Starting phenix.real_space_refine on Tue Feb 20 10:25:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6voo_21271/02_2024/6voo_21271_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6voo_21271/02_2024/6voo_21271.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6voo_21271/02_2024/6voo_21271.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6voo_21271/02_2024/6voo_21271.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6voo_21271/02_2024/6voo_21271_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6voo_21271/02_2024/6voo_21271_updated.pdb" } resolution = 3.05 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= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 104 5.16 5 C 17295 2.51 5 N 4754 2.21 5 O 5382 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 14": "NH1" <-> "NH2" Residue "A GLU 18": "OE1" <-> "OE2" Residue "A GLU 52": "OE1" <-> "OE2" Residue "A GLU 68": "OE1" <-> "OE2" Residue "A GLU 102": "OE1" <-> "OE2" Residue "A TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 121": "OE1" <-> "OE2" Residue "A GLU 126": "OE1" <-> "OE2" Residue "A GLU 131": "OE1" <-> "OE2" Residue "A ARG 140": "NH1" <-> "NH2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A ARG 216": "NH1" <-> "NH2" Residue "A TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 254": "OE1" <-> "OE2" Residue "A ARG 255": "NH1" <-> "NH2" Residue "A GLU 285": "OE1" <-> "OE2" Residue "A GLU 300": "OE1" <-> "OE2" Residue "A GLU 321": "OE1" <-> "OE2" Residue "A ARG 366": "NH1" <-> "NH2" Residue "A GLU 392": "OE1" <-> "OE2" Residue "A PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 413": "NH1" <-> "NH2" Residue "A GLU 419": "OE1" <-> "OE2" Residue "A ASP 447": "OD1" <-> "OD2" Residue "A GLU 460": "OE1" <-> "OE2" Residue "A GLU 474": "OE1" <-> "OE2" Residue "A GLU 484": "OE1" <-> "OE2" Residue "A GLU 496": "OE1" <-> "OE2" Residue "B ASP 7": "OD1" <-> "OD2" Residue "B ARG 14": "NH1" <-> "NH2" Residue "B ARG 22": "NH1" <-> "NH2" Residue "B GLU 68": "OE1" <-> "OE2" Residue "B ASP 79": "OD1" <-> "OD2" Residue "B GLU 102": "OE1" <-> "OE2" Residue "B TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 126": "OE1" <-> "OE2" Residue "B ARG 172": "NH1" <-> "NH2" Residue "B ARG 216": "NH1" <-> "NH2" Residue "B GLU 248": "OE1" <-> "OE2" Residue "B PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 263": "OD1" <-> "OD2" Residue "B ARG 297": "NH1" <-> "NH2" Residue "B ASP 326": "OD1" <-> "OD2" Residue "B ASP 348": "OD1" <-> "OD2" Residue "B GLU 386": "OE1" <-> "OE2" Residue "B GLU 394": "OE1" <-> "OE2" Residue "B PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 402": "OD1" <-> "OD2" Residue "B GLU 450": "OE1" <-> "OE2" Residue "B ARG 455": "NH1" <-> "NH2" Residue "B GLU 460": "OE1" <-> "OE2" Residue "B GLU 471": "OE1" <-> "OE2" Residue "B GLU 484": "OE1" <-> "OE2" Residue "B GLU 496": "OE1" <-> "OE2" Residue "C GLU 15": "OE1" <-> "OE2" Residue "C TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 22": "NH1" <-> "NH2" Residue "C GLU 23": "OE1" <-> "OE2" Residue "C ASP 37": "OD1" <-> "OD2" Residue "C GLU 47": "OE1" <-> "OE2" Residue "C ARG 94": "NH1" <-> "NH2" Residue "C GLU 102": "OE1" <-> "OE2" Residue "C GLU 126": "OE1" <-> "OE2" Residue "C ARG 141": "NH1" <-> "NH2" Residue "C GLU 166": "OE1" <-> "OE2" Residue "C TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 285": "OE1" <-> "OE2" Residue "C PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 301": "NH1" <-> "NH2" Residue "C ASP 326": "OD1" <-> "OD2" Residue "C GLU 386": "OE1" <-> "OE2" Residue "C ASP 404": "OD1" <-> "OD2" Residue "C ARG 416": "NH1" <-> "NH2" Residue "C ASP 447": "OD1" <-> "OD2" Residue "C GLU 450": "OE1" <-> "OE2" Residue "C ARG 462": "NH1" <-> "NH2" Residue "C GLU 487": "OE1" <-> "OE2" Residue "D PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 163": "NH1" <-> "NH2" Residue "D GLU 184": "OE1" <-> "OE2" Residue "D PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 229": "OE1" <-> "OE2" Residue "D GLU 284": "OE1" <-> "OE2" Residue "D GLU 305": "OE1" <-> "OE2" Residue "D ASP 366": "OD1" <-> "OD2" Residue "D GLU 383": "OE1" <-> "OE2" Residue "D GLU 393": "OE1" <-> "OE2" Residue "D ARG 397": "NH1" <-> "NH2" Residue "D GLU 412": "OE1" <-> "OE2" Residue "D GLU 416": "OE1" <-> "OE2" Residue "D GLU 439": "OE1" <-> "OE2" Residue "D GLU 465": "OE1" <-> "OE2" Residue "D GLU 482": "OE1" <-> "OE2" Residue "D GLU 493": "OE1" <-> "OE2" Residue "E ARG 52": "NH1" <-> "NH2" Residue "E GLU 90": "OE1" <-> "OE2" Residue "E GLU 218": "OE1" <-> "OE2" Residue "E GLU 241": "OE1" <-> "OE2" Residue "E ARG 246": "NH1" <-> "NH2" Residue "E GLU 318": "OE1" <-> "OE2" Residue "E ASP 332": "OD1" <-> "OD2" Residue "E ASP 347": "OD1" <-> "OD2" Residue "E GLU 400": "OE1" <-> "OE2" Residue "E ASP 403": "OD1" <-> "OD2" Residue "E GLU 416": "OE1" <-> "OE2" Residue "E ARG 423": "NH1" <-> "NH2" Residue "E PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 52": "NH1" <-> "NH2" Residue "F GLU 90": "OE1" <-> "OE2" Residue "F GLU 204": "OE1" <-> "OE2" Residue "F GLU 208": "OE1" <-> "OE2" Residue "F GLU 215": "OE1" <-> "OE2" Residue "F GLU 258": "OE1" <-> "OE2" Residue "F GLU 318": "OE1" <-> "OE2" Residue "F ASP 332": "OD1" <-> "OD2" Residue "F GLU 382": "OE1" <-> "OE2" Residue "F GLU 383": "OE1" <-> "OE2" Residue "F GLU 386": "OE1" <-> "OE2" Residue "F GLU 393": "OE1" <-> "OE2" Residue "F GLU 412": "OE1" <-> "OE2" Residue "F GLU 415": "OE1" <-> "OE2" Residue "F GLU 416": "OE1" <-> "OE2" Residue "F ARG 425": "NH1" <-> "NH2" Residue "F GLU 428": "OE1" <-> "OE2" Residue "F GLU 465": "OE1" <-> "OE2" Residue "F ASP 481": "OD1" <-> "OD2" Residue "d ARG 77": "NH1" <-> "NH2" Residue "d GLU 93": "OE1" <-> "OE2" Residue "d GLU 108": "OE1" <-> "OE2" Residue "d GLU 131": "OE1" <-> "OE2" Residue "d ASP 151": "OD1" <-> "OD2" Residue "d GLU 176": "OE1" <-> "OE2" Residue "d ARG 208": "NH1" <-> "NH2" Residue "d ASP 214": "OD1" <-> "OD2" Residue "d PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 234": "OD1" <-> "OD2" Residue "d GLU 249": "OE1" <-> "OE2" Residue "g ARG 48": "NH1" <-> "NH2" Residue "g ARG 73": "NH1" <-> "NH2" Residue "g GLU 77": "OE1" <-> "OE2" Residue "g ARG 83": "NH1" <-> "NH2" Residue "g PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 98": "OE1" <-> "OE2" Residue "g GLU 103": "OE1" <-> "OE2" Residue "g ASP 104": "OD1" <-> "OD2" Residue "g ASP 106": "OD1" <-> "OD2" Residue "g ARG 127": "NH1" <-> "NH2" Residue "g ARG 144": "NH1" <-> "NH2" Residue "g TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 170": "NH1" <-> "NH2" Residue "g ASP 181": "OD1" <-> "OD2" Residue "g GLU 190": "OE1" <-> "OE2" Residue "g ASP 196": "OD1" <-> "OD2" Residue "g GLU 238": "OE1" <-> "OE2" Residue "g ASP 241": "OD1" <-> "OD2" Residue "g GLU 261": "OE1" <-> "OE2" Residue "g GLU 285": "OE1" <-> "OE2" Residue "g ASP 293": "OD1" <-> "OD2" Residue "g ARG 306": "NH1" <-> "NH2" Residue "g GLU 315": "OE1" <-> "OE2" Residue "g GLU 332": "OE1" <-> "OE2" Residue "g GLU 352": "OE1" <-> "OE2" Residue "e ARG 12": "NH1" <-> "NH2" Residue "e GLU 21": "OE1" <-> "OE2" Residue "e ARG 50": "NH1" <-> "NH2" Residue "e ARG 68": "NH1" <-> "NH2" Residue "e GLU 73": "OE1" <-> "OE2" Residue "e ARG 104": "NH1" <-> "NH2" Residue "e ARG 120": "NH1" <-> "NH2" Residue "e ARG 123": "NH1" <-> "NH2" Residue "e ARG 125": "NH1" <-> "NH2" Residue "e GLU 127": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 27551 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3850 Classifications: {'peptide': 501} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 483} Chain: "B" Number of atoms: 3854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 3854 Classifications: {'peptide': 502} Link IDs: {'PTRANS': 17, 'TRANS': 484} Chain: "C" Number of atoms: 3843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3843 Classifications: {'peptide': 500} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 482} Chain: "D" Number of atoms: 3619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3619 Classifications: {'peptide': 478} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 452} Chain: "E" Number of atoms: 3645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3645 Classifications: {'peptide': 481} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 455} Chain: "F" Number of atoms: 3636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3636 Classifications: {'peptide': 480} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 454} Chain: "d" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1384 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 4, 'TRANS': 174} Chain: "g" Number of atoms: 2502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2502 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 12, 'TRANS': 309} Chain: "e" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1010 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'ATP': 1, 'TTX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 15.04, per 1000 atoms: 0.55 Number of scatterers: 27551 At special positions: 0 Unit cell: (171.639, 137.943, 131.625, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 104 16.00 P 16 15.00 O 5382 8.00 N 4754 7.00 C 17295 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.33 Conformation dependent library (CDL) restraints added in 5.3 seconds 7112 Ramachandran restraints generated. 