9296 (tm-30) REVERT: E 400 ASP cc_start: 0.8900 (p0) cc_final: 0.8655 (p0) outliers start: 4 outliers final: 0 residues processed: 717 average time/residue: 0.3196 time to fit residues: 363.7624 Evaluate side-chains 548 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 547 time to evaluate : 2.658 ------------------------------------------------------------------------------- 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: 9.9990 chunk 77 optimal weight: 7.9990 chunk 207 optimal weight: 8.9990 chunk 170 optimal weight: 20.0000 chunk 68 optimal weight: 6.9990 chunk 250 optimal weight: 0.9990 chunk 270 optimal weight: 20.0000 chunk 222 optimal weight: 4.9990 chunk 248 optimal weight: 9.9990 chunk 85 optimal weight: 2.9990 chunk 200 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 376 GLN ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 GLN A 254 GLN A 341 ASN ** 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 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 ASN C 365 HIS ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 460 GLN ** E 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 192 ASN ** E 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 372 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 22431 Z= 0.282 Angle : 0.639 8.152 30515 Z= 0.328 Chirality : 0.045 0.160 3307 Planarity : 0.005 0.076 3973 Dihedral : 5.594 65.707 2998 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 0.08 % Allowed : 6.03 % Favored : 93.89 % 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: -3.17 (0.14), residues: 2755 helix: -1.62 (0.32), residues: 195 sheet: -1.50 (0.18), residues: 717 loop : -2.57 (0.13), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 49 HIS 0.007 0.001 HIS B 365 PHE 0.019 0.002 PHE D 50 TYR 0.029 0.002 TYR A 36 ARG 0.010 0.001 ARG B 110 *********************** 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 636 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 634 time to evaluate : 2.527 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: L 21 MET cc_start: 0.5599 (mmm) cc_final: 0.5234 (mtt) REVERT: H 36 VAL cc_start: 0.5835 (m) cc_final: 0.5243 (t) REVERT: B 20 LYS cc_start: 0.9358 (pttp) cc_final: 0.9039 (ptpp) REVERT: B 36 TYR cc_start: 0.9354 (t80) cc_final: 0.9128 (t80) REVERT: B 78 LEU cc_start: 0.9567 (mm) cc_final: 0.9335 (mm) REVERT: B 80 ASP cc_start: 0.9330 (t70) cc_final: 0.9007 (t70) REVERT: B 83 LYS cc_start: 0.9053 (mppt) cc_final: 0.8699 (mmtm) REVERT: B 84 PHE cc_start: 0.8480 (t80) cc_final: 0.8253 (t80) REVERT: B 128 ASP cc_start: 0.9130 (m-30) cc_final: 0.8833 (m-30) REVERT: B 163 LYS cc_start: 0.9458 (tppp) cc_final: 0.9231 (tppp) REVERT: B 237 MET cc_start: 0.9209 (mmm) cc_final: 0.8740 (mmm) REVERT: B 255 MET cc_start: 0.8455 (tmm) cc_final: 0.8003 (tmm) REVERT: B 347 GLU cc_start: 0.9021 (pp20) cc_final: 0.8532 (pp20) REVERT: B 387 MET cc_start: 0.9658 (mtp) cc_final: 0.9435 (mtp) REVERT: B 452 GLU cc_start: 0.9156 (pm20) cc_final: 0.8897 (pm20) REVERT: A 127 PHE cc_start: 0.9207 (t80) cc_final: 0.8612 (t80) REVERT: A 128 ASP cc_start: 0.9051 (m-30) cc_final: 0.8301 (m-30) REVERT: A 168 GLU cc_start: 0.9130 (pm20) cc_final: 0.8833 (pm20) REVERT: A 239 SER cc_start: 0.9039 (t) cc_final: 0.8769 (p) REVERT: A 246 LEU cc_start: 0.9744 (mp) cc_final: 0.9454 (mp) REVERT: A 250 LEU cc_start: 0.9513 (mm) cc_final: 0.9192 (mm) REVERT: A 309 LYS cc_start: 0.9409 (mttp) cc_final: 0.8954 (mmmm) REVERT: A 311 TYR cc_start: 0.9172 (m-80) cc_final: 0.8676 (m-80) REVERT: A 320 ASN cc_start: 0.8280 (t0) cc_final: 0.7996 (t0) REVERT: A 359 PHE cc_start: 0.9253 (m-80) cc_final: 0.8571 (m-10) REVERT: A 387 MET cc_start: 0.9306 (ptp) cc_final: 0.9024 (ptp) REVERT: A 402 GLN cc_start: 0.9150 (tp-100) cc_final: 0.8932 (tp-100) REVERT: C 107 GLU cc_start: 0.8239 (tm-30) cc_final: 0.7755 (tp30) REVERT: C 150 MET cc_start: 0.8886 (mmm) cc_final: 0.8580 (mmm) REVERT: C 154 GLN cc_start: 0.9288 (mm110) cc_final: 0.8576 (mt0) REVERT: C 156 GLN cc_start: 0.8556 (mt0) cc_final: 0.8118 (mt0) REVERT: C 159 LEU cc_start: 0.9323 (mm) cc_final: 0.9096 (mm) REVERT: C 160 ILE cc_start: 0.9338 (mp) cc_final: 0.9105 (mp) REVERT: C 192 ASN cc_start: 0.8825 (m110) cc_final: 0.8484 (m-40) REVERT: C 208 MET cc_start: 0.8931 (ptp) cc_final: 0.7390 (mpp) REVERT: C 229 CYS cc_start: 0.8229 (p) cc_final: 0.7925 (p) REVERT: C 231 TYR cc_start: 0.9232 (t80) cc_final: 0.8963 (t80) REVERT: C 236 LYS cc_start: 0.9445 (tttt) cc_final: 0.9083 (tppt) REVERT: C 237 MET cc_start: 0.9532 (tpp) cc_final: 0.9211 (mmt) REVERT: C 248 PHE cc_start: 0.7299 (t80) cc_final: 0.6883 (t80) REVERT: C 347 GLU cc_start: 0.9214 (pm20) cc_final: 0.8996 (pm20) REVERT: C 369 TYR cc_start: 0.8458 (m-10) cc_final: 0.8006 (m-10) REVERT: C 376 GLN cc_start: 0.8590 (tt0) cc_final: 0.8148 (tm-30) REVERT: C 378 CYS cc_start: 0.7098 (m) cc_final: 0.5469 (m) REVERT: C 387 MET cc_start: 0.9598 (mtm) cc_final: 0.9184 (mtt) REVERT: C 394 ASP cc_start: 0.8999 (t0) cc_final: 0.8637 (t70) REVERT: C 400 ASP cc_start: 0.9121 (p0) cc_final: 0.8519 (p0) REVERT: C 402 GLN cc_start: 0.9463 (mt0) cc_final: 0.9130 (mp10) REVERT: C 451 LYS cc_start: 0.9262 (mttt) cc_final: 0.8880 (mttp) REVERT: D 34 TYR cc_start: 0.9327 (m-80) cc_final: 0.8922 (m-10) REVERT: D 71 TYR cc_start: 0.9024 (m-80) cc_final: 0.8485 (m-80) REVERT: D 78 LEU cc_start: 0.9376 (tt) cc_final: 0.9161 (tt) REVERT: D 126 LYS cc_start: 0.9258 (tmmt) cc_final: 0.8971 (tmtt) REVERT: D 139 GLN cc_start: 0.8827 (tp40) cc_final: 0.7904 (tm-30) REVERT: D 150 MET cc_start: 0.8858 (pmm) cc_final: 0.8571 (pmm) REVERT: D 156 GLN cc_start: 0.7825 (tt0) cc_final: 0.6961 (tt0) REVERT: D 168 GLU cc_start: 0.9252 (pm20) cc_final: 0.8983 (pm20) REVERT: D 210 PHE cc_start: 0.9343 (m-80) cc_final: 0.8977 (m-80) REVERT: D 222 ILE cc_start: 0.9333 (mp) cc_final: 0.9002 (pt) REVERT: D 229 CYS cc_start: 0.7897 (p) cc_final: 0.7391 (p) REVERT: D 231 TYR cc_start: 0.9112 (t80) cc_final: 0.8102 (t80) REVERT: D 234 TYR cc_start: 0.9261 (m-80) cc_final: 0.8876 (m-80) REVERT: D 255 MET cc_start: 0.8868 (ptm) cc_final: 0.8271 (ppp) REVERT: D 303 GLU cc_start: 0.9322 (tm-30) cc_final: 0.9081 (tm-30) REVERT: D 306 LEU cc_start: 0.9687 (mm) cc_final: 0.9110 (mm) REVERT: D 321 ASN cc_start: 0.9435 (t0) cc_final: 0.9009 (t0) REVERT: D 360 LYS cc_start: 0.9655 (mttt) cc_final: 0.9380 (tppt) REVERT: D 369 TYR cc_start: 0.8920 (m-80) cc_final: 0.8609 (m-10) REVERT: D 393 MET cc_start: 0.9364 (tpp) cc_final: 0.9152 (tpp) REVERT: D 401 TRP cc_start: 0.9532 (m-10) cc_final: 0.9327 (m-10) REVERT: D 443 TYR cc_start: 0.9544 (m-80) cc_final: 0.9258 (m-80) REVERT: D 444 THR cc_start: 0.8755 (p) cc_final: 0.8046 (p) REVERT: E 97 GLN cc_start: 0.9256 (mt0) cc_final: 0.8905 (mp10) REVERT: E 125 ASN cc_start: 0.9589 (t0) cc_final: 0.8935 (p0) REVERT: E 150 MET cc_start: 0.8529 (mtm) cc_final: 0.8066 (mtm) REVERT: E 172 LYS cc_start: 0.8422 (tptm) cc_final: 0.8058 (tppt) REVERT: E 193 SER cc_start: 0.9466 (t) cc_final: 0.9231 (p) REVERT: E 200 MET cc_start: 0.9355 (mmm) cc_final: 0.8783 (tpp) REVERT: E 234 TYR cc_start: 0.9318 (m-80) cc_final: 0.8611 (m-10) REVERT: E 242 TYR cc_start: 0.8302 (m-80) cc_final: 0.7424 (m-80) REVERT: E 251 ARG cc_start: 0.9194 (ptt90) cc_final: 0.8371 (ptt90) REVERT: E 259 HIS cc_start: 0.8997 (m-70) cc_final: 0.8744 (m-70) REVERT: E 311 TYR cc_start: 0.9141 (m-80) cc_final: 0.8801 (m-80) REVERT: E 314 GLN cc_start: 0.9341 (mt0) cc_final: 0.8642 (pm20) REVERT: E 324 CYS cc_start: 0.9183 (p) cc_final: 0.8854 (p) REVERT: E 338 ARG cc_start: 0.9407 (mtt-85) cc_final: 0.8692 (mtp85) REVERT: E 354 TYR cc_start: 0.8557 (t80) cc_final: 0.8314 (t80) REVERT: E 393 MET cc_start: 0.8832 (tpt) cc_final: 0.8128 (tpt) REVERT: E 399 GLU cc_start: 0.9520 (tm-30) cc_final: 0.9310 (tm-30) REVERT: E 400 ASP cc_start: 0.8907 (p0) cc_final: 0.8586 (p0) REVERT: E 451 LYS cc_start: 0.9379 (mttm) cc_final: 0.8632 (mmmm) outliers start: 2 outliers final: 0 residues processed: 634 average time/residue: 0.3044 time to fit residues: 304.8614 Evaluate side-chains 503 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 503 