3556 Oldfield, 0 Emsley, 3556 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6570 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 124 helices and 25 sheets defined 40.6% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.25 Creating SS restraints... Processing helix chain 'A' and resid 11 through 23 removed outlier: 3.825A pdb=" N GLU A 23 " --> pdb=" O GLY A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 157 removed outlier: 3.873A pdb=" N MET A 157 " --> pdb=" O ALA A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 187 removed outlier: 3.837A pdb=" N GLN A 187 " --> pdb=" O THR A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 215 Processing helix chain 'A' and resid 233 through 252 Proline residue: A 240 - end of helix removed outlier: 3.874A pdb=" N PHE A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 277 Processing helix chain 'A' and resid 284 through 286 No H-bonds generated for 'chain 'A' and resid 284 through 286' Processing helix chain 'A' and resid 289 through 301 removed outlier: 4.345A pdb=" N PHE A 292 " --> pdb=" O GLY A 289 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N TYR A 293 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ARG A 297 " --> pdb=" O LEU A 294 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLU A 300 " --> pdb=" O ARG A 297 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG A 301 " --> pdb=" O LEU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 338 removed outlier: 3.851A pdb=" N SER A 337 " --> pdb=" O THR A 333 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE A 338 " --> pdb=" O ASN A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 352 Processing helix chain 'A' and resid 368 through 371 Processing helix chain 'A' and resid 374 through 379 Processing helix chain 'A' and resid 383 through 396 Processing helix chain 'A' and resid 405 through 420 Processing helix chain 'A' and resid 431 through 442 Processing helix chain 'A' and resid 454 through 467 Processing helix chain 'A' and resid 471 through 478 Processing helix chain 'A' and resid 484 through 504 Processing helix chain 'B' and resid 10 through 18 Processing helix chain 'B' and resid 152 through 157 Processing helix chain 'B' and resid 177 through 185 Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 233 through 253 Proline residue: B 240 - end of helix removed outlier: 3.880A pdb=" N PHE B 250 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG B 253 " --> pdb=" O TYR B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 277 Processing helix chain 'B' and resid 284 through 286 No H-bonds generated for 'chain 'B' and resid 284 through 286' Processing helix chain 'B' and resid 291 through 301 removed outlier: 3.903A pdb=" N LEU B 298 " --> pdb=" O LEU B 294 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ARG B 301 " --> pdb=" O ARG B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 309 No H-bonds generated for 'chain 'B' and resid 307 through 309' Processing helix chain 'B' and resid 330 through 338 Processing helix chain 'B' and resid 347 through 351 Processing helix chain 'B' and resid 360 through 362 No H-bonds generated for 'chain 'B' and resid 360 through 362' Processing helix chain 'B' and resid 368 through 370 No H-bonds generated for 'chain 'B' and resid 368 through 370' Processing helix chain 'B' and resid 374 through 396 removed outlier: 4.913A pdb=" N LYS B 382 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU B 383 " --> pdb=" O VAL B 379 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU B 392 " --> pdb=" O ALA B 388 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA B 395 " --> pdb=" O ALA B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 409 removed outlier: 3.552A pdb=" N THR B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 421 removed outlier: 3.823A pdb=" N GLU B 419 " --> pdb=" O GLN B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 442 Processing helix chain 'B' and resid 454 through 468 Processing helix chain 'B' and resid 470 through 479 removed outlier: 3.678A pdb=" N THR B 479 " --> pdb=" O ILE B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 502 Processing helix chain 'C' and resid 7 through 19 Processing helix chain 'C' and resid 102 through 104 No H-bonds generated for 'chain 'C' and resid 102 through 104' Processing helix chain 'C' and resid 152 through 157 Processing helix chain 'C' and resid 176 through 188 removed outlier: 4.388A pdb=" N GLN C 188 " --> pdb=" O ILE C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 Processing helix chain 'C' and resid 233 through 252 Proline residue: C 240 - end of helix Processing helix chain 'C' and resid 264 through 277 Processing helix chain 'C' and resid 284 through 286 No H-bonds generated for 'chain 'C' and resid 284 through 286' Processing helix chain 'C' and resid 291 through 301 removed outlier: 3.609A pdb=" N LEU C 298 " --> pdb=" O LEU C 294 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ARG C 301 " --> pdb=" O ARG C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 338 Processing helix chain 'C' and resid 347 through 351 Processing helix chain 'C' and resid 368 through 371 Processing helix chain 'C' and resid 374 through 399 removed outlier: 3.955A pdb=" N LYS C 378 " --> pdb=" O LYS C 374 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N VAL C 379 " --> pdb=" O ALA C 375 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LYS C 382 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ALA C 395 " --> pdb=" O ALA C 391 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N PHE C 396 " --> pdb=" O GLU C 392 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA C 397 " --> pdb=" O LEU C 393 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N GLN C 398 " --> pdb=" O GLU C 394 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N PHE C 399 " --> pdb=" O ALA C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 417 Processing helix chain 'C' and resid 431 through 443 Processing helix chain 'C' and resid 454 through 468 Processing helix chain 'C' and resid 470 through 478 Processing helix chain 'C' and resid 484 through 502 Processing helix chain 'D' and resid 104 through 106 No H-bonds generated for 'chain 'D' and resid 104 through 106' Processing helix chain 'D' and resid 154 through 159 Processing helix chain 'D' and resid 178 through 189 Processing helix chain 'D' and resid 206 through 219 Processing helix chain 'D' and resid 243 through 262 removed outlier: 3.740A pdb=" N ARG D 248 " --> pdb=" O GLY D 244 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N GLY D 250 " --> pdb=" O ARG D 246 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N LEU D 251 " --> pdb=" O MET D 247 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE D 260 " --> pdb=" O MET D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 288 removed outlier: 3.850A pdb=" N LEU D 288 " --> pdb=" O GLU D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 310 removed outlier: 3.598A pdb=" N LEU D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 332 No H-bonds generated for 'chain 'D' and resid 330 through 332' Processing helix chain 'D' and resid 337 through 345 removed outlier: 4.544A pdb=" N ALA D 344 " --> pdb=" O ALA D 340 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N HIS D 345 " --> pdb=" O THR D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 358 Processing helix chain 'D' and resid 382 through 407 removed outlier: 4.861A pdb=" N ASP D 403 " --> pdb=" O LYS D 399 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ILE D 404 " --> pdb=" O GLU D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 412 No H-bonds generated for 'chain 'D' and resid 410 through 412' Processing helix chain 'D' and resid 415 through 430 Processing helix chain 'D' and resid 439 through 442 No H-bonds generated for 'chain 'D' and resid 439 through 442' Processing helix chain 'D' and resid 451 through 462 Processing helix chain 'D' and resid 471 through 473 No H-bonds generated for 'chain 'D' and resid 471 through 473' Processing helix chain 'D' and resid 481 through 493 Processing helix chain 'E' and resid 154 through 159 Processing helix chain 'E' and resid 179 through 192 Processing helix chain 'E' and resid 206 through 218 Processing helix chain 'E' and resid 243 through 262 removed outlier: 5.359A pdb=" N GLY E 250 " --> pdb=" O ARG E 246 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N LEU E 251 " --> pdb=" O MET E 247 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE E 260 " --> pdb=" O MET E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 289 Processing helix chain 'E' and resid 302 through 312 removed outlier: 3.681A pdb=" N LEU E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ARG E 312 " --> pdb=" O SER E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 332 No H-bonds generated for 'chain 'E' and resid 330 through 332' Processing helix chain 'E' and resid 337 through 342 Processing helix chain 'E' and resid 354 through 358 Processing helix chain 'E' and resid 377 through 380 No H-bonds generated for 'chain 'E' and resid 377 through 380' Processing helix chain 'E' and resid 382 through 407 removed outlier: 5.098A pdb=" N ASP E 403 " --> pdb=" O LYS E 399 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ILE E 404 " --> pdb=" O GLU E 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 410 through 412 No H-bonds generated for 'chain 'E' and resid 410 through 412' Processing helix chain 'E' and resid 415 through 430 Processing helix chain 'E' and resid 438 through 442 removed outlier: 3.592A pdb=" N THR E 442 " --> pdb=" O GLU E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 451 through 462 Processing helix chain 'E' and resid 481 through 495 removed outlier: 3.731A pdb=" N SER E 494 " --> pdb=" O LEU E 490 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 106 No H-bonds generated for 'chain 'F' and resid 104 through 106' Processing helix chain 'F' and resid 154 through 158 Processing helix chain 'F' and resid 179 through 189 Processing helix chain 'F' and resid 206 through 218 Processing helix chain 'F' and resid 227 through 229 No H-bonds generated for 'chain 'F' and resid 227 through 229' Processing helix chain 'F' and resid 243 through 246 No H-bonds generated for 'chain 'F' and resid 243 through 246' Processing helix chain 'F' and resid 249 through 262 removed outlier: 3.508A pdb=" N PHE F 260 " --> pdb=" O MET F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 288 removed outlier: 3.730A pdb=" N GLY F 282 " --> pdb=" O PHE F 278 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALA F 287 " --> pdb=" O SER F 283 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N LEU F 288 " --> pdb=" O GLU F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 312 removed outlier: 3.789A pdb=" N LEU F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 332 No H-bonds generated for 'chain 'F' and resid 330 through 332' Processing helix chain 'F' and resid 337 through 343 Processing helix chain 'F' and resid 354 through 357 No H-bonds generated for 'chain 'F' and resid 354 through 357' Processing helix chain 'F' and resid 377 through 380 No H-bonds generated for 'chain 'F' and resid 377 through 380' Processing helix chain 'F' and resid 382 through 400 Processing helix chain 'F' and resid 402 through 406 Processing helix chain 'F' and resid 415 through 431 removed outlier: 3.542A pdb=" N LEU F 419 " --> pdb=" O GLU F 415 " (cutoff:3.500A) Processing helix chain 'F' and resid 451 through 463 Processing helix chain 'F' and resid 471 through 474 Processing helix chain 'F' and resid 480 through 495 Processing helix chain 'd' and resid 74 through 88 Processing helix chain 'd' and resid 92 through 106 removed outlier: 3.711A pdb=" N ARG d 104 " --> pdb=" O GLU d 100 " (cutoff:3.500A) Processing helix chain 'd' and resid 109 through 115 Processing helix chain 'd' and resid 122 through 136 removed outlier: 3.531A pdb=" N VAL d 128 " --> pdb=" O ASN d 124 " (cutoff:3.500A) Processing helix chain 'd' and resid 142 through 151 Processing helix chain 'd' and resid 155 through 172 removed outlier: 5.148A pdb=" N LYS d 159 " --> pdb=" O ASN d 156 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE d 165 " --> pdb=" O LEU d 162 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLU d 166 " --> pdb=" O ASN d 163 " (cutoff:3.500A) Processing helix chain 'd' and resid 189 through 200 Processing helix chain 'd' and resid 238 through 248 Processing helix chain 'g' and resid 43 through 98 Proline residue: g 84 - end of helix Processing helix chain 'g' and resid 133 through 151 removed outlier: 3.945A pdb=" N LYS g 150 " --> pdb=" O ALA g 146 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU g 151 " --> pdb=" O GLU g 147 " (cutoff:3.500A) Processing helix chain 'g' and resid 162 through 170 Processing helix chain 'g' and resid 189 through 203 Processing helix chain 'g' and resid 247 through 250 removed outlier: 3.575A pdb=" N ALA g 250 " --> pdb=" O VAL g 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 247 through 250' Processing helix chain 'g' and resid 288 through 362 removed outlier: 3.841A pdb=" N LEU g 292 " --> pdb=" O PRO g 288 " (cutoff:3.500A) Proline residue: g 297 - end of helix Processing helix chain 'e' and resid 89 through 105 removed outlier: 4.030A pdb=" N ILE e 98 " --> pdb=" O GLN e 94 " (cutoff:3.500A) Processing helix chain 'e' and resid 109 through 129 removed outlier: 3.605A pdb=" N ILE e 113 " --> pdb=" O LYS e 109 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR e 124 " --> pdb=" O ARG e 120 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 88 through 90 removed outlier: 6.471A pdb=" N ARG A 41 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N VAL A 35 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ILE A 39 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N VAL A 75 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ALA A 64 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLU A 52 " --> pdb=" O ALA A 64 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 341 through 345 removed outlier: 4.133A pdb=" N ASP A 171 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 222 through 227 removed outlier: 6.738A pdb=" N CYS A 194 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N VAL A 225 " --> pdb=" O CYS A 194 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N TYR A 196 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N GLU A 227 " --> pdb=" O TYR A 196 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ALA A 198 " --> pdb=" O GLU A 227 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N SER A 313 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ILE A 259 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N THR A 315 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N TYR A 261 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LEU A 317 " --> pdb=" O TYR A 261 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.462A pdb=" N GLY B 73 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N LEU B 67 " --> pdb=" O ASN B 71 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ASN B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N GLN B 34 " --> pdb=" O ARG B 41 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N HIS B 43 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N VAL B 32 " --> pdb=" O HIS B 43 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 342 through 345 removed outlier: 6.769A pdb=" N LEU B 167 " --> pdb=" O ILE B 343 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N LEU B 345 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE B 169 " --> pdb=" O LEU B 345 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 222 through 226 removed outlier: 8.317A pdb=" N ILE B 223 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N CYS B 194 " --> pdb=" O ILE B 223 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N VAL B 225 " --> pdb=" O CYS B 194 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N TYR B 196 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N HIS B 256 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N VAL B 195 " --> pdb=" O HIS B 256 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LEU B 258 " --> pdb=" O VAL B 195 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N VAL B 197 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ILE B 260 " --> pdb=" O VAL B 197 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N SER B 313 " --> pdb=" O THR B 257 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N ILE B 259 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N THR B 315 " --> pdb=" O ILE B 259 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N TYR B 261 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LEU B 317 " --> pdb=" O TYR B 261 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'C' and resid 88 through 90 removed outlier: 6.750A pdb=" N ARG C 41 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N VAL C 35 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE C 39 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN C 66 " --> pdb=" O GLY C 73 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N VAL C 75 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N ALA C 64 " --> pdb=" O VAL C 75 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU C 52 " --> pdb=" O ALA C 64 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 97 through 100 removed outlier: 3.639A pdb=" N GLU C 126 " --> pdb=" O VAL C 100 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 341 through 345 Processing sheet with id= J, first strand: chain 'C' and resid 222 through 227 removed outlier: 8.178A pdb=" N ILE C 223 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N CYS C 194 " --> pdb=" O ILE C 223 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N VAL C 225 " --> pdb=" O CYS C 194 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N TYR C 196 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N GLU C 227 " --> pdb=" O TYR C 196 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ALA C 198 " --> pdb=" O GLU C 227 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N HIS C 256 " --> pdb=" O ILE C 193 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N VAL C 195 " --> pdb=" O HIS C 256 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU C 258 " --> pdb=" O VAL C 195 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N VAL C 197 " --> pdb=" O LEU C 258 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE C 260 " --> pdb=" O VAL C 197 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ILE C 199 " --> pdb=" O ILE C 260 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ASP C 262 " --> pdb=" O ILE C 199 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N SER C 313 " --> pdb=" O THR C 257 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N ILE C 259 " --> pdb=" O SER C 313 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N THR C 315 " --> pdb=" O ILE C 259 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N TYR C 261 " --> pdb=" O THR C 315 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'D' and resid 20 through 22 removed outlier: 4.292A pdb=" N VAL D 61 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ARG D 75 " --> pdb=" O GLN D 66 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N LEU D 68 " --> pdb=" O ARG D 73 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ARG D 73 " --> pdb=" O LEU D 68 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ALA D 34 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ILE D 23 " --> pdb=" O ALA D 34 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 