time to evaluate : 2.673 ------------------------------------------------------------------------------- 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: 10.0000 chunk 188 optimal weight: 9.9990 chunk 129 optimal weight: 5.9990 chunk 27 optimal weight: 40.0000 chunk 119 optimal weight: 0.4980 chunk 167 optimal weight: 8.9990 chunk 251 optimal weight: 0.6980 chunk 265 optimal weight: 7.9990 chunk 131 optimal weight: 10.0000 chunk 237 optimal weight: 5.9990 chunk 71 optimal weight: 20.0000 overall best weight: 4.2386 ------------------------------------------------------------------------------- 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 327 ASN ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 GLN A 139 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN C 214 GLN C 319 HIS C 321 ASN ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 254 GLN ** D 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 305 GLN E 341 ASN ** E 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 22431 Z= 0.250 Angle : 0.617 7.828 30515 Z= 0.314 Chirality : 0.044 0.156 3307 Planarity : 0.005 0.071 3973 Dihedral : 5.430 63.764 2998 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % 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: -2.90 (0.15), residues: 2755 helix: -1.22 (0.35), residues: 189 sheet: -1.39 (0.18), residues: 709 loop : -2.36 (0.13), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 101 HIS 0.009 0.001 HIS B 365 PHE 0.020 0.002 PHE A 291 TYR 0.017 0.001 TYR A 369 ARG 0.006 0.001 ARG B 338 *********************** 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 636 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 636 time to evaluate : 2.580 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: L 21 MET cc_start: 0.5447 (mmm) cc_final: 0.4993 (mtt) REVERT: H 36 VAL cc_start: 0.5366 (m) cc_final: 0.4769 (t) REVERT: B 20 LYS cc_start: 0.9346 (pttp) cc_final: 0.9048 (ptpp) REVERT: B 71 TYR cc_start: 0.9019 (m-80) cc_final: 0.8786 (m-80) REVERT: B 78 LEU cc_start: 0.9511 (mm) cc_final: 0.9301 (mm) REVERT: B 80 ASP cc_start: 0.9314 (t70) cc_final: 0.8965 (t70) REVERT: B 83 LYS cc_start: 0.9050 (mppt) cc_final: 0.8723 (mmtm) REVERT: B 84 PHE cc_start: 0.8490 (t80) cc_final: 0.8254 (t80) REVERT: B 128 ASP cc_start: 0.9153 (m-30) cc_final: 0.8840 (m-30) REVERT: B 163 LYS cc_start: 0.9473 (tppp) cc_final: 0.9210 (tppp) REVERT: B 237 MET cc_start: 0.9209 (mmm) cc_final: 0.8745 (mmm) REVERT: B 255 MET cc_start: 0.8516 (tmm) cc_final: 0.7995 (tmm) REVERT: B 347 GLU cc_start: 0.8992 (pp20) cc_final: 0.8498 (pp20) REVERT: B 387 MET cc_start: 0.9658 (mtp) cc_final: 0.9075 (mtt) REVERT: B 452 GLU cc_start: 0.9191 (pm20) cc_final: 0.8757 (pm20) REVERT: A 127 PHE cc_start: 0.9228 (t80) cc_final: 0.8688 (t80) REVERT: A 128 ASP cc_start: 0.9124 (m-30) cc_final: 0.8407 (m-30) REVERT: A 166 THR cc_start: 0.9235 (p) cc_final: 0.8574 (p) REVERT: A 239 SER cc_start: 0.9023 (t) cc_final: 0.8780 (p) REVERT: A 309 LYS cc_start: 0.9380 (mttp) cc_final: 0.9092 (mmmm) REVERT: A 320 ASN cc_start: 0.8223 (t0) cc_final: 0.7989 (t0) REVERT: A 359 PHE cc_start: 0.9249 (m-80) cc_final: 0.8629 (m-10) REVERT: A 387 MET cc_start: 0.9278 (ptp) cc_final: 0.8955 (ptp) REVERT: A 402 GLN cc_start: 0.9125 (tp-100) cc_final: 0.8893 (tp-100) REVERT: C 107 GLU cc_start: 0.8243 (tm-30) cc_final: 0.7855 (tp30) REVERT: C 150 MET cc_start: 0.8854 (mmm) cc_final: 0.8539 (mmm) REVERT: C 154 GLN cc_start: 0.9326 (mm110) cc_final: 0.8724 (mt0) REVERT: C 156 GLN cc_start: 0.8679 (mt0) cc_final: 0.8193 (mt0) REVERT: C 159 LEU cc_start: 0.9422 (mm) cc_final: 0.9193 (mm) REVERT: C 160 ILE cc_start: 0.9310 (mp) cc_final: 0.9104 (mp) REVERT: C 192 ASN cc_start: 0.8876 (m110) cc_final: 0.8539 (m-40) REVERT: C 200 MET cc_start: 0.9418 (mmp) cc_final: 0.9172 (mmp) REVERT: C 208 MET cc_start: 0.8433 (ptp) cc_final: 0.7982 (ptp) REVERT: C 229 CYS cc_start: 0.8304 (p) cc_final: 0.8064 (p) REVERT: C 231 TYR cc_start: 0.9200 (t80) cc_final: 0.8988 (t80) REVERT: C 236 LYS cc_start: 0.9528 (tttt) cc_final: 0.9043 (tppt) REVERT: C 237 MET cc_start: 0.9522 (tpp) cc_final: 0.9243 (mmt) REVERT: C 248 PHE cc_start: 0.7263 (t80) cc_final: 0.6848 (t80) REVERT: C 253 GLU cc_start: 0.9479 (mm-30) cc_final: 0.9260 (mm-30) REVERT: C 342 MET cc_start: 0.6717 (mmm) cc_final: 0.6301 (mmm) REVERT: C 347 GLU cc_start: 0.9223 (pm20) cc_final: 0.8969 (pm20) REVERT: C 376 GLN cc_start: 0.8617 (tt0) cc_final: 0.8165 (tm-30) REVERT: C 378 CYS cc_start: 0.7038 (m) cc_final: 0.5343 (m) REVERT: C 387 MET cc_start: 0.9580 (mtm) cc_final: 0.9179 (mtt) REVERT: C 394 ASP cc_start: 0.8928 (t0) cc_final: 0.8619 (t70) REVERT: C 400 ASP cc_start: 0.9122 (p0) cc_final: 0.8628 (p0) REVERT: C 402 GLN cc_start: 0.9490 (mt0) cc_final: 0.9180 (mp10) REVERT: C 451 LYS cc_start: 0.9256 (mttt) cc_final: 0.8843 (mttm) REVERT: D 34 TYR cc_start: 0.9360 (m-80) cc_final: 0.9037 (m-80) REVERT: D 65 LYS cc_start: 0.9426 (ttpt) cc_final: 0.8934 (tptm) REVERT: D 71 TYR cc_start: 0.9067 (m-80) cc_final: 0.8542 (m-80) REVERT: D 126 LYS cc_start: 0.9351 (tmmt) cc_final: 0.9048 (tmtt) REVERT: D 139 GLN cc_start: 0.8807 (tp40) cc_final: 0.7916 (tm-30) REVERT: D 156 GLN cc_start: 0.7789 (tt0) cc_final: 0.7080 (tt0) REVERT: D 168 GLU cc_start: 0.9268 (pm20) cc_final: 0.9008 (pm20) REVERT: D 189 GLU cc_start: 0.9130 (tp30) cc_final: 0.8908 (tp30) REVERT: D 210 PHE cc_start: 0.9331 (m-80) cc_final: 0.8845 (m-80) REVERT: D 229 CYS cc_start: 0.8020 (p) cc_final: 0.7355 (p) REVERT: D 231 TYR cc_start: 0.9080 (t80) cc_final: 0.8081 (t80) REVERT: D 234 TYR cc_start: 0.9247 (m-80) cc_final: 0.8795 (m-80) REVERT: D 247 PHE cc_start: 0.8646 (m-10) cc_final: 0.8168 (m-80) REVERT: D 255 MET cc_start: 0.8805 (ptm) cc_final: 0.8275 (ppp) REVERT: D 298 SER cc_start: 0.9558 (t) cc_final: 0.9313 (p) REVERT: D 306 LEU cc_start: 0.9632 (mm) cc_final: 0.9136 (mm) REVERT: D 315 ARG cc_start: 0.9143 (mtp-110) cc_final: 0.8791 (mtp85) REVERT: D 321 ASN cc_start: 0.9419 (t0) cc_final: 0.9061 (t0) REVERT: D 369 TYR cc_start: 0.8969 (m-80) cc_final: 0.8574 (m-10) REVERT: D 393 MET cc_start: 0.9338 (tpp) cc_final: 0.9134 (tpp) REVERT: E 97 GLN cc_start: 0.9271 (mt0) cc_final: 0.8855 (mp10) REVERT: E 150 MET cc_start: 0.8503 (mtm) cc_final: 0.8225 (mtm) REVERT: E 172 LYS cc_start: 0.8401 (tptm) cc_final: 0.7765 (tptm) REVERT: E 193 SER cc_start: 0.9256 (t) cc_final: 0.9038 (p) REVERT: E 200 MET cc_start: 0.9310 (mmm) cc_final: 0.8490 (tpp) REVERT: E 224 ILE cc_start: 0.9769 (pt) cc_final: 0.9162 (mm) REVERT: E 234 TYR cc_start: 0.9330 (m-80) cc_final: 0.9080 (m-10) REVERT: E 251 ARG cc_start: 0.9192 (ptt90) cc_final: 0.8932 (ptt90) REVERT: E 259 HIS cc_start: 0.8980 (m-70) cc_final: 0.8710 (m-70) REVERT: E 311 TYR cc_start: 0.9145 (m-80) cc_final: 0.8887 (m-80) REVERT: E 314 GLN cc_start: 0.9322 (mt0) cc_final: 0.8616 (pm20) REVERT: E 324 CYS cc_start: 0.9204 (p) cc_final: 0.8831 (p) REVERT: E 338 ARG cc_start: 0.9449 (mtt-85) cc_final: 0.8760 (mtp85) REVERT: E 354 TYR cc_start: 0.8517 (t80) cc_final: 0.8271 (t80) REVERT: E 361 GLU cc_start: 0.9024 (mm-30) cc_final: 0.8636 (mm-30) REVERT: E 400 ASP cc_start: 0.8846 (p0) cc_final: 0.8555 (p0) REVERT: E 416 THR cc_start: 0.8838 (t) cc_final: 0.6469 (t) outliers start: 0 outliers final: 0 residues processed: 636 average time/residue: 0.3042 time to fit residues: 308.1115 Evaluate side-chains 504 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 504 time to evaluate : 2.797 ------------------------------------------------------------------------------- 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: 1.9990 chunk 150 optimal weight: 20.0000 chunk 3 optimal weight: 30.0000 chunk 197 optimal weight: 5.9990 chunk 109 optimal weight: 7.9990 chunk 226 optimal weight: 4.9990 chunk 183 optimal weight: 6.9990 chunk 0 optimal weight: 60.0000 chunk 135 optimal weight: 9.9990 chunk 238 optimal weight: 7.9990 chunk 67 optimal weight: 0.9980 overall best weight: 4.1988 ------------------------------------------------------------------------------- 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 