99 through 101 Processing sheet with id= M, first strand: chain 'D' and resid 348 through 351 removed outlier: 3.680A pdb=" N ALA D 348 " --> pdb=" O LYS D 167 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ILE D 168 " --> pdb=" O ILE D 321 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N SER D 323 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N LEU D 170 " --> pdb=" O SER D 323 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N GLN D 325 " --> pdb=" O LEU D 170 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N GLY D 172 " --> pdb=" O GLN D 325 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N VAL D 327 " --> pdb=" O GLY D 172 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP D 273 " --> pdb=" O GLY D 200 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA D 233 " --> pdb=" O SER D 197 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 20 through 22 removed outlier: 6.774A pdb=" N ARG E 75 " --> pdb=" O GLN E 66 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N LEU E 68 " --> pdb=" O ARG E 73 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ARG E 73 " --> pdb=" O LEU E 68 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N ALA E 34 " --> pdb=" O ILE E 23 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ILE E 23 " --> pdb=" O ALA E 34 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 99 through 101 Processing sheet with id= P, first strand: chain 'E' and resid 348 through 350 removed outlier: 8.466A pdb=" N ILE E 168 " --> pdb=" O ILE E 321 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N SER E 323 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N LEU E 170 " --> pdb=" O SER E 323 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLN E 325 " --> pdb=" O LEU E 170 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA E 326 " --> pdb=" O ILE E 272 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL E 196 " --> pdb=" O LEU E 269 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N PHE E 271 " --> pdb=" O VAL E 196 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL E 198 " --> pdb=" O PHE E 271 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 20 through 22 removed outlier: 5.222A pdb=" N GLU F 90 " --> pdb=" O LYS F 50 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ARG F 75 " --> pdb=" O GLN F 66 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N LEU F 68 " --> pdb=" O ARG F 73 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ARG F 73 " --> pdb=" O LEU F 68 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ALA F 34 " --> pdb=" O ILE F 23 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ILE F 23 " --> pdb=" O ALA F 34 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 99 through 101 Processing sheet with id= S, first strand: chain 'F' and resid 167 through 172 removed outlier: 7.371A pdb=" N ILE F 168 " --> pdb=" O ILE F 321 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N SER F 323 " --> pdb=" O ILE F 168 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N LEU F 170 " --> pdb=" O SER F 323 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLN F 325 " --> pdb=" O LEU F 170 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N GLY F 172 " --> pdb=" O GLN F 325 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N VAL F 327 " --> pdb=" O GLY F 172 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL F 268 " --> pdb=" O THR F 322 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N ILE F 324 " --> pdb=" O VAL F 268 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU F 270 " --> pdb=" O ILE F 324 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ALA F 326 " --> pdb=" O LEU F 270 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ILE F 272 " --> pdb=" O ALA F 326 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N TYR F 328 " --> pdb=" O ILE F 272 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'd' and resid 208 through 213 removed outlier: 3.860A pdb=" N ALA d 178 " --> pdb=" O ARG d 208 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER d 182 " --> pdb=" O VAL d 212 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N PHE d 221 " --> pdb=" O MET d 235 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET d 235 " --> pdb=" O PHE d 221 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL d 233 " --> pdb=" O ILE d 223 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'g' and resid 157 through 159 removed outlier: 7.240A pdb=" N LEU g 120 " --> pdb=" O ILE g 158 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'g' and resid 256 through 259 Processing sheet with id= W, first strand: chain 'e' and resid 4 through 8 removed outlier: 3.582A pdb=" N CYS e 6 " --> pdb=" O ILE e 74 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLY e 65 " --> pdb=" O VAL e 44 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'e' and resid 22 through 24 removed outlier: 3.903A pdb=" N ILE e 22 " --> pdb=" O VAL e 33 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'e' and resid 48 through 52 1100 hydrogen bonds defined for protein. 3204 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: 9.61 Time building geometry restraints manager: 11.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4830 1.32 - 1.44: 6493 1.44 - 1.57: 16390 1.57 - 1.69: 26 1.69 - 1.81: 197 Bond restraints: 27936 Sorted by residual: bond pdb=" C4 ATP D 502 " pdb=" C5 ATP D 502 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.07e+01 bond pdb=" C4 ATP A 601 " pdb=" C5 ATP A 601 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.05e+01 bond pdb=" C4 ATP B 601 " pdb=" C5 ATP B 601 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.89e+01 bond pdb=" C4 ATP C 601 " pdb=" C5 ATP C 601 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.88e+01 bond pdb=" C5 ATP A 601 " pdb=" C6 ATP A 601 " ideal model delta sigma weight residual 1.409 1.477 -0.068 1.00e-02 1.00e+04 4.68e+01 ... (remaining 27931 not shown) Histogram of bond angle deviations from ideal: 97.69 - 105.38: 549 105.38 - 113.07: 15523 113.07 - 120.76: 13109 120.76 - 128.45: 8604 128.45 - 136.15: 80 Bond angle restraints: 37865 Sorted by residual: angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 115.72 24.15 1.00e+00 1.00e+00 5.83e+02 angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 120.06 19.81 1.00e+00 1.00e+00 3.92e+02 angle pdb=" PB ATP D 502 " pdb=" O3B ATP D 502 " pdb=" PG ATP D 502 " ideal model delta sigma weight residual 139.87 122.14 17.73 1.00e+00 1.00e+00 3.14e+02 angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 124.07 15.80 1.00e+00 1.00e+00 2.50e+02 angle pdb=" PA ATP A 601 " pdb=" O3A ATP A 601 " pdb=" PB ATP A 601 " ideal model delta sigma weight residual 136.83 122.09 14.74 1.00e+00 1.00e+00 2.17e+02 ... (remaining 37860 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.00: 16405 28.00 - 56.00: 709 56.00 - 84.00: 74 84.00 - 112.00: 17 112.00 - 140.00: 1 Dihedral angle restraints: 17206 sinusoidal: 6970 harmonic: 10236 Sorted by residual: dihedral pdb=" CA ALA F 295 " pdb=" C ALA F 295 " pdb=" N VAL F 296 " pdb=" CA VAL F 296 " ideal model delta harmonic sigma weight residual -180.00 -135.50 -44.50 0 5.00e+00 4.00e-02 7.92e+01 dihedral pdb=" CA LEU g 129 " pdb=" C LEU g 129 " pdb=" N CYS g 130 " pdb=" CA CYS g 130 " ideal model delta harmonic sigma weight residual 180.00 137.65 42.35 0 5.00e+00 4.00e-02 7.17e+01 dihedral pdb=" CA LYS g 116 " pdb=" C LYS g 116 " pdb=" N LYS g 117 " pdb=" CA LYS g 117 " ideal model delta harmonic sigma weight residual 180.00 144.24 35.76 0 5.00e+00 4.00e-02 5.12e+01 ... (remaining 17203 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 4001 0.083 - 0.165: 437 0.165 - 0.248: 12 0.248 - 0.331: 0 0.331 - 0.413: 1 Chirality restraints: 4451 Sorted by residual: chirality pdb=" C9 TTX D 501 " pdb=" C10 TTX D 501 " pdb=" C8 TTX D 501 " pdb=" N3 TTX D 501 " both_signs ideal model delta sigma weight residual False -2.28 -2.69 0.41 2.00e-01 2.50e+01 4.27e+00 chirality pdb=" CB VAL F 380 " pdb=" CA VAL F 380 " pdb=" CG1 VAL F 380 " pdb=" CG2 VAL F 380 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA ASN D 479 " pdb=" N ASN D 479 " pdb=" C ASN D 479 " pdb=" CB ASN D 479 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 4448 not shown) Planarity restraints: 4918 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 176 " -0.017 2.00e-02 2.50e+03 3.48e-02 1.21e+01 pdb=" C LYS B 176 " 0.060 2.00e-02 2.50e+03 pdb=" O LYS B 176 " -0.022 2.00e-02 2.50e+03 pdb=" N THR B 177 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 178 " -0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C LYS F 178 " 0.056 2.00e-02 2.50e+03 pdb=" O LYS F 178 " -0.021 2.00e-02 2.50e+03 pdb=" N THR F 179 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU g 296 " -0.039 5.00e-02 4.00e+02 5.92e-02 5.62e+00 pdb=" N PRO g 297 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO g 297 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO g 297 " -0.033 5.00e-02 4.00e+02 ... (remaining 4915 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1075 2.71 - 3.26: 28530 3.26 - 3.80: 46478 3.80 - 4.35: 60898 4.35 - 4.90: 100694 Nonbonded interactions: 237675 Sorted by model distance: nonbonded pdb=" OG1 THR C 228 " pdb=" OD1 ASP C 230 " model vdw 2.159 2.440 nonbonded pdb=" OH TYR C 464 " pdb=" OE1 GLU C 496 " model vdw 2.186 2.440 nonbonded pdb=" O ALA F 295 " pdb=" N GLY F 297 " model vdw 2.187 2.520 nonbonded pdb=" O ALA C 218 " pdb=" OG1 THR C 222 " model vdw 2.218 2.440 nonbonded pdb=" O ILE C 475 " pdb=" OG1 THR C 479 " model vdw 2.218 2.440 ... (remaining 237670 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 6 through 503 or resid 601)) selection = (chain 'B' and (resid 6 through 503 or resid 601)) selection = (chain 'C' and (resid 6 through 503 or resid 601)) } ncs_group { reference = (chain 'D' and resid 17 through 494) selection = (chain 'E' and resid 17 through 494) selection = (chain 'F' and resid 17 through 494) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.140 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: 0.000 Extract box with map and model: 17.790 Check model and map are aligned: 0.400 Set scattering table: 0.270 Process input model: 74.130 Find NCS groups from input model: 1.950 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 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 : 0.006 0.093 27936 Z= 0.407 Angle : 0.857 24.149 37865 Z= 0.529 Chirality : 0.050 0.413 4451 Planarity : 0.005 0.059 4918 Dihedral : 15.432 140.000 10636 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.21 % Favored : 93.64 % Rotamer: Outliers : 0.03 % Allowed : 7.34 % Favored : 92.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.12), residues: 3556 helix: -1.18 (0.12), residues: 1482 sheet: -2.05 (0.18), residues: 629 loop : -2.29 (0.15), residues: 1445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP e 15 HIS 0.005 0.001 HIS F 384 PHE 0.036 0.002 PHE C 482 TYR 0.018 0.002 TYR B 457 ARG 0.010 0.001 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7112 Ramachandran restraints generated. 3556 Oldfield, 0 Emsley, 3556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7112 Ramachandran restraints generated. 3556 Oldfield, 0 Emsley, 3556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 737 residues out of total 2942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 736 time to evaluate : 3.479 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: A 63 ILE cc_start: 0.8286 (mt) cc_final: 0.7989 (mt) REVERT: A 290 ASP cc_start: 0.7611 (p0) cc_final: 0.7316 (p0) REVERT: A 330 TYR cc_start: 0.8181 (t80) cc_final: 0.7861 (t80) REVERT: B 20 TYR cc_start: 0.6032 (t80) cc_final: 0.5774 (t80) REVERT: B 58 GLU cc_start: 0.7066 (tt0) cc_final: 0.6796 (tp30) REVERT: B 260 ILE cc_start: 0.8964 (mt) cc_final: 0.8668 (mt) REVERT: B 359 ASN cc_start: 0.7846 (t0) cc_final: 0.7262 (t0) REVERT: B 378 LYS cc_start: 0.7753 (mtpt) cc_final: 0.7454 (mtmt) REVERT: B 419 GLU cc_start: 0.6791 (mm-30) cc_final: 0.6561 (mp0) REVERT: B 453 GLN cc_start: 0.8000 (mt0) cc_final: 0.7573 (mt0) REVERT: B 474 GLU cc_start: 0.6840 (tp30) cc_final: 0.6388 (mm-30) REVERT: B 498 MET cc_start: 0.7030 (tpt) cc_final: 0.4959 (tmm) REVERT: C 90 LYS cc_start: 0.8133 (ttpp) cc_final: 0.7563 (pptt) REVERT: C 155 ASP cc_start: 0.8324 (m-30) cc_final: 0.8113 (m-30) REVERT: C 402 ASP cc_start: 0.7463 (p0) cc_final: 0.6989 (p0) REVERT: C 456 LYS cc_start: 0.8050 (ttpt) cc_final: 0.7820 (tppt) REVERT: D 22 ARG cc_start: 0.7776 (mmt-90) cc_final: 0.7540 (mpt180) REVERT: D 32 ASP cc_start: 0.8019 (p0) cc_final: 0.7761 (p0) REVERT: D 59 MET cc_start: 0.5518 (mpp) cc_final: 0.5272 (mpp) REVERT: D 92 ILE cc_start: 0.8169 (mt) cc_final: 0.7891 (pt) REVERT: D 229 GLU cc_start: 0.7583 (pp20) cc_final: 0.7287 (pp20) REVERT: D 231 LYS cc_start: 0.8222 (mptt) cc_final: 0.7940 (mtmt) REVERT: D 258 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7874 (mt-10) REVERT: D 306 MET cc_start: 0.7974 (tpp) cc_final: 0.7755 (tpp) REVERT: D 401 LEU cc_start: 0.8452 (pp) cc_final: 0.8127 (pp) REVERT: E 31 LEU cc_start: 0.8210 (mt) cc_final: 0.7835 (mt) REVERT: E 184 GLU cc_start: 0.7618 (tp30) cc_final: 0.7357 (tp30) REVERT: E 275 ILE cc_start: 0.8661 (tp) cc_final: 0.8439 (tt) REVERT: E 292 MET cc_start: 0.7955 (ttm) cc_final: 0.7543 (ttm) REVERT: E 328 TYR cc_start: 0.8228 (t80) cc_final: 0.7992 (t80) REVERT: E 397 ARG cc_start: 0.7537 (tpp80) cc_final: 0.7094 (tpp-160) REVERT: E 398 TYR cc_start: 0.8265 (t80) cc_final: 0.7821 (t80) REVERT: F 66 GLN cc_start: 0.7962 (mm110) cc_final: 0.7630 (mm-40) REVERT: F 71 ASN cc_start: 0.6926 (t0) cc_final: 0.6574 (t0) REVERT: F 241 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7456 (mm-30) REVERT: F 248 ARG cc_start: 0.7129 (mmt-90) cc_final: 0.6815 (mmt-90) REVERT: g 71 LYS cc_start: 0.8419 (mtmt) cc_final: 0.8105 (mtpt) REVERT: g 113 ARG cc_start: 0.5101 (ttp-170) cc_final: 0.4535 (ttp-170) REVERT: g 139 LYS cc_start: 0.7089 (ttmt) cc_final: 0.6746 (mtmt) REVERT: g 163 LYS cc_start: 0.8165 (mmpt) cc_final: 0.7853 (mmtm) REVERT: g 178 ARG cc_start: 0.7060 (tpp80) cc_final: 0.6604 (tpp80) REVERT: g 211 GLU cc_start: 0.6964 (pm20) cc_final: 0.6478 (pm20) REVERT: g 214 TYR cc_start: 0.8303 (p90) cc_final: 0.7625 (p90) REVERT: g 306 ARG cc_start: 0.7651 (tpt-90) cc_final: 0.6940 (tpp-160) REVERT: g 309 GLN cc_start: 0.7807 (mt0) cc_final: 0.7209 (mt0) REVERT: g 353 ILE cc_start: 0.8867 (mt) cc_final: 0.8302 (pt) REVERT: e 4 ASN cc_start: 0.3766 (t0) cc_final: 0.3466 (t0) REVERT: e 110 ARG cc_start: 0.5655 (ptm-80) cc_final: 0.5356 (ptm-80) REVERT: e 125 ARG cc_start: 0.7076 (ttm170) cc_final: 0.6673 (ttp80) outliers start: 1 outliers final: 1 residues processed: 737 average time/residue: 0.4975 time to fit residues: 540.0787 Evaluate side-chains 618 residues out of total 2942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 617 time to evaluate : 3.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 237 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 299 optimal weight: 2.9990 chunk 269 optimal weight: 0.6980 chunk 149 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 181 optimal weight: 0.8980 chunk 143 optimal weight: 0.8980 chunk 278 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 169 optimal weight: 0.7980 chunk 207 optimal weight: 3.9990 chunk 322 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 GLN A 190 GLN A 201 GLN A 351 ASN A 408 GLN A 410 GLN A 415 GLN A 423 GLN A 434 GLN A 468 ASN B 148 GLN B 186 ASN B 208 GLN B 425 GLN B 453 GLN C 34 GLN C 43 HIS C 186 ASN C 342 GLN C 415 GLN C 423 GLN D 25 GLN D 60 ASN D 67 GLN ** D 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 389 GLN D 402 GLN E 42 ASN E 45 ASN E 66 GLN F 25 GLN F 71 ASN F 120 ASN ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 266 GLN F 325 GLN F 489 ASN d 147 ASN g 76 GLN ** g 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 36 ASN ** e 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 27936 Z= 0.260 Angle : 0.627 12.252 37865 Z= 0.321 Chirality : 0.045 0.171 4451 Planarity : 0.004 0.048 4918 Dihedral : 7.586 129.041 4054 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.74 % Favored : 94.12 % Rotamer: Outliers : 1.70 % Allowed : 12.92 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.13), residues: 3556 helix: -0.01 (0.13), residues: 1485 sheet: -1.63 (0.19), residues: 641 loop : -1.83 (0.15), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP e 15 HIS 0.005 0.001 HIS C 43 PHE 0.020 0.001 PHE D 458 TYR 0.018 0.001 TYR C 464 ARG 0.008 0.000 ARG C 94 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7112 Ramachandran restraints generated. 3556 Oldfield, 0 Emsley, 3556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7112 Ramachandran restraints generated. 3556 Oldfield, 0 Emsley, 3556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 2942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 636 time to evaluate : 3.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 LYS cc_start: 0.6809 (mttp) cc_final: 0.6607 (mttp) REVERT: A 330 TYR cc_start: 0.8143 (t80) cc_final: 0.7848 (t80) REVERT: A 382 LYS cc_start: 0.8211 (mttp) cc_final: 0.7885 (mttm) REVERT: B 20 TYR cc_start: 0.6029 (t80) cc_final: 0.5746 (t80) REVERT: B 58 GLU cc_start: 0.7073 (tt0) cc_final: 0.6804 (tp30) REVERT: B 66 ASN cc_start: 0.8091 (t0) cc_final: 0.7787 (t0) REVERT: B 77 MET cc_start: 0.7778 (mmm) cc_final: 0.7512 (mmp) REVERT: B 260 ILE cc_start: 0.8967 (mt) cc_final: 0.8673 (mp) REVERT: B 359 ASN cc_start: 0.7847 (t0) cc_final: 0.7434 (t0) REVERT: B 378 LYS cc_start: 0.7666 (mtpt) cc_final: 0.7386 (mtmt) REVERT: B 387 LEU cc_start: 0.7911 (mt) cc_final: 0.7634 (mt) REVERT: B 415 GLN cc_start: 0.7877 (mt0) cc_final: 0.7605 (mt0) REVERT: B 419 GLU cc_start: 0.6800 (mm-30) cc_final: 0.6591 (mp0) REVERT: B 450 GLU cc_start: 0.6766 (mp0) cc_final: 0.6493 (mp0) REVERT: B 453 GLN cc_start: 0.7903 (mt0) cc_final: 0.7225 (mt0) REVERT: B 498 MET cc_start: 0.6952 (tpt) cc_final: 0.4957 (tmm) REVERT: C 85 GLU cc_start: 0.7640 (tm-30) cc_final: 0.7370 (tm-30) REVERT: C 90 LYS cc_start: 0.8091 (ttpp) cc_final: 0.7604 (pptt) REVERT: C 155 ASP cc_start: 0.8343 (m-30) cc_final: 0.8059 (m-30) REVERT: C 402 ASP cc_start: 0.7470 (p0) cc_final: 0.6979 (p0) REVERT: C 456 LYS cc_start: 0.7995 (ttpt) cc_final: 0.7765 (tppt) REVERT: D 32 ASP cc_start: 0.7756 (p0) cc_final: 0.7556 (p0) REVERT: D 59 MET cc_start: 0.5587 (mpp) cc_final: 0.5343 (mpp) REVERT: D 216 MET cc_start: 0.8244 (mmm) cc_final: 0.8019 (mtt) REVERT: D 231 LYS cc_start: 0.8294 (mptt) cc_final: 0.8041 (mtpt) REVERT: D 258 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7805 (mt-10) REVERT: D 306 MET cc_start: 0.7940 (tpp) cc_final: 0.7721 (tpp) REVERT: D 311 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7403 (mm-30) REVERT: D 374 MET cc_start: 0.8867 (mmm) cc_final: 0.8636 (mmm) REVERT: E 47 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8359 (pp) REVERT: E 184 GLU cc_start: 0.7587 (tp30) cc_final: 0.7308 (tp30) REVERT: E 397 ARG cc_start: 0.7479 (tpp80) cc_final: 0.7071 (tpp-160) REVERT: E 398 TYR cc_start: 0.8213 (t80) cc_final: 0.7863 (t80) REVERT: F 44 TYR cc_start: 0.7922 (m-10) cc_final: 0.7526 (m-10) REVERT: F 64 GLU cc_start: 0.7797 (tt0) cc_final: 0.7573 (tt0) REVERT: F 71 ASN