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 ASN ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 ASN ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN D 391 HIS ** D 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7776 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 22431 Z= 0.254 Angle : 0.614 7.670 30515 Z= 0.314 Chirality : 0.044 0.159 3307 Planarity : 0.005 0.070 3973 Dihedral : 5.334 62.355 2998 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 0.04 % Allowed : 3.14 % Favored : 96.82 % 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: -2.80 (0.15), residues: 2755 helix: -1.12 (0.36), residues: 198 sheet: -1.31 (0.19), residues: 697 loop : -2.30 (0.13), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP D 401 HIS 0.009 0.001 HIS B 365 PHE 0.019 0.001 PHE A 291 TYR 0.031 0.001 TYR A 36 ARG 0.005 0.000 ARG B 98 *********************** 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 646 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 645 time to evaluate : 2.781 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: L 21 MET cc_start: 0.5644 (mmm) cc_final: 0.5214 (mtt) REVERT: H 36 VAL cc_start: 0.5694 (m) cc_final: 0.5181 (t) REVERT: B 20 LYS cc_start: 0.9354 (pttp) cc_final: 0.9057 (ptpp) REVERT: B 33 ILE cc_start: 0.9480 (mm) cc_final: 0.9180 (mm) REVERT: B 70 GLN cc_start: 0.9083 (mt0) cc_final: 0.8793 (mt0) REVERT: B 71 TYR cc_start: 0.8938 (m-80) cc_final: 0.8558 (m-80) REVERT: B 78 LEU cc_start: 0.9536 (mm) cc_final: 0.9312 (mm) REVERT: B 80 ASP cc_start: 0.9302 (t70) cc_final: 0.9014 (t70) REVERT: B 83 LYS cc_start: 0.9013 (mppt) cc_final: 0.8685 (mmtm) REVERT: B 84 PHE cc_start: 0.8480 (t80) cc_final: 0.8255 (t80) REVERT: B 128 ASP cc_start: 0.9157 (m-30) cc_final: 0.8813 (m-30) REVERT: B 163 LYS cc_start: 0.9482 (tppp) cc_final: 0.9203 (tppp) REVERT: B 237 MET cc_start: 0.9270 (mmm) cc_final: 0.8769 (mmm) REVERT: B 254 GLN cc_start: 0.9318 (pt0) cc_final: 0.9099 (pm20) REVERT: B 255 MET cc_start: 0.8551 (tmm) cc_final: 0.8141 (tmm) REVERT: B 347 GLU cc_start: 0.8940 (pp20) cc_final: 0.8454 (pp20) REVERT: B 387 MET cc_start: 0.9658 (mtp) cc_final: 0.9413 (mtp) REVERT: B 452 GLU cc_start: 0.9176 (pm20) cc_final: 0.8736 (pm20) REVERT: A 127 PHE cc_start: 0.9307 (t80) cc_final: 0.8641 (t80) REVERT: A 128 ASP cc_start: 0.9141 (m-30) cc_final: 0.8366 (m-30) REVERT: A 153 LYS cc_start: 0.9260 (ptmm) cc_final: 0.8672 (ttpp) REVERT: A 166 THR cc_start: 0.9156 (p) cc_final: 0.8351 (p) REVERT: A 168 GLU cc_start: 0.9090 (pm20) cc_final: 0.8791 (pm20) REVERT: A 244 ASP cc_start: 0.8306 (m-30) cc_final: 0.8007 (m-30) REVERT: A 246 LEU cc_start: 0.9654 (mp) cc_final: 0.9424 (mp) REVERT: A 255 MET cc_start: 0.8361 (ptt) cc_final: 0.7647 (ptt) REVERT: A 309 LYS cc_start: 0.9465 (mttp) cc_final: 0.9140 (mmmm) REVERT: A 320 ASN cc_start: 0.8221 (t0) cc_final: 0.7805 (t0) REVERT: A 331 VAL cc_start: 0.9819 (t) cc_final: 0.9593 (p) REVERT: A 338 ARG cc_start: 0.8863 (mtt90) cc_final: 0.8603 (mtm-85) REVERT: A 359 PHE cc_start: 0.9249 (m-80) cc_final: 0.8603 (m-10) REVERT: A 387 MET cc_start: 0.9278 (ptp) cc_final: 0.8989 (ptp) REVERT: A 402 GLN cc_start: 0.9109 (tp-100) cc_final: 0.8833 (tp-100) REVERT: A 451 LYS cc_start: 0.8777 (mttt) cc_final: 0.8535 (mtpt) REVERT: C 107 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7754 (tp30) REVERT: C 150 MET cc_start: 0.8839 (mmm) cc_final: 0.8509 (mmm) REVERT: C 154 GLN cc_start: 0.9297 (mm110) cc_final: 0.8749 (mt0) REVERT: C 156 GLN cc_start: 0.8685 (mt0) cc_final: 0.8186 (mt0) REVERT: C 160 ILE cc_start: 0.9331 (mp) cc_final: 0.9112 (mp) REVERT: C 192 ASN cc_start: 0.8920 (m110) cc_final: 0.8565 (m-40) REVERT: C 208 MET cc_start: 0.8820 (ptp) cc_final: 0.8152 (ptp) REVERT: C 229 CYS cc_start: 0.8238 (p) cc_final: 0.8025 (p) REVERT: C 234 TYR cc_start: 0.9021 (m-80) cc_final: 0.8590 (m-10) REVERT: C 236 LYS cc_start: 0.9406 (tttt) cc_final: 0.8840 (tppt) REVERT: C 248 PHE cc_start: 0.7262 (t80) cc_final: 0.6878 (t80) REVERT: C 342 MET cc_start: 0.6692 (mmm) cc_final: 0.6462 (mmm) REVERT: C 347 GLU cc_start: 0.9266 (pm20) cc_final: 0.8685 (pp20) REVERT: C 376 GLN cc_start: 0.8640 (tt0) cc_final: 0.8160 (tm-30) REVERT: C 378 CYS cc_start: 0.7150 (m) cc_final: 0.5402 (m) REVERT: C 400 ASP cc_start: 0.9105 (p0) cc_final: 0.8677 (p0) REVERT: C 402 GLN cc_start: 0.9499 (mt0) cc_final: 0.9206 (mp10) REVERT: C 451 LYS cc_start: 0.9212 (mttt) cc_final: 0.8801 (mttm) REVERT: D 34 TYR cc_start: 0.9318 (m-80) cc_final: 0.9015 (m-80) REVERT: D 71 TYR cc_start: 0.9045 (m-80) cc_final: 0.8503 (m-80) REVERT: D 101 TRP cc_start: 0.8203 (m100) cc_final: 0.7680 (m100) REVERT: D 126 LYS cc_start: 0.9294 (tmmt) cc_final: 0.8947 (tmtt) REVERT: D 156 GLN cc_start: 0.7821 (tt0) cc_final: 0.7064 (tt0) REVERT: D 168 GLU cc_start: 0.9240 (pm20) cc_final: 0.8996 (pm20) REVERT: D 189 GLU cc_start: 0.9151 (tp30) cc_final: 0.8914 (tp30) REVERT: D 210 PHE cc_start: 0.9364 (m-80) cc_final: 0.8781 (m-80) REVERT: D 229 CYS cc_start: 0.8053 (p) cc_final: 0.7296 (p) REVERT: D 231 TYR cc_start: 0.9044 (t80) cc_final: 0.7956 (t80) REVERT: D 234 TYR cc_start: 0.9254 (m-80) cc_final: 0.8723 (m-80) REVERT: D 247 PHE cc_start: 0.8820 (m-10) cc_final: 0.8376 (m-80) REVERT: D 255 MET cc_start: 0.8869 (ptm) cc_final: 0.8287 (ppp) REVERT: D 262 ASN cc_start: 0.8174 (p0) cc_final: 0.7969 (p0) REVERT: D 298 SER cc_start: 0.9589 (t) cc_final: 0.9284 (p) REVERT: D 306 LEU cc_start: 0.9657 (mm) cc_final: 0.9116 (mm) REVERT: D 315 ARG cc_start: 0.9193 (mtp-110) cc_final: 0.8944 (mtp85) REVERT: D 321 ASN cc_start: 0.9386 (t0) cc_final: 0.9117 (t0) REVERT: D 369 TYR cc_start: 0.8986 (m-80) cc_final: 0.8587 (m-10) REVERT: D 378 CYS cc_start: 0.8864 (m) cc_final: 0.8315 (t) REVERT: D 393 MET cc_start: 0.9329 (tpp) cc_final: 0.9106 (tpp) REVERT: D 396 ASN cc_start: 0.9226 (p0) cc_final: 0.8995 (p0) REVERT: D 401 TRP cc_start: 0.9081 (m-10) cc_final: 0.8866 (m100) REVERT: E 97 GLN cc_start: 0.9256 (mt0) cc_final: 0.8827 (mp10) REVERT: E 172 LYS cc_start: 0.8418 (tptm) cc_final: 0.7765 (tptm) REVERT: E 193 SER cc_start: 0.9292 (t) cc_final: 0.9087 (p) REVERT: E 200 MET cc_start: 0.9368 (mmm) cc_final: 0.8451 (tpp) REVERT: E 224 ILE cc_start: 0.9774 (pt) cc_final: 0.9176 (mm) REVERT: E 234 TYR cc_start: 0.9377 (m-80) cc_final: 0.9017 (m-10) REVERT: E 242 TYR cc_start: 0.8418 (m-80) cc_final: 0.7688 (m-80) REVERT: E 251 ARG cc_start: 0.9252 (ptt90) cc_final: 0.8899 (ptt90) REVERT: E 259 HIS cc_start: 0.9017 (m-70) cc_final: 0.8756 (m-70) REVERT: E 311 TYR cc_start: 0.9213 (m-80) cc_final: 0.8996 (m-80) REVERT: E 314 GLN cc_start: 0.9309 (mt0) cc_final: 0.8615 (pm20) REVERT: E 324 CYS cc_start: 0.9216 (p) cc_final: 0.8799 (p) REVERT: E 338 ARG cc_start: 0.9378 (mtt-85) cc_final: 0.8732 (mtp85) REVERT: E 354 TYR cc_start: 0.8612 (t80) cc_final: 0.8297 (t80) REVERT: E 361 GLU cc_start: 0.9015 (mm-30) cc_final: 0.8638 (mm-30) REVERT: E 393 MET cc_start: 0.8831 (tpt) cc_final: 0.8550 (tpt) REVERT: E 399 GLU cc_start: 0.9511 (tm-30) cc_final: 0.9298 (tm-30) REVERT: E 400 ASP cc_start: 0.8863 (p0) cc_final: 0.8557 (p0) REVERT: E 454 PHE cc_start: 0.8625 (m-80) cc_final: 0.8364 (m-10) outliers start: 1 outliers final: 0 residues processed: 646 average time/residue: 0.3062 time to fit residues: 311.3174 Evaluate side-chains 513 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 513 time to evaluate : 2.582 ------------------------------------------------------------------------------- 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: 4.9990 chunk 239 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 156 optimal weight: 20.0000 chunk 65 optimal weight: 20.0000 chunk 266 optimal weight: 9.9990 chunk 220 optimal weight: 9.9990 chunk 123 optimal weight: 9.9990 chunk 22 optimal weight: 50.0000 chunk 88 optimal weight: 10.0000 chunk 139 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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 112 GLN ** 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 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 GLN B 327 ASN ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 112 GLN A 192 ASN ** 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 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 ASN C 321 ASN ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 22431 Z= 0.387 Angle : 0.709 13.245 30515 Z= 0.364 Chirality : 0.046 0.221 3307 Planarity : 0.006 0.081 3973 Dihedral : 5.687 60.638 2998 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 19.