cc_start: 0.7054 (t0) cc_final: 0.6612 (t0) REVERT: F 236 TYR cc_start: 0.8281 (m-80) cc_final: 0.8045 (m-80) REVERT: F 241 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7450 (mm-30) REVERT: F 248 ARG cc_start: 0.7095 (mmt-90) cc_final: 0.6788 (mmt-90) REVERT: F 385 TYR cc_start: 0.8500 (t80) cc_final: 0.8213 (t80) REVERT: F 418 ARG cc_start: 0.7578 (mtm180) cc_final: 0.7209 (mtm180) REVERT: d 130 ASP cc_start: 0.6334 (m-30) cc_final: 0.6119 (m-30) REVERT: d 250 MET cc_start: -0.0431 (ttt) cc_final: -0.0639 (ttt) REVERT: g 71 LYS cc_start: 0.8359 (mtmt) cc_final: 0.8014 (mtpt) REVERT: g 139 LYS cc_start: 0.7117 (ttmt) cc_final: 0.6733 (mtmt) REVERT: g 163 LYS cc_start: 0.8212 (mmpt) cc_final: 0.7923 (mmtm) REVERT: g 211 GLU cc_start: 0.6905 (pm20) cc_final: 0.6402 (pm20) REVERT: g 214 TYR cc_start: 0.8164 (p90) cc_final: 0.7508 (p90) REVERT: g 306 ARG cc_start: 0.7650 (tpt-90) cc_final: 0.6949 (tpp-160) REVERT: g 309 GLN cc_start: 0.7695 (mt0) cc_final: 0.7423 (mt0) REVERT: g 353 ILE cc_start: 0.8713 (mt) cc_final: 0.8277 (pt) REVERT: e 110 ARG cc_start: 0.5642 (ptm-80) cc_final: 0.5356 (ptm-80) REVERT: e 117 LEU cc_start: 0.7143 (tp) cc_final: 0.6669 (tt) REVERT: e 125 ARG cc_start: 0.7073 (ttm170) cc_final: 0.6679 (ttp80) outliers start: 50 outliers final: 34 residues processed: 659 average time/residue: 0.4725 time to fit residues: 461.6871 Evaluate side-chains 634 residues out of total 2942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 599 time to evaluate : 3.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 452 ASP Chi-restraints excluded: chain C residue 495 GLN Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 59 MET Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain d residue 184 VAL Chi-restraints excluded: chain d residue 237 VAL Chi-restraints excluded: chain g residue 287 ASP Chi-restraints excluded: chain e residue 5 LEU Chi-restraints excluded: chain e residue 9 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 179 optimal weight: 4.9990 chunk 100 optimal weight: 10.0000 chunk 268 optimal weight: 0.8980 chunk 219 optimal weight: 0.0470 chunk 88 optimal weight: 0.9990 chunk 322 optimal weight: 0.9980 chunk 348 optimal weight: 6.9990 chunk 287 optimal weight: 2.9990 chunk 320 optimal weight: 0.9980 chunk 110 optimal weight: 0.8980 chunk 259 optimal weight: 0.6980 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 GLN A 443 ASN C 28 ASN ** D 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 210 ASN F 389 GLN ** g 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 325 ASN ** g 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 27936 Z= 0.240 Angle : 0.602 10.218 37865 Z= 0.306 Chirality : 0.044 0.194 4451 Planarity : 0.004 0.045 4918 Dihedral : 7.294 120.074 4054 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.74 % Favored : 94.12 % Rotamer: Outliers : 2.79 % Allowed : 15.13 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.14), residues: 3556 helix: 0.50 (0.14), residues: 1487 sheet: -1.32 (0.19), residues: 630 loop : -1.56 (0.16), residues: 1439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP e 15 HIS 0.004 0.001 HIS D 384 PHE 0.023 0.001 PHE B 390 TYR 0.018 0.001 TYR C 464 ARG 0.009 0.000 ARG e 104 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7112 Ramachandran restraints generated. 3556 Oldfield, 0 Emsley, 3556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7112 Ramachandran restraints generated. 3556 Oldfield, 0 Emsley, 3556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 2942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 616 time to evaluate : 3.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ILE cc_start: 0.8540 (mp) cc_final: 0.8256 (mp) REVERT: A 330 TYR cc_start: 0.8165 (t80) cc_final: 0.7945 (t80) REVERT: A 382 LYS cc_start: 0.8204 (mttp) cc_final: 0.7868 (mttm) REVERT: B 20 TYR cc_start: 0.5984 (t80) cc_final: 0.5713 (t80) REVERT: B 37 ASP cc_start: 0.4957 (OUTLIER) cc_final: 0.4405 (p0) REVERT: B 58 GLU cc_start: 0.7059 (tt0) cc_final: 0.6842 (tp30) REVERT: B 66 ASN cc_start: 0.8060 (t0) cc_final: 0.7849 (t0) REVERT: B 260 ILE cc_start: 0.8959 (mt) cc_final: 0.8657 (mp) REVERT: B 359 ASN cc_start: 0.7872 (t0) cc_final: 0.7454 (t0) REVERT: B 378 LYS cc_start: 0.7609 (mtpt) cc_final: 0.7343 (mtmt) REVERT: B 384 LYS cc_start: 0.6886 (tmtt) cc_final: 0.6663 (tptt) REVERT: B 387 LEU cc_start: 0.8004 (mt) cc_final: 0.7792 (mt) REVERT: B 415 GLN cc_start: 0.7818 (mt0) cc_final: 0.7507 (mt0) REVERT: B 419 GLU cc_start: 0.6789 (mm-30) cc_final: 0.6542 (mp0) REVERT: B 450 GLU cc_start: 0.6809 (mp0) cc_final: 0.6466 (tp30) REVERT: B 498 MET cc_start: 0.6854 (tpt) cc_final: 0.4885 (tmm) REVERT: C 90 LYS cc_start: 0.8074 (ttpp) cc_final: 0.7601 (pptt) REVERT: C 155 ASP cc_start: 0.8323 (m-30) cc_final: 0.8077 (m-30) REVERT: C 321 GLU cc_start: 0.7198 (tt0) cc_final: 0.6893 (tt0) REVERT: C 402 ASP cc_start: 0.7438 (p0) cc_final: 0.6989 (p0) REVERT: C 456 LYS cc_start: 0.7983 (ttpt) cc_final: 0.7741 (tppt) REVERT: D 20 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.7168 (mp) REVERT: D 22 ARG cc_start: 0.7727 (mmt-90) cc_final: 0.7506 (mpt180) REVERT: D 59 MET cc_start: 0.5532 (mpp) cc_final: 0.5320 (mpp) REVERT: D 306 MET cc_start: 0.7942 (tpp) cc_final: 0.7654 (tpp) REVERT: D 311 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7403 (mm-30) REVERT: D 374 MET cc_start: 0.8893 (mmm) cc_final: 0.8661 (mmm) REVERT: E 47 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8309 (pp) REVERT: E 397 ARG cc_start: 0.7480 (tpp80) cc_final: 0.7067 (tpp-160) REVERT: E 398 TYR cc_start: 0.8174 (t80) cc_final: 0.7826 (t80) REVERT: F 22 ARG cc_start: 0.7478 (mmt90) cc_final: 0.7236 (mmm-85) REVERT: F 44 TYR cc_start: 0.7881 (m-10) cc_final: 0.7446 (m-10) REVERT: F 64 GLU cc_start: 0.7838 (tt0) cc_final: 0.7557 (tt0) REVERT: F 71 ASN cc_start: 0.7020 (t0) cc_final: 0.6613 (t0) REVERT: F 183 MET cc_start: 0.7207 (mmt) cc_final: 0.6952 (mmt) REVERT: F 204 GLU cc_start: 0.5875 (tp30) cc_final: 0.5675 (tp30) REVERT: F 248 ARG cc_start: 0.7114 (mmt-90) cc_final: 0.6734 (mmt-90) REVERT: F 385 TYR cc_start: 0.8488 (t80) cc_final: 0.8188 (t80) REVERT: F 428 GLU cc_start: 0.7323 (tt0) cc_final: 0.6878 (tt0) REVERT: d 103 ILE cc_start: 0.6331 (OUTLIER) cc_final: 0.6057 (mt) REVERT: d 176 GLU cc_start: 0.5688 (mm-30) cc_final: 0.5293 (mp0) REVERT: g 76 GLN cc_start: 0.6514 (tt0) cc_final: 0.6092 (tt0) REVERT: g 139 LYS cc_start: 0.7219 (ttmt) cc_final: 0.6857 (mtmt) REVERT: g 163 LYS cc_start: 0.8153 (mmpt) cc_final: 0.7820 (mmtm) REVERT: g 211 GLU cc_start: 0.6947 (pm20) cc_final: 0.6445 (pm20) REVERT: g 214 TYR cc_start: 0.8123 (p90) cc_final: 0.7448 (p90) REVERT: g 353 ILE cc_start: 0.8719 (mt) cc_final: 0.8258 (pt) REVERT: e 12 ARG cc_start: 0.5835 (OUTLIER) cc_final: 0.5434 (ttp80) REVERT: e 24 LEU cc_start: 0.6526 (tp) cc_final: 0.6240 (tt) REVERT: e 110 ARG cc_start: 0.5829 (ptm-80) cc_final: 0.5620 (ptm-80) REVERT: e 117 LEU cc_start: 0.7157 (tp) cc_final: 0.6716 (tt) REVERT: e 125 ARG cc_start: 0.7084 (ttm170) cc_final: 0.6673 (ttp80) outliers start: 82 outliers final: 53 residues processed: 666 average time/residue: 0.4712 time to fit residues: 467.6584 Evaluate side-chains 656 residues out of total 2942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 598 time to evaluate : 2.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 452 ASP Chi-restraints excluded: chain C residue 495 GLN Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 230 SER Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 488 MET Chi-restraints excluded: chain d residue 103 ILE Chi-restraints excluded: chain d residue 179 VAL Chi-restraints excluded: chain d residue 184 VAL Chi-restraints excluded: chain d residue 237 VAL Chi-restraints excluded: chain g residue 135 ASN Chi-restraints excluded: chain g residue 181 ASP Chi-restraints excluded: chain g residue 287 ASP Chi-restraints excluded: chain e residue 5 LEU Chi-restraints excluded: chain e residue 9 THR Chi-restraints excluded: chain e residue 12 ARG Chi-restraints excluded: chain e residue 58 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 319 optimal weight: 2.9990 chunk 242 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 154 optimal weight: 0.9990 chunk 216 optimal weight: 2.9990 chunk 324 optimal weight: 0.7980 chunk 343 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 307 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 GLN A 212 ASN C 28 ASN ** D 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 389 GLN ** g 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 27936 Z= 0.345 Angle : 0.649 10.047 37865 Z= 0.330 Chirality : 0.046 0.201 4451 Planarity : 0.004 0.054 4918 Dihedral : 7.389 118.068 4054 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.24 % Favored : 93.62 % Rotamer: Outliers : 3.16 % Allowed : 17.47 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.14), residues: 3556 helix: 0.53 (0.13), residues: 1487 sheet: -1.26 (0.20), residues: 637 loop : -1.47 (0.16), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP e 57 HIS 0.005 0.001 HIS F 384 PHE 0.019 0.002 PHE F 458 TYR 0.022 0.002 TYR d 112 ARG 0.007 0.001 ARG D 425 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7112 Ramachandran restraints generated. 3556 Oldfield, 0 Emsley, 3556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7112 Ramachandran restraints generated. 3556 Oldfield, 0 Emsley, 3556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 695 residues out of total 2942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 602 time to evaluate : 3.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ILE cc_start: 0.8616 (mp) cc_final: 0.8404 (mp) REVERT: A 266 LYS cc_start: 0.6698 (mttp) cc_final: 0.6364 (tppt) REVERT: A 330 TYR cc_start: 0.8214 (t80) cc_final: 0.7887 (t80) REVERT: A 420 LEU cc_start: 0.8171 (mp) cc_final: 0.7864 (mt) REVERT: A 500 ARG cc_start: 0.6449 (mtt180) cc_final: 0.6247 (mtt180) REVERT: B 77 MET cc_start: 0.7876 (OUTLIER) cc_final: 0.7642 (mmp) REVERT: B 260 ILE cc_start: 0.8973 (mt) cc_final: 0.8690 (mt) REVERT: B 378 LYS cc_start: 0.7626 (mtpt) cc_final: 0.7369 (mtmt) REVERT: B 387 LEU cc_start: 0.7941 (mt) cc_final: 0.7688 (mt) REVERT: B 419 GLU cc_start: 0.6825 (mm-30) cc_final: 0.6574 (mm-30) REVERT: B 450 GLU cc_start: 0.6944 (mp0) cc_final: 0.6528 (tp30) REVERT: B 474 GLU cc_start: 0.6835 (tp30) cc_final: 0.6368 (mm-30) REVERT: B 489 LEU cc_start: 0.6175 (OUTLIER) cc_final: 0.5620 (pp) REVERT: B 498 MET cc_start: 0.6769 (tpt) cc_final: 0.4775 (tmm) REVERT: C 90 LYS cc_start: 0.8095 (ttpp) cc_final: 0.7603 (pptt) REVERT: C 155 ASP cc_start: 0.8357 (m-30) cc_final: 0.8139 (m-30) REVERT: C 402 ASP cc_start: 0.7502 (p0) cc_final: 0.7053 (p0) REVERT: C 456 LYS cc_start: 0.8022 (ttpt) cc_final: 0.7768 (tppt) REVERT: D 20 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.7293 (mp) REVERT: D 22 ARG cc_start: 0.7770 (mmt-90) cc_final: 0.7551 (mpt180) REVERT: D 59 MET cc_start: 0.5632 (mpp) cc_final: 0.5374 (mpp) REVERT: D 134 ARG cc_start: 0.7696 (ptm-80) cc_final: 0.7083 (ptp-110) REVERT: D 218 GLU cc_start: 0.6764 (mp0) cc_final: 0.6521 (mp0) REVERT: D 306 MET cc_start: 0.7978 (tpp) cc_final: 0.7663 (tpp) REVERT: D 481 ASP cc_start: 0.7093 (p0) cc_final: 0.6817 (p0) REVERT: E 47 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8351 (pp) REVERT: E 397 ARG cc_start: 0.7501 (tpp80) cc_final: 0.7074 (tpp-160) REVERT: E 398 TYR cc_start: 0.8243 (t80) cc_final: 0.7888 (t80) REVERT: F 22 ARG cc_start: 0.7477 (mmt90) cc_final: 0.7225 (mmm-85) REVERT: F 44 TYR cc_start: 0.7959 (m-10) cc_final: 0.7516 (m-10) REVERT: F 71 ASN cc_start: 0.7102 (t0) cc_final: 0.6659 (t0) REVERT: F 236 TYR cc_start: 0.8321 (m-80) cc_final: 0.8060 (m-80) REVERT: F 385 TYR cc_start: 0.8571 (t80) cc_final: 0.8258 (t80) REVERT: F 428 GLU cc_start: 0.7365 (tt0) cc_final: 0.6969 (tt0) REVERT: d 103 ILE cc_start: 0.6469 (OUTLIER) cc_final: 0.6189 (mt) REVERT: d 250 MET cc_start: 0.0264 (ttt) cc_final: -0.0112 (ttt) REVERT: g 76 GLN cc_start: 0.6582 (tt0) cc_final: 0.6119 (tt0) REVERT: g 139 LYS cc_start: 0.7212 (ttmt) cc_final: 0.6852 (mtmt) REVERT: g 173 GLU cc_start: 0.6381 (mp0) cc_final: 0.6028 (pm20) REVERT: g 211 GLU cc_start: 0.6972 (pm20) cc_final: 0.6399 (pm20) REVERT: g 214 TYR cc_start: 0.8170 (p90) cc_final: 0.7375 (p90) REVERT: g 306 ARG cc_start: 0.7755 (tpp80) cc_final: 0.6882 (tpp-160) REVERT: g 309 GLN cc_start: 0.7817 (mt0) cc_final: 0.7551 (mt0) REVERT: g 353 ILE cc_start: 0.8712 (mt) cc_final: 0.8264 (pt) REVERT: e 110 ARG cc_start: 0.5788 (ptm-80) cc_final: 0.5537 (ptm-80) REVERT: e 125 ARG cc_start: 0.7058 (ttm170) cc_final: 0.6696 (ttp80) outliers start: 93 outliers final: 68 residues processed: 659 average time/residue: 0.4562 time to fit residues: 448.4597 Evaluate side-chains 653 residues out of total 2942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 580 time to evaluate : 3.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 77 MET Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 452 ASP Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 193 HIS Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 467 ASP Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 59 MET Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 230 SER Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 414 SER Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 280 GLN Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 463 SER Chi-restraints excluded: chain F residue 488 MET Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain d residue 103 ILE Chi-restraints excluded: chain d residue 142 THR Chi-restraints excluded: chain d residue 156 ASN Chi-restraints excluded: chain d residue 179 VAL Chi-restraints excluded: chain d residue 184 VAL Chi-restraints excluded: chain d residue 237 VAL Chi-restraints excluded: chain g residue 135 ASN Chi-restraints excluded: chain g residue 181 ASP Chi-restraints excluded: chain g residue 348 LYS Chi-restraints excluded: chain e residue 5 LEU Chi-restraints excluded: chain e residue 9 THR Chi-restraints excluded: chain e residue 12 ARG Chi-restraints excluded: chain e residue 34 LEU Chi-restraints excluded: chain e residue 58 LEU Chi-restraints excluded: chain e residue 62 LEU Chi-restraints excluded: chain e residue 124 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 285 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 255 optimal weight: 1.9990 chunk 141 optimal weight: 0.0470 chunk 292 optimal weight: 0.6980 chunk 237 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 175 optimal weight: 0.9980 chunk 307 optimal weight: 8.9990 chunk 86 optimal weight: 3.9990 overall best weight: 0.9482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 GLN C 28 ASN ** D 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 25 GLN F 389 GLN ** g 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 27936 Z= 0.294 Angle : 0.627 11.712 37865 Z= 0.318 Chirality : 0.045 0.211 4451 Planarity : 0.004 0.047 4918 Dihedral : 7.304 114.944 4054 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.76 % Favored : 94.09 % Rotamer: Outliers : 3.26 % Allowed : 18.86 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.14), residues: 3556 helix: 0.66 (0.14), residues: 1487 sheet: -1.15 (0.20), residues: 642 loop : -1.38 (0.16), residues: 1427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP e 15 HIS 0.004 0.001 HIS F 384 PHE 0.018 0.001 PHE D 343 TYR 0.022 0.002 TYR d 112 ARG 0.008 0.000 ARG g 171 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7112 Ramachandran restraints generated. 3556 Oldfield, 0 Emsley, 3556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7112 Ramachandran restraints generated. 3556 Oldfield, 0 Emsley, 3556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 2942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 600 time to evaluate : 2.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 LYS cc_start: 0.6707 (mttp) cc_final: 0.6444 (mttm) REVERT: A 330 TYR cc_start: 0.8226 (t80) cc_final: 0.7914 (t80) REVERT: A 382 LYS cc_start: 0.8220 (mttp) cc_final: 0.7854 (mttm) REVERT: A 420 LEU cc_start: 0.8190 (mp) cc_final: 0.7860 (mt) REVERT: A 500 ARG cc_start: 0.6453 (mtt180) cc_final: 0.6178 (mtt180) REVERT: B 37 ASP cc_start: 0.4916 (OUTLIER) cc_final: 0.4343 (p0) REVERT: B 68 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7517 (mt-10) REVERT: B 77 MET cc_start: 0.7816 (OUTLIER) cc_final: 0.7563 (mmp) REVERT: B 260 ILE cc_start: 0.8971 (mt) cc_final: 0.8671 (mp) REVERT: B 378 LYS cc_start: 0.7621 (mtpt) cc_final: 0.7357 (mtmt) REVERT: B 387 LEU cc_start: 0.7885 (mt) cc_final: 0.7617 (mt) REVERT: B 419 GLU cc_start: 0.6817 (mm-30) cc_final: 0.6566 (mm-30) REVERT: B 450 GLU cc_start: 0.6888 (mp0) cc_final: 0.6510 (tp30) REVERT: B 489 LEU cc_start: 0.6161 (OUTLIER) cc_final: 0.5602 (pp) REVERT: B 498 MET cc_start: 0.6706 (tpt) cc_final: 0.4679 (tmm) REVERT: C 90 LYS cc_start: 0.8085 (ttpp) cc_final: 0.7596 (pptt) REVERT: C 155 ASP cc_start: 0.8326 (m-30) cc_final: 0.8117 (m-30) REVERT: C 402 ASP cc_start: 0.7446 (p0) cc_final: 0.7008 (p0) REVERT: C 456 LYS cc_start: 0.8003 (ttpt) cc_final: 0.7750 (tppt) REVERT: D 22 ARG cc_start: 0.7763 (mmt-90) cc_final: 0.7530 (mpt180) REVERT: D 59 MET cc_start: 0.5513 (mpp) cc_final: 0.5257 (mpp) REVERT: D 134 ARG cc_start: 0.7670 (ptm-80) cc_final: 0.7060 (ptp-110) REVERT: D 218 GLU cc_start: 0.6710 (mp0) cc_final: 0.6448 (mp0) REVERT: D 306 MET cc_start: 0.7942 (tpp) cc_final: 0.7650 (tpp) REVERT: D 481 ASP cc_start: 0.7131 (p0) cc_final: 0.6914 (p0) REVERT: E 47 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8366 (pp) REVERT: E 397 ARG cc_start: 0.7491 (tpp80) cc_final: 0.7061 (tpp-160) REVERT: E 398 TYR cc_start: 0.8229 (t80) cc_final: 0.7877 (t80) REVERT: F 22 ARG cc_start: 0.7473 (mmt90) cc_final: 0.7225 (mmm-85) REVERT: F 32 ASP cc_start: 0.7470 (p0) cc_final: 0.7078 (p0) REVERT: F 44 TYR cc_start: 0.7934 (m-10) cc_final: 0.7484 (m-10) REVERT: F 71 ASN cc_start: 0.7120 (t0) cc_final: 0.6686 (t0) REVERT: F 183 MET cc_start: 0.7227 (mmt) cc_final: 0.6991 (mmt) REVERT: F 248 ARG cc_start: 0.7151 (mmt-90) cc_final: 0.6850 (mmt-90) REVERT: F 385 TYR cc_start: 0.8553 (t80) cc_final: 0.8237 (t80) REVERT: F 428 GLU cc_start: 0.7314 (tt0) cc_final: 0.6957 (tt0) REVERT: d 103 ILE cc_start: 0.6484 (OUTLIER) cc_final: 0.6210 (mt) REVERT: d 164 GLU cc_start: 0.6490 (tm-30) cc_final: 0.6238 (tm-30) REVERT: g 76 GLN cc_start: 0.6566 (tt0) cc_final: 0.6107 (tt0) REVERT: g 139 LYS cc_start: 0.7211 (ttmt) cc_final: 0.6853 (mtmt) REVERT: g 163 LYS cc_start: 0.8183 (mmpt) cc_final: 0.7913 (mmtm) REVERT: g 173 GLU cc_start: 0.6411 (mp0) cc_final: 0.6100 (pm20) REVERT: g 211 GLU cc_start: 0.6961 (pm20) cc_final: 0.6451 (pm20) REVERT: g 214 TYR cc_start: 0.8139 (p90) cc_final: 0.7266 (p90) REVERT: g 306 ARG cc_start: 0.7757 (tpp80) cc_final: 0.6873 (tpp-160) REVERT: g 309 GLN cc_start: 0.7824 (mt0) cc_final: 0.7569 (mt0) REVERT: g 353 ILE cc_start: 0.8731 (mt) cc_final: 0.8268 (pt) REVERT: e 110 ARG cc_start: 0.5758 (ptm-80) cc_final: 0.5522 (ptm-80) REVERT: e 125 ARG cc_start: 0.6874 (ttm170) cc_final: 0.6610 (ttp80) outliers start: 96 outliers final: 70 residues processed: 656 average time/residue: 0.4682 time to fit residues: 459.9399 Evaluate side-chains 659 residues out of total 2942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 584 time to evaluate : 3.