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.47 % Favored : 90.53 % Rotamer: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % 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: -2.88 (0.15), residues: 2755 helix: -1.11 (0.35), residues: 197 sheet: -1.27 (0.18), residues: 728 loop : -2.42 (0.13), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP C 401 HIS 0.007 0.002 HIS C 365 PHE 0.019 0.002 PHE A 291 TYR 0.022 0.002 TYR B 34 ARG 0.009 0.001 ARG B 98 *********************** 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 588 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 588 time to evaluate : 2.704 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: L 21 MET cc_start: 0.5550 (mmm) cc_final: 0.5056 (mtt) REVERT: H 36 VAL cc_start: 0.5909 (m) cc_final: 0.5337 (t) REVERT: B 20 LYS cc_start: 0.9415 (pttp) cc_final: 0.9122 (ptpp) REVERT: B 35 TYR cc_start: 0.9468 (m-80) cc_final: 0.8923 (m-80) REVERT: B 70 GLN cc_start: 0.9131 (mt0) cc_final: 0.8711 (mt0) REVERT: B 78 LEU cc_start: 0.9524 (mm) cc_final: 0.9305 (mm) REVERT: B 128 ASP cc_start: 0.9140 (m-30) cc_final: 0.8802 (m-30) REVERT: B 255 MET cc_start: 0.8610 (tmm) cc_final: 0.8162 (tmm) REVERT: B 266 LYS cc_start: 0.9127 (ptpt) cc_final: 0.8819 (ptpt) REVERT: B 347 GLU cc_start: 0.8865 (pp20) cc_final: 0.8353 (pp20) REVERT: B 387 MET cc_start: 0.9665 (mtp) cc_final: 0.9420 (mtp) REVERT: B 403 PHE cc_start: 0.8434 (m-80) cc_final: 0.8202 (m-80) REVERT: B 437 GLU cc_start: 0.7325 (pm20) cc_final: 0.7102 (tp30) REVERT: B 452 GLU cc_start: 0.9213 (pm20) cc_final: 0.8770 (pm20) REVERT: A 106 LEU cc_start: 0.9622 (tp) cc_final: 0.9324 (tp) REVERT: A 127 PHE cc_start: 0.9327 (t80) cc_final: 0.8591 (t80) REVERT: A 128 ASP cc_start: 0.9139 (m-30) cc_final: 0.8268 (m-30) REVERT: A 148 LEU cc_start: 0.8689 (tp) cc_final: 0.8470 (tp) REVERT: A 151 ASP cc_start: 0.8902 (t0) cc_final: 0.8649 (t0) REVERT: A 166 THR cc_start: 0.8772 (p) cc_final: 0.8538 (p) REVERT: A 168 GLU cc_start: 0.9097 (pm20) cc_final: 0.8883 (pm20) REVERT: A 200 MET cc_start: 0.9221 (mmt) cc_final: 0.8990 (mmt) REVERT: A 239 SER cc_start: 0.9058 (t) cc_final: 0.8805 (p) REVERT: A 244 ASP cc_start: 0.8215 (m-30) cc_final: 0.7875 (m-30) REVERT: A 255 MET cc_start: 0.8488 (ptt) cc_final: 0.7917 (ptt) REVERT: A 262 ASN cc_start: 0.8634 (p0) cc_final: 0.8160 (p0) REVERT: A 309 LYS cc_start: 0.9494 (mttp) cc_final: 0.9135 (mmmm) REVERT: A 320 ASN cc_start: 0.8273 (t0) cc_final: 0.7906 (t0) REVERT: A 331 VAL cc_start: 0.9829 (t) cc_final: 0.9596 (p) REVERT: A 359 PHE cc_start: 0.9258 (m-80) cc_final: 0.8639 (m-10) REVERT: A 387 MET cc_start: 0.9320 (ptp) cc_final: 0.9057 (ptp) REVERT: A 402 GLN cc_start: 0.9147 (tp-100) cc_final: 0.8245 (tm-30) REVERT: A 418 ARG cc_start: 0.4341 (mpp-170) cc_final: 0.3134 (mpt-90) REVERT: A 451 LYS cc_start: 0.8767 (mttt) cc_final: 0.8479 (mtpt) REVERT: C 107 GLU cc_start: 0.8255 (tm-30) cc_final: 0.7785 (tp30) REVERT: C 150 MET cc_start: 0.8778 (mmm) cc_final: 0.8462 (mmm) REVERT: C 151 ASP cc_start: 0.7903 (p0) cc_final: 0.7435 (p0) REVERT: C 154 GLN cc_start: 0.9202 (mm110) cc_final: 0.8581 (mp-120) REVERT: C 156 GLN cc_start: 0.8614 (mt0) cc_final: 0.8202 (mt0) REVERT: C 160 ILE cc_start: 0.9319 (mp) cc_final: 0.9081 (mp) REVERT: C 208 MET cc_start: 0.8896 (ptp) cc_final: 0.8104 (ptp) REVERT: C 229 CYS cc_start: 0.8558 (p) cc_final: 0.8313 (p) REVERT: C 231 TYR cc_start: 0.9243 (t80) cc_final: 0.9029 (t80) REVERT: C 236 LYS cc_start: 0.9440 (tttt) cc_final: 0.8928 (tppt) REVERT: C 248 PHE cc_start: 0.7275 (t80) cc_final: 0.6910 (t80) REVERT: C 296 SER cc_start: 0.7412 (p) cc_final: 0.6554 (t) REVERT: C 342 MET cc_start: 0.6740 (mmm) cc_final: 0.6410 (mmm) REVERT: C 347 GLU cc_start: 0.9341 (pm20) cc_final: 0.8759 (pp20) REVERT: C 376 GLN cc_start: 0.8587 (tt0) cc_final: 0.8131 (tm-30) REVERT: C 378 CYS cc_start: 0.7474 (m) cc_final: 0.5604 (m) REVERT: C 387 MET cc_start: 0.9481 (mtm) cc_final: 0.9237 (mtt) REVERT: C 394 ASP cc_start: 0.9006 (t0) cc_final: 0.8680 (t70) REVERT: C 451 LYS cc_start: 0.9222 (mttt) cc_final: 0.8751 (mttp) REVERT: D 101 TRP cc_start: 0.8280 (m100) cc_final: 0.7879 (m100) REVERT: D 126 LYS cc_start: 0.9355 (tmmt) cc_final: 0.9118 (tmtt) REVERT: D 150 MET cc_start: 0.8866 (pmm) cc_final: 0.8615 (pmm) REVERT: D 156 GLN cc_start: 0.8010 (tt0) cc_final: 0.7355 (tt0) REVERT: D 210 PHE cc_start: 0.9322 (m-80) cc_final: 0.8810 (m-80) REVERT: D 229 CYS cc_start: 0.8138 (p) cc_final: 0.7349 (p) REVERT: D 234 TYR cc_start: 0.9268 (m-80) cc_final: 0.8905 (m-80) REVERT: D 242 TYR cc_start: 0.8349 (m-80) cc_final: 0.8102 (m-80) REVERT: D 255 MET cc_start: 0.8922 (ptm) cc_final: 0.8327 (ppp) REVERT: D 306 LEU cc_start: 0.9670 (mm) cc_final: 0.9211 (mm) REVERT: D 315 ARG cc_start: 0.9249 (mtp-110) cc_final: 0.8986 (mtp85) REVERT: D 321 ASN cc_start: 0.9403 (t0) cc_final: 0.9141 (t0) REVERT: D 330 PHE cc_start: 0.8759 (m-10) cc_final: 0.8554 (m-10) REVERT: D 338 ARG cc_start: 0.9475 (mtt90) cc_final: 0.9046 (tpp80) REVERT: D 369 TYR cc_start: 0.9006 (m-80) cc_final: 0.8631 (m-10) REVERT: D 396 ASN cc_start: 0.9166 (p0) cc_final: 0.8927 (p0) REVERT: E 21 VAL cc_start: 0.9518 (t) cc_final: 0.9171 (p) REVERT: E 107 GLU cc_start: 0.8804 (mm-30) cc_final: 0.8401 (mm-30) REVERT: E 110 ARG cc_start: 0.8389 (mmm-85) cc_final: 0.8103 (mmm-85) REVERT: E 172 LYS cc_start: 0.8455 (tptm) cc_final: 0.8227 (tppt) REVERT: E 200 MET cc_start: 0.9289 (mmm) cc_final: 0.8486 (tpp) REVERT: E 208 MET cc_start: 0.8949 (ppp) cc_final: 0.8352 (ppp) REVERT: E 209 ASP cc_start: 0.9193 (t70) cc_final: 0.8825 (t70) REVERT: E 218 SER cc_start: 0.9314 (p) cc_final: 0.9098 (t) REVERT: E 222 ILE cc_start: 0.9281 (mm) cc_final: 0.9069 (mm) REVERT: E 229 CYS cc_start: 0.8250 (m) cc_final: 0.7808 (p) REVERT: E 234 TYR cc_start: 0.9423 (m-80) cc_final: 0.9027 (m-10) REVERT: E 251 ARG cc_start: 0.9271 (ptt90) cc_final: 0.8838 (ptt90) REVERT: E 253 GLU cc_start: 0.9292 (pm20) cc_final: 0.8890 (pm20) REVERT: E 305 GLN cc_start: 0.9211 (tp40) cc_final: 0.8848 (tp40) REVERT: E 314 GLN cc_start: 0.9365 (mt0) cc_final: 0.8669 (pm20) REVERT: E 324 CYS cc_start: 0.9281 (p) cc_final: 0.8775 (p) REVERT: E 335 ASP cc_start: 0.8568 (t0) cc_final: 0.8131 (t0) REVERT: E 354 TYR cc_start: 0.8544 (t80) cc_final: 0.8328 (t80) REVERT: E 400 ASP cc_start: 0.8858 (p0) cc_final: 0.8572 (p0) REVERT: E 416 THR cc_start: 0.7632 (t) cc_final: 0.7190 (t) outliers start: 0 outliers final: 0 residues processed: 588 average time/residue: 0.3074 time to fit residues: 287.5018 Evaluate side-chains 465 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 465 time to evaluate : 2.611 ------------------------------------------------------------------------------- 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: 20.0000 chunk 29 optimal weight: 30.0000 chunk 151 optimal weight: 1.9990 chunk 194 optimal weight: 20.0000 chunk 150 optimal weight: 3.9990 chunk 223 optimal weight: 0.8980 chunk 148 optimal weight: 3.9990 chunk 265 optimal weight: 5.9990 chunk 165 optimal weight: 6.9990 chunk 161 optimal weight: 8.9990 chunk 122 optimal weight: 1.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 ** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 ASN ** B 423 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 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 ASN ** D 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 402 GLN ** 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** E 460 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22431 Z= 0.197 Angle : 0.630 11.856 30515 Z= 0.314 Chirality : 0.045 0.196 3307 Planarity : 0.005 0.071 3973 Dihedral : 5.288 58.024 2998 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % 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: -2.63 (0.15), residues: 2755 helix: -1.06 (0.36), residues: 197 sheet: -1.12 (0.19), residues: 703 loop : -2.21 (0.14), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP D 401 HIS 0.011 0.001 HIS E 259 PHE 0.017 0.001 PHE A 291 TYR 0.045 0.001 TYR A 36 ARG 0.011 0.000 ARG B 98 *********************** 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 664 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 664 time to evaluate : 2.482 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: H 36 VAL cc_start: 0.5866 (m) cc_final: 0.5305 (t) REVERT: B 20 LYS cc_start: 0.9368 (pttp) cc_final: 0.9095 (ptpp) REVERT: B 35 TYR cc_start: 0.9283 (m-80) cc_final: 0.8730 (m-80) REVERT: B 70 GLN cc_start: 0.9078 (mt0) cc_final: 0.8742 (mt0) REVERT: B 71 TYR cc_start: 0.9008 (m-80) cc_final: 0.8665 (m-10) REVERT: B 84 PHE cc_start: 0.8470 (t80) cc_final: 0.8042 (t80) REVERT: B 128 ASP cc_start: 0.9204 (m-30) cc_final: 0.8901 (m-30) REVERT: B 163 LYS cc_start: 0.9449 (tppp) cc_final: 0.9222 (tppp) REVERT: B 255 MET cc_start: 0.8563 (tmm) cc_final: 0.8086 (tmm) REVERT: B 266 LYS cc_start: 0.9132 (ptpt) cc_final: 0.8798 (ptpt) REVERT: B 347 GLU cc_start: 0.8926 (pp20) cc_final: 0.8458 (pp20) REVERT: B 387 MET cc_start: 0.9660 (mtp) cc_final: 0.9073 (mtt) REVERT: B 437 GLU cc_start: 0.7247 (pm20) cc_final: 0.6965 (tp30) REVERT: B 452 GLU cc_start: 0.9195 (pm20) cc_final: 0.8801 (pm20) REVERT: A 31 THR cc_start: 0.9624 (p) cc_final: 0.9199 (p) REVERT: A 127 PHE cc_start: 0.9316 (t80) cc_final: 0.8635 (t80) REVERT: A 128 ASP cc_start: 0.9138 (m-30) cc_final: 0.8297 (m-30) REVERT: A 151 ASP cc_start: 0.8865 (t0) cc_final: 0.8662 (t0) REVERT: A 153 LYS cc_start: 0.9243 (ptmm) cc_final: 0.8427 (ttpp) REVERT: A 244 ASP cc_start: 0.8139 (m-30) cc_final: 0.7794 (m-30) REVERT: A 246 LEU cc_start: 0.9714 (mp) cc_final: 0.9513 (mp) REVERT: A 253 GLU cc_start: 0.9118 (pm20) cc_final: 0.8866 (pm20) REVERT: A 255 MET cc_start: 0.8361 (ptt) cc_final: 0.7645 (ptt) REVERT: A 262 ASN cc_start: 0.8633 (p0) cc_final: 0.8123 (p0) REVERT: A 309 LYS cc_start: 0.9494 (mttp) cc_final: 0.9136 (mmmm) REVERT: A 320 ASN cc_start: 0.8056 (t0) cc_final: 0.7688 (t0) REVERT: A 331 VAL cc_start: 0.9815 (t) cc_final: 0.9588 (p) REVERT: A 359 PHE cc_start: 0.9216 (m-80) cc_final: 0.8617 (m-10) REVERT: A 372 GLN cc_start: 0.8428 (mt0) cc_final: 0.7874 (mp-120) REVERT: A 387 MET cc_start: 0.9299 (ptp) cc_final: 0.9065 (ptp) REVERT: A 402 GLN cc_start: 0.9070 (tp-100) cc_final: 0.8096 (pp30) REVERT: A 451 LYS cc_start: 0.8658 (mttt) cc_final: 0.8381 (mtpt) REVERT: C 107 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7771 (tp30) REVERT: C 150 MET cc_start: 0.8801 (mmm) cc_final: 0.8496 (mmm) REVERT: C 151 ASP cc_start: 0.7781 (p0) cc_final: 0.7429 (p0) REVERT: C 153 LYS cc_start: 0.8867 (ttpt) cc_final: 0.8651 (ttpp) REVERT: C 160 ILE cc_start: 0.9263 (mp) cc_final: 0.9061 (mp) REVERT: C 208 MET cc_start: 0.8789 (ptp) cc_final: 0.8187 (ptp) REVERT: C 209 ASP cc_start: 0.8956 (m-30) cc_final: 0.8720 (m-30) REVERT: C 229 CYS cc_start: 0.8210 (p) cc_final: 0.7970 (p) REVERT: C 236 LYS cc_start: 0.9475 (tttt) cc_final: 0.8924 (mmtt) REVERT: C 242 TYR cc_start: 0.9165 (m-10) cc_final: 0.8840 (m-10) REVERT: C 296 SER cc_start: 0.7486 (p) cc_final: 0.6240 (t) REVERT: C 342 MET cc_start: 0.6659 (mmm) cc_final: 0.6414 (mmm) REVERT: C 347 GLU cc_start: 0.9310 (pm20) cc_final: 0.8744 (pp20) REVERT: C 376 GLN cc_start: 0.8610 (tt0) cc_final: 0.8154 (tm-30) REVERT: C 378 CYS cc_start: 0.7290 (m) cc_final: 0.5620 (m) REVERT: C 385 GLU cc_start: 0.9448 (pm20) cc_final: 0.9228 (pm20) REVERT: C 387 MET cc_start: 0.9447 (mtm) cc_final: 0.9232 (mtt) REVERT: C 394 ASP cc_start: 0.8936 (t0) cc_final: 0.8634 (t70) REVERT: C 400 ASP cc_start: 0.9231 (p0) cc_final: 0.8694 (p0) REVERT: C 402 GLN cc_start: 0.9505 (mt0) cc_final: 0.9190 (mp10) REVERT: C 451 LYS cc_start: 0.9142 (mttt) cc_final: 0.8756 (mttm) REVERT: D 34 TYR cc_start: 0.9336 (m-80) cc_final: 0.9006 (m-10) REVERT: D 101 TRP cc_start: 0.8181 (m100) cc_final: 0.7726 (m100) REVERT: D 126 LYS cc_start: 0.9289 (tmmt) cc_final: 0.9006 (tmtt) REVERT: D 156 GLN cc_start: 0.7800 (tt0) cc_final: 0.7028 (tt0) REVERT: D 189 GLU cc_start: 0.9164 (tp30) cc_final: 0.8716 (mp0) REVERT: D 199 ASP cc_start: 0.8984 (m-30) cc_final: 0.8760 (m-30) REVERT: D 210 PHE cc_start: 0.9333 (m-80) cc_final: 0.8812 (m-80) REVERT: D 229 CYS cc_start: 0.7890 (p) cc_final: 0.7391 (p) REVERT: D 231 TYR cc_start: 0.8796 (t80) cc_final: 0.7757 (t80) REVERT: D 233 ASP cc_start: 0.8975 (t0) cc_final: 0.8482 (t0) REVERT: D 234 TYR cc_start: 0.9235 (m-80) cc_final: 0.8611 (m-80) REVERT: D 237 MET cc_start: 0.9527 (mmt) cc_final: 0.8370 (mmt) REVERT: D 240 GLU cc_start: 0.8821 (tm-30) cc_final: 0.8332 (tm-30) REVERT: D 242 TYR cc_start: 0.8228 (m-80) cc_final: 0.7881 (m-80) REVERT: D 255 MET cc_start: 0.8864 (ptm) cc_final: 0.8391 (ppp) REVERT: D 303 GLU cc_start: 0.9434 (tm-30) cc_final: 0.9185 (tm-30) REVERT: D 306 LEU cc_start: 0.9690 (mm) cc_final: 0.9118 (mm) REVERT: D 321 ASN cc_start: 0.9386 (t0) cc_final: 0.9060 (t0) REVERT: D 369 TYR cc_start: 0.9050 (m-80) cc_final: 0.8597 (m-10) REVERT: D 399 GLU cc_start: 0.9110 (pp20) cc_final: 0.8871 (pp20) REVERT: D 400 ASP cc_start: 0.8902 (m-30) cc_final: 0.8446 (m-30) REVERT: D 470 GLN cc_start: 0.8964 (tp-100) cc_final: 0.8709 (tt0) REVERT: E 21 VAL cc_start: 0.9501 (t) cc_final: 0.9137 (p) REVERT: E 107 GLU cc_start: 0.8782 (mm-30) cc_final: 0.8458 (mm-30) REVERT: E 193 SER cc_start: 0.9194 (t) cc_final: 0.8967 (p) REVERT: E 200 MET cc_start: 0.9283 (mmm) cc_final: 0.8546 (tpp) REVERT: E 218 SER cc_start: 0.9307 (p) cc_final: 0.9094 (t) REVERT: E 224 ILE cc_start: 0.9772 (pt) cc_final: 0.9212 (mm) REVERT: E 229 CYS cc_start: 0.8269 (m) cc_final: 0.8053 (p) REVERT: E 234 TYR cc_start: 0.9359 (m-80) cc_final: 0.8989 (m-10) REVERT: E 251 ARG cc_start: 0.9234 (ptt90) cc_final: 0.8808 (ptt90) REVERT: E 253 GLU cc_start: 0.9215 (pm20) cc_final: 0.8780 (pm20) REVERT: E 305 GLN cc_start: 0.9161 (tp40) cc_final: 0.8831 (tp40) REVERT: E 314 GLN cc_start: 0.9302 (mt0) cc_final: 0.8632 (pm20) REVERT: E 338 ARG cc_start: 0.9357 (mtt-85) cc_final: 0.8836 (mtp85) REVERT: E 400 ASP cc_start: 0.8816 (p0) cc_final: 0.8543 (p0) REVERT: E 416 THR cc_start: 0.7821 (t) cc_final: 0.7574 (t) outliers start: 0 outliers final: 0 residues processed: 664 average time/residue: 0.3081 time to fit residues: 324.3312 Evaluate side-chains 521 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 521 time to evaluate : 2.535 ------------------------------------------------------------------------------- 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: 3.9990 chunk 105 optimal weight: 10.0000 chunk 158 optimal weight: 10.0000 chunk 79 optimal weight: 6.9990 chunk 52 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 168 optimal weight: 9.9990 chunk 180 optimal weight: 10.0000 chunk 131 optimal weight: 20.0000 chunk 24 optimal weight: 50.0000 chunk 208 optimal weight: 9.9990 overall best weight: 4.4586 ------------------------------------------------------------------------------- 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 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 GLN ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 GLN ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 ASN ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN ** D 402 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 22431 Z= 0.271 Angle : 0.649 11.334 30515 Z= 0.328 Chirality : 0.045 0.202 3307 Planarity : 0.005 0.102 3973 Dihedral : 5.364 63.797 2998 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 0.04 % Allowed : 1.59 % Favored : 98.37 % 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: -2.59 (0.15), residues: 2755 helix: -0.94 (0.37), residues: 198 sheet: -1.06 (0.19), residues: 713 loop : -2.22 (0.14), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP B 312 HIS 0.011 0.002 HIS E 259 PHE 0.018 0.002 PHE A 291 TYR 0.021 0.002 TYR A 234 ARG 0.010 0.001 ARG A 251 *********************** 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 617 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 616 time to evaluate : 3.116 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: H 36 VAL cc_start: 0.5737 (m) cc_final: 0.5100 (t) REVERT: B 20 LYS cc_start: 0.9377 (pttp) cc_final: 0.9113 (ptpp) REVERT: B 35 TYR cc_start: 0.9346 (m-80) cc_final: 0.8805 (m-80) REVERT: B 70 GLN cc_start: 0.9052 (mt0) cc_final: 0.8735 (mt0) REVERT: B 71 TYR cc_start: 0.9017 (m-80) cc_final: 0.8675 (m-10) REVERT: B 78 LEU cc_start: 0.9522 (mm) cc_final: 0.9293 (mm) REVERT: B 80 ASP cc_start: 0.9182 (t0) cc_final: 0.8869 (t0) REVERT: B 84 PHE cc_start: 0.8619 (t80) cc_final: 0.8277 (t80) REVERT: B 128 ASP cc_start: 0.9197 (m-30) cc_final: 0.8908 (m-30) REVERT: B 163 LYS cc_start: 0.9420 (tppp) cc_final: 0.9201 (tppp) REVERT: B 255 MET cc_start: 0.8608 (tmm) cc_final: 0.8132 (tmm) REVERT: B 266 LYS cc_start: 0.9050 (ptpt) cc_final: 0.8725 (ptpt) REVERT: B 347 GLU cc_start: 0.8892 (pp20) cc_final: 0.8395 (pp20) REVERT: B 387 MET cc_start: 0.9671 (mtp) cc_final: 0.9425 (mtp) REVERT: B 437 GLU cc_start: 0.7306 (pm20) cc_final: 0.7020 (tp30) REVERT: B 452 GLU cc_start: 0.9191 (pm20) cc_final: 0.8747 (pm20) REVERT: A 127 PHE cc_start: 0.9318 (t80) cc_final: 0.8592 (t80) REVERT: A 128 ASP cc_start: 0.9148 (m-30) cc_final: 0.8296 (m-30) REVERT: A 151 ASP cc_start: 0.8930 (t0) cc_final: 0.8679 (t0) REVERT: A 153 LYS cc_start: 0.9270 (ptmm) cc_final: 0.8455 (ttpp) REVERT: A 168 GLU cc_start: 0.9079 (pm20) cc_final: 0.8851 (pm20) REVERT: A 244 ASP cc_start: 0.8074 (m-30) cc_final: 0.7799 (m-30) REVERT: A 246 LEU cc_start: 0.9720 (mp) cc_final: 0.9507 (mp) REVERT: A 253 GLU cc_start: 0.9239 (pm20) cc_final: 0.9034 (pm20) REVERT: A 255 MET cc_start: 0.8480 (ptt) cc_final: 0.7831 (ptt) REVERT: A 262 ASN cc_start: 0.8659 (p0) cc_final: 0.8117 (p0) REVERT: A 305 GLN cc_start: 0.9258 (mt0) cc_final: 0.8920 (mm-40) REVERT: A 309 LYS cc_start: 0.9576 (mttp) cc_final: 0.9129 (mmmm) REVERT: A 320 ASN cc_start: 0.8131 (t0) cc_final: 0.7749 (t0) REVERT: A 331 VAL cc_start: 0.9828 (t) cc_final: 0.9613 (p) REVERT: A 372 GLN cc_start: 0.8815 (mt0) cc_final: 0.8343 (mp-120) REVERT: A 387 MET cc_start: 0.9294 (ptp) cc_final: 0.9063 (ptp) REVERT: A 402 GLN cc_start: 0.9151 (tp-100) cc_final: 0.8248 (tm-30) REVERT: A 451 LYS cc_start: 0.8699 (mttt) cc_final: 0.8418 (mtpt) REVERT: C 107 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7756 (tp30) REVERT: C 150 MET cc_start: 0.8822 (mmm) cc_final: 0.8533 (mmm) REVERT: C 151 ASP cc_start: 0.7853 (p0) cc_final: 0.7489 (p0) REVERT: C 153 LYS cc_start: 0.9102 (ttpt) cc_final: 0.8801 (ttpp) REVERT: C 159 LEU cc_start: 0.9394 (mm) cc_final: 0.9150 (mm) REVERT: C 208 MET cc_start: 0.9090 (ptp) cc_final: 0.8239 (ptp) REVERT: C 209 ASP cc_start: 0.8949 (m-30) cc_final: 0.8713 (m-30) REVERT: C 229 CYS cc_start: 0.8232 (p) cc_final: 0.7963 (p) REVERT: C 236 LYS cc_start: 0.9525 (tttt) cc_final: 0.9200 (tptt) REVERT: C 237 MET cc_start: 0.9433 (mmt) cc_final: 0.9078 (mmm) REVERT: C 246 LEU cc_start: 0.9356 (tp) cc_final: 0.9029 (tt) REVERT: C 296 SER cc_start: 0.7393 (p) cc_final: 0.6205 (t) REVERT: C 317 GLN cc_start: 0.8301 (pm20) cc_final: 0.7740 (pp30) REVERT: C 342 MET cc_start: 0.6686 (mmm) cc_final: 0.6441 (mmm) REVERT: C 347 GLU cc_start: 0.9299 (pm20) cc_final: 0.8750 (pp20) REVERT: C 376 GLN cc_start: 0.8648 (tt0) cc_final: 0.8169 (tm-30) REVERT: C 378 CYS cc_start: 0.7408 (m) cc_final: 0.5609 (m) REVERT: C 387 MET cc_start: 0.9463 (mtm) cc_final: 0.9230 (mtt) REVERT: C 394 ASP cc_start: 0.9041 (t0) cc_final: 0.8605 (t70) REVERT: C 451 LYS cc_start: 0.9179 (mttt) cc_final: 0.8491 (mptp) REVERT: D 34 TYR cc_start: 0.9327 (m-80) cc_final: 0.9016 (m-10) REVERT: D 65 LYS cc_start: 0.9263 (tttt) cc_final: 0.8727 (tptm) REVERT: D 101 TRP cc_start: 0.8307 (m100) cc_final: 0.7847 (m100) REVERT: D 121 HIS cc_start: 0.9123 (t70) cc_final: 0.8889 (t70) REVERT: D 150 MET cc_start: 0.8874 (pmm) cc_final: 0.8620 (pmm) REVERT: D 156 GLN cc_start: 0.7850 (tt0) cc_final: 0.7182 (tt0) REVERT: D 168 GLU cc_start: 0.9119 (pm20) cc_final: 0.8908 (pm20) REVERT: D 196 GLU cc_start: 0.8616 (tt0) cc_final: 0.8223 (tp30) REVERT: D 210 PHE cc_start: 0.9328 (m-80) cc_final: 0.8840 (m-80) REVERT: D 229 CYS cc_start: 0.7792 (p) cc_final: 0.7305 (p) REVERT: D 231 TYR cc_start: 0.8808 (t80) cc_final: 0.7899 (t80) REVERT: D 234 TYR cc_start: 0.9235 (m-80) cc_final: 0.8544 (m-80) REVERT: D 237 MET cc_start: 0.9547 (mmt) cc_final: 0.8486 (mmt) REVERT: D 242 TYR cc_start: 0.8265 (m-80) cc_final: 0.8061 (m-80) REVERT: D 255 MET cc_start: 0.8908 (ptm) cc_final: 0.8377 (ppp) REVERT: D 306 LEU cc_start: 0.9622 (mm) cc_final: 0.9110 (mm) REVERT: D 315 ARG cc_start: 0.9179 (mtp-110) cc_final: 0.8906 (mtp85) REVERT: D 321 ASN cc_start: 0.9422 (t0) cc_final: 0.9174 (t0) REVERT: D 338 ARG cc_start: 0.9399 (mtt90) cc_final: 0.8837 (tpp80) REVERT: D 369 TYR cc_start: 0.9029 (m-80) cc_final: 0.8622 (m-10) REVERT: D 396 ASN cc_start: 0.8896 (p0) cc_final: 0.8589 (p0) REVERT: D 443 TYR cc_start: 0.9364 (m-80) cc_final: 0.9097 (m-80) REVERT: D 470 GLN cc_start: 0.8982 (tp-100) cc_final: 0.8715 (tt0) REVERT: E 107 GLU cc_start: 0.8793 (mm-30) cc_final: 0.8407 (mm-30) REVERT: E 200 MET cc_start: 0.9377 (mmm) cc_final: 0.8401 (tpp) REVERT: E 208 MET cc_start: 0.8795 (ppp) cc_final: 0.8086 (ppp) REVERT: E 229 CYS cc_start: 0.8217 (m) cc_final: 0.7957 (p) REVERT: E 234 TYR cc_start: 0.9424 (m-80) cc_final: 0.9005 (m-10) REVERT: E 251 ARG cc_start: 0.9249 (ptt90) cc_final: 0.8820 (ptt90) REVERT: E 253 GLU cc_start: 0.9241 (pm20) cc_final: 0.8769 (pm20) REVERT: E 314 GLN cc_start: 0.9305 (mt0) cc_final: 0.8649 (pm20) REVERT: E 324 CYS cc_start: 0.9168 (p) cc_final: 0.8862 (p) REVERT: E 338 ARG cc_start: 0.9355 (mtt-85) cc_final: 0.8824 (mtp85) REVERT: E 400 ASP cc_start: 0.8818 (p0) cc_final: 0.8504 (p0) REVERT: E 416 THR cc_start: 0.8082 (t) cc_final: 0.7705 (t) outliers start: 1 outliers final: 0 residues processed: 617 average time/residue: 0.3030 time to fit residues: 297.1687 Evaluate side-chains 489 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 489 time to evaluate : 2.852 ------------------------------------------------------------------------------- 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: 0.9990 chunk 253 optimal weight: 6.9990 chunk 231 optimal weight: 10.0000 chunk 246 optimal weight: 10.0000 chunk 148 optimal weight: 20.0000 chunk 107 optimal weight: 3.9990 chunk 193 optimal weight: 9.9990 chunk 75 optimal weight: 6.9990 chunk 223 optimal weight: 0.4980 chunk 233 optimal weight: 20.0000 chunk 162 optimal weight: 9.9990 overall best weight: 3.8988 ------------------------------------------------------------------------------- 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 139 GLN ** 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 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 423 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 ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN ** D 402 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 22431 Z= 0.245 Angle : 0.638 11.471 30515 Z= 0.321 Chirality : 0.045 0.184 3307 Planarity : 0.005 0.080 3973 Dihedral : 5.267 62.448 2998 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 0.04 % Allowed : 0.45 % Favored : 99.51 % 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: -2.51 (0.15), residues: 2755 helix: -0.98 (0.36), residues: 198 sheet: -1.00 (0.19), residues: 713 loop : -2.14 (0.14), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP D 401 HIS 0.012 0.001 HIS E 259 PHE 0.018 0.001 PHE A 291 TYR 0.043 0.002 TYR A 36 ARG 0.008 0.001 ARG B 98 *********************** 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 612 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 611 time to evaluate : 2.573 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: H 36 VAL cc_start: 0.5971 (m) cc_final: 0.5317 (t) REVERT: B 20 LYS cc_start: 0.9362 (pttp) cc_final: 0.9095 (ptpp) REVERT: B 35 TYR cc_start: 0.9332 (m-80) cc_final: 0.8778 (m-80) REVERT: B 70 GLN cc_start: 0.9072 (mt0) cc_final: 0.8719 (mt0) REVERT: B 71 TYR cc_start: 0.8973 (m-80) cc_final: 0.8597 (m-10) REVERT: B 80 ASP cc_start: 0.9183 (t0) cc_final: 0.8871 (t0) REVERT: B 84 PHE cc_start: 0.8609 (t80) cc_final: 0.8237 (t80) REVERT: B 128 ASP cc_start: 0.9206 (m-30) cc_final: 0.8893 (m-30) REVERT: B 156 GLN cc_start: 0.9316 (mt0) cc_final: 0.8906 (mt0) REVERT: B 163 LYS cc_start: 0.9399 (tppp) cc_final: 0.9182 (tppp) REVERT: B 255 MET cc_start: 0.8559 (tmm) cc_final: 0.8150 (tmm) REVERT: B 266 LYS cc_start: 0.9001 (ptpt) cc_final: 0.8705 (ptpt) REVERT: B 291 PHE cc_start: 0.8782 (m-80) cc_final: 0.8545 (m-10) REVERT: B 347 GLU cc_start: 0.8863 (pp20) cc_final: 0.8376 (pp20) REVERT: B 387 MET cc_start: 0.9674 (mtp) cc_final: 0.9430 (mtp) REVERT: B 437 GLU cc_start: 0.7408 (pm20) cc_final: 0.7056 (tp30) REVERT: B 452 GLU cc_start: 0.9182 (pm20) cc_final: 0.8844 (pm20) REVERT: A 32 SER cc_start: 0.9244 (p) cc_final: 0.9042 (p) REVERT: A 107 GLU cc_start: 0.8944 (mm-30) cc_final: 0.8433 (mm-30) REVERT: A 127 PHE cc_start: 0.9310 (t80) cc_final: 0.8693 (t80) REVERT: A 128 ASP cc_start: 0.9135 (m-30) cc_final: 0.8342 (m-30) REVERT: A 151 ASP cc_start: 0.8911 (t0) cc_final: 0.8698 (t0) REVERT: A 153 LYS cc_start: 0.9252 (ptmm) cc_final: 0.8432 (ttpp) REVERT: A 244 ASP cc_start: 0.8083 (m-30) cc_final: 0.7806 (m-30) REVERT: A 255 MET cc_start: 0.8497 (ptt) cc_final: 0.7836 (ptt) REVERT: A 262 ASN cc_start: 0.8669 (p0) cc_final: 0.8177 (p0) REVERT: A 305 GLN cc_start: 0.9266 (mt0) cc_final: 0.9034 (mt0) REVERT: A 309 LYS cc_start: 0.9588 (mttp) cc_final: 0.9089 (mmmm) REVERT: A 320 ASN cc_start: 0.8193 (t0) cc_final: 0.7820 (t0) REVERT: A 330 PHE cc_start: 0.9488 (m-80) cc_final: 0.8855 (m-10) REVERT: A 331 VAL cc_start: 0.9823 (t) cc_final: 0.9611 (p) REVERT: A 338 ARG cc_start: 0.9067 (mtm-85) cc_final: 0.8680 (mtm-85) REVERT: A 372 GLN cc_start: 0.8408 (mt0) cc_final: 0.8070 (mp-120) REVERT: A 387 MET cc_start: 0.9279 (ptp) cc_final: 0.9014 (ptp) REVERT: A 402 GLN cc_start: 0.9138 (tp-100) cc_final: 0.8279 (tm-30) REVERT: A 451 LYS cc_start: 0.8612 (mttt) cc_final: 0.8405 (mtpt) REVERT: C 107 GLU cc_start: 0.8299 (tm-30) cc_final: 0.7820 (tp30) REVERT: C 150 MET cc_start: 0.8824 (mmm) cc_final: 0.8523 (mmm) REVERT: C 151 ASP cc_start: 0.7694 (p0) cc_final: 0.7302 (p0) REVERT: C 160 ILE cc_start: 0.9209 (mp) cc_final: 0.8989 (mp) REVERT: C 208 MET cc_start: 0.9146 (ptp) cc_final: 0.8378 (ptp) REVERT: C 209 ASP cc_start: 0.8944 (m-30) cc_final: 0.8707 (m-30) REVERT: C 229 CYS cc_start: 0.8178 (p) cc_final: 0.7974 (p) REVERT: C 236 LYS cc_start: 0.9482 (tttt) cc_final: 0.9150 (mmtt) REVERT: C 237 MET cc_start: 0.9485 (mmt) cc_final: 0.9154 (mmm) REVERT: C 248 PHE cc_start: 0.7075 (t80) cc_final: 0.6831 (t80) REVERT: C 296 SER cc_start: 0.7484 (p) cc_final: 0.6418 (t) REVERT: C 342 MET cc_start: 0.6666 (mmm) cc_final: 0.6396 (mmm) REVERT: C 347 GLU cc_start: 0.9266 (pm20) cc_final: 0.8733 (pp20) REVERT: C 376 GLN cc_start: 0.8644 (tt0) cc_final: 0.8172 (tm-30) REVERT: C 378 CYS cc_start: 0.7388 (m) cc_final: 0.5636 (m) REVERT: C 394 ASP cc_start: 0.9015 (t0) cc_final: 0.8583 (t70) REVERT: C 402 GLN cc_start: 0.9515 (mt0) cc_final: 0.9191 (mp10) REVERT: C 451 LYS cc_start: 0.9161 (mttt) cc_final: 0.8769 (mttm) REVERT: D 34 TYR cc_start: 0.9331 (m-80) cc_final: 0.9056 (m-10) REVERT: D 65 LYS cc_start: 0.9289 (tttt) cc_final: 0.8752 (tptm) REVERT: D 101 TRP cc_start: 0.8343 (m100) cc_final: 0.7838 (m100) REVERT: D 121 HIS cc_start: 0.9145 (t70) cc_final: 0.8929 (t70) REVERT: D 126 LYS cc_start: 0.9355 (tmtt) cc_final: 0.9130 (tmtt) REVERT: D 150 MET cc_start: 0.8893 (pmm) cc_final: 0.8542 (pmm) REVERT: D 156 GLN cc_start: 0.7817 (tt0) cc_final: 0.7098 (tt0) REVERT: D 196 GLU cc_start: 0.8633 (tt0) cc_final: 0.8200 (tp30) REVERT: D 229 CYS cc_start: 0.7650 (p) cc_final: 0.7175 (p) REVERT: D 231 TYR cc_start: 0.8852 (t80) cc_final: 0.7799 (t80) REVERT: D 234 TYR cc_start: 0.9233 (m-80) cc_final: 0.8593 (m-80) REVERT: D 242 TYR cc_start: 0.8241 (m-80) cc_final: 0.8008 (m-80) REVERT: D 255 MET cc_start: 0.8887 (ptm) cc_final: 0.8362 (ppp) REVERT: D 269 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8108 (mp0) REVERT: D 306 LEU cc_start: 0.9620 (mm) cc_final: 0.9101 (mm) REVERT: D 315 ARG cc_start: 0.9153 (mtp-110) cc_final: 0.8933 (mtp85) REVERT: D 321 ASN cc_start: 0.9440 (t0) cc_final: 0.9220 (t0) REVERT: D 338 ARG cc_start: 0.9372 (mtt90) cc_final: 0.8942 (tpp80) REVERT: D 368 GLU cc_start: 0.8529 (tt0) cc_final: 0.8313 (tt0) REVERT: D 369 TYR cc_start: 0.9035 (m-80) cc_final: 0.8612 (m-10) REVERT: D 396 ASN cc_start: 0.8844 (p0) cc_final: 0.8545 (p0) REVERT: D 443 TYR cc_start: 0.9446 (m-80) cc_final: 0.9127 (m-80) REVERT: D 470 GLN cc_start: 0.8980 (tp-100) cc_final: 0.8718 (tt0) REVERT: E 107 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8490 (mm-30) REVERT: E 193 SER cc_start: 0.9313 (t) cc_final: 0.9063 (p) REVERT: E 200 MET cc_start: 0.9380 (mmm) cc_final: 0.8441 (tpp) REVERT: E 222 ILE cc_start: 0.9464 (mm) cc_final: 0.9222 (pt) REVERT: E 234 TYR cc_start: 0.9453 (m-80) cc_final: 0.9055 (m-10) REVERT: E 237 MET cc_start: 0.9075 (mmt) cc_final: 0.8604 (mmm) REVERT: E 251 ARG cc_start: 0.9232 (ptt90) cc_final: 0.8794 (ptt90) REVERT: E 253 GLU cc_start: 0.9142 (pm20) cc_final: 0.8750 (pm20) REVERT: E 314 GLN cc_start: 0.9293 (mt0) cc_final: 0.8667 (pm20) REVERT: E 324 CYS cc_start: 0.9174 (p) cc_final: 0.8875 (p) REVERT: E 338 ARG cc_start: 0.9347 (mtt-85) cc_final: 0.8821 (mtp85) REVERT: E 400 ASP cc_start: 0.8809 (p0) cc_final: 0.8493 (p0) REVERT: E 417 TYR cc_start: 0.8673 (m-80) cc_final: 0.8448 (m-80) outliers start: 1 outliers final: 0 residues processed: 612 average time/residue: 0.3120 time to fit residues: 303.5474 Evaluate side-chains 497 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 497 time to evaluate : 2.841 ------------------------------------------------------------------------------- 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: 0.4980 chunk 159 optimal weight: 0.9980 chunk 123 optimal weight: 0.9980 chunk 181 optimal weight: 10.0000 chunk 273 optimal weight: 0.1980 chunk 252 optimal weight: 9.9990 chunk 218 optimal weight: 8.9990 chunk 22 optimal weight: 50.0000 chunk 168 optimal weight: 9.9990 chunk 133 optimal weight: 8.9990 chunk 173 optimal weight: 3.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- 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 52 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 139 GLN ** 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 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 GLN ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 GLN ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** 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 82 ASN D 192 ASN ** D 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN ** E 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 259 HIS ** E 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 22431 Z= 0.164 Angle : 0.622 9.655 30515 Z= 0.307 Chirality : 0.045 0.180 3307 Planarity : 0.005 0.070 3973 Dihedral : 4.979 61.065 2998 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.42 % Favored : 93.54 % Rotamer: Outliers : 0.08 % Allowed : 0.24 % Favored : 99.67 % 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: -2.33 (0.15), residues: 2755 helix: -1.03 (0.35), residues: 200 sheet: -0.82 (0.19), residues: 684 loop : -2.01 (0.14), residues: 1871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP D 401 HIS 0.010 0.001 HIS E 259 PHE 0.013 0.001 PHE C 256 TYR 0.015 0.001 TYR C 389 ARG 0.006 0.000 ARG D 315 ********************** 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 668 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 666 time to evaluate : 2.558 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: L 21 MET cc_start: 0.4749 (mmp) cc_final: 0.4404 (mmt) REVERT: H 36 VAL cc_start: 0.5818 (m) cc_final: 0.5134 (t) REVERT: B 20 LYS cc_start: 0.9314 (pttp) cc_final: 0.9073 (ptpp) REVERT: B 35 TYR cc_start: 0.9276 (m-80) cc_final: 0.8756 (m-80) REVERT: B 70 GLN cc_start: 0.9081 (mt0) cc_final: 0.8693 (mt0) REVERT: B 71 TYR cc_start: 0.8959 (m-80) cc_final: 0.8596 (m-10) REVERT: B 80 ASP cc_start: 0.9140 (t0) cc_final: 0.8872 (t0) REVERT: B 128 ASP cc_start: 0.9187 (m-30) cc_final: 0.8867 (m-30) REVERT: B 156 GLN cc_start: 0.9328 (mt0) cc_final: 0.8952 (mt0) REVERT: B 163 LYS cc_start: 0.9383 (tppp) cc_final: 0.9146 (tppp) REVERT: B 255 MET cc_start: 0.8600 (tmm) cc_final: 0.8103 (tmm) REVERT: B 266 LYS cc_start: 0.9031 (ptpt) cc_final: 0.8749 (ptpt) REVERT: B 291 PHE cc_start: 0.8753 (m-80) cc_final: 0.8537 (m-10) REVERT: B 347 GLU cc_start: 0.8827 (pp20) cc_final: 0.8325 (pp20) REVERT: B 387 MET cc_start: 0.9663 (mtp) cc_final: 0.9067 (mtt) REVERT: B 437 GLU cc_start: 0.7358 (pm20) cc_final: 0.7016 (tp30) REVERT: B 452 GLU cc_start: 0.9275 (pm20) cc_final: 0.8977 (pm20) REVERT: A 127 PHE cc_start: 0.9262 (t80) cc_final: 0.8756 (t80) REVERT: A 128 ASP cc_start: 0.9094 (m-30) cc_final: 0.8338 (m-30) REVERT: A 151 ASP cc_start: 0.9207 (t0) cc_final: 0.8648 (t0) REVERT: A 153 LYS cc_start: 0.9134 (ptmm) cc_final: 0.8404 (ttpp) REVERT: A 169 HIS cc_start: 0.9370 (p-80) cc_final: 0.8849 (p-80) REVERT: A 244 ASP cc_start: 0.8059 (m-30) cc_final: 0.7758 (m-30) REVERT: A 255 MET cc_start: 0.8259 (ptt) cc_final: 0.7679 (ptt) REVERT: A 305 GLN cc_start: 0.9215 (mt0) cc_final: 0.8993 (mt0) REVERT: A 309 LYS cc_start: 0.9626 (mttp) cc_final: 0.9111 (mmmm) REVERT: A 320 ASN cc_start: 0.8130 (t0) cc_final: 0.7753 (t0) REVERT: A 330 PHE cc_start: 0.9359 (m-80) cc_final: 0.8743 (m-10) REVERT: A 331 VAL cc_start: 0.9814 (t) cc_final: 0.9609 (p) REVERT: A 387 MET cc_start: 0.9259 (ptp) cc_final: 0.9033 (ptp) REVERT: A 402 GLN cc_start: 0.9076 (tp-100) cc_final: 0.8744 (tp-100) REVERT: A 451 LYS cc_start: 0.8603 (mttt) cc_final: 0.8338 (mtpt) REVERT: C 107 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7723 (tp30) REVERT: C 159 LEU cc_start: 0.9376 (mm) cc_final: 0.9159 (mm) REVERT: C 160 ILE cc_start: 0.9116 (mp) cc_final: 0.8880 (mp) REVERT: C 208 MET cc_start: 0.9177 (ptp) cc_final: 0.8506 (ptp) REVERT: C 209 ASP cc_start: 0.8982 (m-30) cc_final: 0.8742 (m-30) REVERT: C 236 LYS cc_start: 0.9433 (tttt) cc_final: 0.9088 (mmtt) REVERT: C 248 PHE cc_start: 0.7097 (t80) cc_final: 0.6876 (t80) REVERT: C 296 SER cc_start: 0.7326 (p) cc_final: 0.5942 (t) REVERT: C 342 MET cc_start: 0.6603 (mmm) cc_final: 0.6391 (mmm) REVERT: C 347 GLU cc_start: 0.9190 (pm20) cc_final: 0.8662 (pp20) REVERT: C 376 GLN cc_start: 0.8617 (tt0) cc_final: 0.8161 (tm-30) REVERT: C 378 CYS cc_start: 0.7436 (m) cc_final: 0.5950 (m) REVERT: C 385 GLU cc_start: 0.9455 (pm20) cc_final: 0.9216 (pm20) REVERT: C 387 MET cc_start: 0.9419 (mtm) cc_final: 0.9175 (mtt) REVERT: C 394 ASP cc_start: 0.9007 (t0) cc_final: 0.8563 (t70) REVERT: C 400 ASP cc_start: 0.9231 (p0) cc_final: 0.8715 (p0) REVERT: C 402 GLN cc_start: 0.9451 (mt0) cc_final: 0.9137 (mp10) REVERT: C 451 LYS cc_start: 0.9090 (mttt) cc_final: 0.8748 (mttm) REVERT: D 34 TYR cc_start: 0.9334 (m-80) cc_final: 0.9071 (m-10) REVERT: D 65 LYS cc_start: 0.9316 (tttt) cc_final: 0.8921 (tttm) REVERT: D 101 TRP cc_start: 0.8332 (m100) cc_final: 0.7813 (m100) REVERT: D 121 HIS cc_start: 0.9132 (t70) cc_final: 0.8921 (t70) REVERT: D 126 LYS cc_start: 0.9344 (tmtt) cc_final: 0.8972 (tmtt) REVERT: D 146 GLU cc_start: 0.9536 (pt0) cc_final: 0.9307 (pt0) REVERT: D 150 MET cc_start: 0.8918 (pmm) cc_final: 0.8455 (pmm) REVERT: D 156 GLN cc_start: 0.7592 (tt0) cc_final: 0.7256 (tt0) REVERT: D 176 CYS cc_start: 0.7656 (p) cc_final: 0.7200 (p) REVERT: D 189 GLU cc_start: 0.9152 (tp30) cc_final: 0.8730 (mp0) REVERT: D 196 GLU cc_start: 0.8472 (tt0) cc_final: 0.8094 (tp30) REVERT: D 229 CYS cc_start: 0.7514 (p) cc_final: 0.7077 (p) REVERT: D 231 TYR cc_start: 0.8922 (t80) cc_final: 0.7875 (t80) REVERT: D 234 TYR cc_start: 0.9216 (m-80) cc_final: 0.8672 (m-80) REVERT: D 240 GLU cc_start: 0.8877 (tm-30) cc_final: 0.8296 (tm-30) REVERT: D 242 TYR cc_start: 0.8251 (m-80) cc_final: 0.7930 (m-80) REVERT: D 247 PHE cc_start: 0.8932 (m-10) cc_final: 0.8317 (m-80) REVERT: D 255 MET cc_start: 0.8823 (ptm) cc_final: 0.8327 (ppp) REVERT: D 269 GLU cc_start: 0.8527 (mm-30) cc_final: 0.7993 (mp0) REVERT: D 306 LEU cc_start: 0.9598 (mm) cc_final: 0.9143 (mm) REVERT: D 315 ARG cc_start: 0.9125 (mtp-110) cc_final: 0.8895 (mtp85) REVERT: D 321 ASN cc_start: 0.9439 (t0) cc_final: 0.9126 (t0) REVERT: D 338 ARG cc_start: 0.9133 (mtt90) cc_final: 0.8911 (tpp80) REVERT: D 362 TYR cc_start: 0.9207 (m-10) cc_final: 0.8935 (m-10) REVERT: D 369 TYR cc_start: 0.9063 (m-80) cc_final: 0.8574 (m-10) REVERT: D 399 GLU cc_start: 0.8917 (pp20) cc_final: 0.8669 (pp20) REVERT: D 400 ASP cc_start: 0.8594 (m-30) cc_final: 0.8092 (m-30) REVERT: D 452 GLU cc_start: 0.4043 (mm-30) cc_final: 0.3566 (tt0) REVERT: D 470 GLN cc_start: 0.8994 (tp-100) cc_final: 0.8759 (tt0) REVERT: E 107 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8550 (mm-30) REVERT: E 193 SER cc_start: 0.9291 (t) cc_final: 0.9038 (p) REVERT: E 200 MET cc_start: 0.9264 (mmm) cc_final: 0.8645 (tpp) REVERT: E 208 MET cc_start: 0.8783 (ppp) cc_final: 0.8276 (ppp) REVERT: E 229 CYS cc_start: 0.7704 (p) cc_final: 0.7335 (p) REVERT: E 234 TYR cc_start: 0.9423 (m-80) cc_final: 0.9001 (m-10) REVERT: E 237 MET cc_start: 0.9057 (mmt) cc_final: 0.8618 (mmm) REVERT: E 251 ARG cc_start: 0.9216 (ptt90) cc_final: 0.8762 (ptt90) REVERT: E 253 GLU cc_start: 0.9056 (pm20) cc_final: 0.8682 (pm20) REVERT: E 305 GLN cc_start: 0.9076 (tp40) cc_final: 0.8546 (tp-100) REVERT: E 314 GLN cc_start: 0.9273 (mt0) cc_final: 0.8667 (pm20) REVERT: E 324 CYS cc_start: 0.9209 (p) cc_final: 0.8976 (p) REVERT: E 338 ARG cc_start: 0.9310 (mtt-85) cc_final: 0.8853 (mtp85) REVERT: E 342 MET cc_start: 0.9175 (mmm) cc_final: 0.8810 (mmm) REVERT: E 400 ASP cc_start: 0.8821 (p0) cc_final: 0.8590 (p0) REVERT: E 416 THR cc_start: 0.8457 (t) cc_final: 0.7697 (t) outliers start: 2 outliers final: 0 residues processed: 668 average time/residue: 0.2943 time to fit residues: 311.9910 Evaluate side-chains 532 residues out of total 2453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 532 time to evaluate : 2.551 ------------------------------------------------------------------------------- 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: 10.0000 chunk 66 optimal weight: 9.9990 chunk 201 optimal weight: 9.9990 chunk 32 optimal weight: 40.0000 chunk 60 optimal weight: 20.0000 chunk 218 optimal weight: 6.9990 chunk 91 optimal weight: 8.9990 chunk 224 optimal weight: 6.9990 chunk 27 optimal weight: 50.0000 chunk 40 optimal weight: 9.9990 chunk 191 optimal weight: 0.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 GLN ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 470 GLN ** C 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 ASN ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 192 ASN ** D 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 402 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.136774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.093677 restraints weight = 56928.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.096620 restraints weight = 29353.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.098521 restraints weight = 18939.596| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.105 22431 Z= 0.374 Angle : 0.701 11.600 30515 Z= 0.358 Chirality : 0.046 0.182 3307 Planarity : 0.006 0.072 3973 Dihedral : 5.410 60.069 2998 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 18.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.40 % Favored : 90.60 % Rotamer: Outliers : 0.08 % Allowed : 0.53 % Favored : 99.39 % 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: -2.48 (0.15), residues: 2755 helix: -0.88 (0.37), residues: 199 sheet: -0.94 (0.19), residues: 704 loop : -2.15 (0.14), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP D 401 HIS 0.012 0.002 HIS E 259 PHE 0.019 0.002 PHE A 359 TYR 0.021 0.002 TYR A 71 ARG 0.011 0.001 ARG B 110 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6016.89 seconds wall clock time: 109 minutes 7.49 seconds (6547.49 seconds total)