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 77 MET Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 452 ASP Chi-restraints excluded: chain C residue 495 GLN Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 193 HIS Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 467 ASP Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 59 MET Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 230 SER Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 280 GLN Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain F residue 488 MET Chi-restraints excluded: chain d residue 103 ILE Chi-restraints excluded: chain d residue 142 THR Chi-restraints excluded: chain d residue 156 ASN Chi-restraints excluded: chain d residue 179 VAL Chi-restraints excluded: chain d residue 184 VAL Chi-restraints excluded: chain d residue 237 VAL Chi-restraints excluded: chain g residue 135 ASN Chi-restraints excluded: chain g residue 181 ASP Chi-restraints excluded: chain e residue 5 LEU Chi-restraints excluded: chain e residue 9 THR Chi-restraints excluded: chain e residue 12 ARG Chi-restraints excluded: chain e residue 34 LEU Chi-restraints excluded: chain e residue 58 LEU Chi-restraints excluded: chain e residue 124 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 115 optimal weight: 0.8980 chunk 309 optimal weight: 0.9980 chunk 67 optimal weight: 0.2980 chunk 201 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 343 optimal weight: 4.9990 chunk 285 optimal weight: 2.9990 chunk 159 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 180 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 GLN B 212 ASN ** D 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 389 GLN F 389 GLN ** g 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 27936 Z= 0.237 Angle : 0.600 11.758 37865 Z= 0.303 Chirality : 0.044 0.228 4451 Planarity : 0.004 0.045 4918 Dihedral : 7.136 112.674 4054 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.82 % Favored : 94.04 % Rotamer: Outliers : 3.60 % Allowed : 19.44 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.14), residues: 3556 helix: 0.85 (0.14), residues: 1487 sheet: -1.04 (0.20), residues: 650 loop : -1.30 (0.16), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP e 15 HIS 0.004 0.001 HIS C 43 PHE 0.019 0.001 PHE E 441 TYR 0.017 0.001 TYR d 112 ARG 0.010 0.000 ARG g 171 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7112 Ramachandran restraints generated. 3556 Oldfield, 0 Emsley, 3556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7112 Ramachandran restraints generated. 3556 Oldfield, 0 Emsley, 3556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 2942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 600 time to evaluate : 3.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 330 TYR cc_start: 0.8217 (t80) cc_final: 0.7990 (t80) REVERT: A 382 LYS cc_start: 0.8205 (mttp) cc_final: 0.7812 (mttm) REVERT: A 420 LEU cc_start: 0.8183 (mp) cc_final: 0.7796 (mt) REVERT: B 37 ASP cc_start: 0.4853 (OUTLIER) cc_final: 0.4277 (p0) REVERT: B 68 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7505 (mt-10) REVERT: B 77 MET cc_start: 0.7807 (OUTLIER) cc_final: 0.7558 (mmp) REVERT: B 260 ILE cc_start: 0.8959 (mt) cc_final: 0.8652 (mp) REVERT: B 378 LYS cc_start: 0.7595 (mtpt) cc_final: 0.7329 (mtmt) REVERT: B 387 LEU cc_start: 0.7900 (mt) cc_final: 0.7690 (mt) REVERT: B 419 GLU cc_start: 0.6750 (mm-30) cc_final: 0.6506 (mm-30) REVERT: B 450 GLU cc_start: 0.6645 (mp0) cc_final: 0.6316 (tp30) REVERT: B 489 LEU cc_start: 0.6123 (OUTLIER) cc_final: 0.5568 (pp) REVERT: B 498 MET cc_start: 0.6779 (tpt) cc_final: 0.4765 (tmm) REVERT: C 90 LYS cc_start: 0.8070 (ttpp) cc_final: 0.7583 (pptt) REVERT: C 402 ASP cc_start: 0.7423 (p0) cc_final: 0.6989 (p0) REVERT: C 456 LYS cc_start: 0.7990 (ttpt) cc_final: 0.7725 (tppt) REVERT: D 22 ARG cc_start: 0.7758 (mmt-90) cc_final: 0.7528 (mpt180) REVERT: D 59 MET cc_start: 0.5472 (mpp) cc_final: 0.5248 (mpp) REVERT: D 134 ARG cc_start: 0.7645 (ptm-80) cc_final: 0.6935 (ptp-110) REVERT: D 218 GLU cc_start: 0.6721 (mp0) cc_final: 0.6463 (mp0) REVERT: D 306 MET cc_start: 0.7918 (tpp) cc_final: 0.7619 (tpp) REVERT: D 481 ASP cc_start: 0.7187 (p0) cc_final: 0.6974 (p0) REVERT: E 47 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8322 (pp) REVERT: E 397 ARG cc_start: 0.7495 (tpp80) cc_final: 0.7070 (tpp-160) REVERT: E 398 TYR cc_start: 0.8209 (t80) cc_final: 0.7863 (t80) REVERT: F 22 ARG cc_start: 0.7463 (mmt90) cc_final: 0.7210 (mmm-85) REVERT: F 71 ASN cc_start: 0.7132 (t0) cc_final: 0.6691 (t0) REVERT: F 183 MET cc_start: 0.7212 (mmt) cc_final: 0.7010 (mmt) REVERT: F 248 ARG cc_start: 0.7140 (mmt-90) cc_final: 0.6867 (mmt-90) REVERT: F 428 GLU cc_start: 0.7292 (tt0) cc_final: 0.6941 (tt0) REVERT: d 103 ILE cc_start: 0.6422 (OUTLIER) cc_final: 0.6161 (mt) REVERT: g 76 GLN cc_start: 0.6591 (tt0) cc_final: 0.6152 (tt0) REVERT: g 139 LYS cc_start: 0.7215 (ttmt) cc_final: 0.6863 (mtmt) REVERT: g 173 GLU cc_start: 0.6431 (mp0) cc_final: 0.6169 (pm20) REVERT: g 211 GLU cc_start: 0.6989 (pm20) cc_final: 0.6445 (pm20) REVERT: g 214 TYR cc_start: 0.8071 (p90) cc_final: 0.7198 (p90) REVERT: g 306 ARG cc_start: 0.7728 (tpp80) cc_final: 0.6898 (tpp-160) REVERT: g 353 ILE cc_start: 0.8729 (mt) cc_final: 0.8260 (pt) REVERT: e 12 ARG cc_start: 0.6029 (OUTLIER) cc_final: 0.5751 (ttp80) REVERT: e 110 ARG cc_start: 0.5733 (ptm-80) cc_final: 0.5502 (ptm-80) REVERT: e 125 ARG cc_start: 0.6845 (ttm170) cc_final: 0.6577 (ttp80) outliers start: 106 outliers final: 80 residues processed: 666 average time/residue: 0.4694 time to fit residues: 470.0378 Evaluate side-chains 666 residues out of total 2942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 580 time to evaluate : 2.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 77 MET Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 452 ASP Chi-restraints excluded: chain C residue 495 GLN Chi-restraints excluded: chain C residue 496 GLU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 193 HIS Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 305 GLU Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 467 ASP Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 59 MET Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 193 HIS Chi-restraints excluded: chain E residue 230 SER Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 414 SER Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 292 MET Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain F residue 488 MET Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain d residue 103 ILE Chi-restraints excluded: chain d residue 142 THR Chi-restraints excluded: chain d residue 156 ASN Chi-restraints excluded: chain d residue 179 VAL Chi-restraints excluded: chain d residue 184 VAL Chi-restraints excluded: chain d residue 237 VAL Chi-restraints excluded: chain g residue 53 SER Chi-restraints excluded: chain g residue 129 LEU Chi-restraints excluded: chain g residue 135 ASN Chi-restraints excluded: chain g residue 181 ASP Chi-restraints excluded: chain e residue 5 LEU Chi-restraints excluded: chain e residue 9 THR Chi-restraints excluded: chain e residue 12 ARG Chi-restraints excluded: chain e residue 34 LEU Chi-restraints excluded: chain e residue 58 LEU Chi-restraints excluded: chain e residue 62 LEU Chi-restraints excluded: chain e residue 124 THR Chi-restraints excluded: chain e residue 126 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 331 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 195 optimal weight: 0.9980 chunk 250 optimal weight: 0.9990 chunk 194 optimal weight: 1.9990 chunk 289 optimal weight: 0.3980 chunk 191 optimal weight: 0.5980 chunk 342 optimal weight: 0.9990 chunk 214 optimal weight: 1.9990 chunk 208 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 GLN D 25 GLN ** D 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 389 GLN ** g 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 27936 Z= 0.258 Angle : 0.613 12.135 37865 Z= 0.310 Chirality : 0.045 0.326 4451 Planarity : 0.004 0.090 4918 Dihedral : 7.124 112.233 4054 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.02 % Favored : 93.84 % Rotamer: Outliers : 3.54 % Allowed : 19.92 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.14), residues: 3556 helix: 0.86 (0.14), residues: 1488 sheet: -0.99 (0.20), residues: 648 loop : -1.27 (0.16), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP e 15 HIS 0.004 0.001 HIS C 43 PHE 0.019 0.001 PHE E 441 TYR 0.017 0.001 TYR d 112 ARG 0.015 0.000 ARG e 104 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7112 Ramachandran restraints generated. 3556 Oldfield, 0 Emsley, 3556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7112 Ramachandran restraints generated. 3556 Oldfield, 0 Emsley, 3556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 2942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 589 time to evaluate : 3.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 LYS cc_start: 0.6683 (mttp) cc_final: 0.6414 (mttt) REVERT: A 330 TYR cc_start: 0.8238 (t80) cc_final: 0.7903 (t80) REVERT: A 382 LYS cc_start: 0.8224 (mttp) cc_final: 0.7815 (mttm) REVERT: A 420 LEU cc_start: 0.8033 (mp) cc_final: 0.7751 (mt) REVERT: B 37 ASP cc_start: 0.4897 (OUTLIER) cc_final: 0.4298 (p0) REVERT: B 68 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7505 (mt-10) REVERT: B 77 MET cc_start: 0.7835 (OUTLIER) cc_final: 0.7578 (mmp) REVERT: B 260 ILE cc_start: 0.8966 (mt) cc_final: 0.8670 (mp) REVERT: B 266 LYS cc_start: 0.7007 (tppt) cc_final: 0.6671 (tppt) REVERT: B 378 LYS cc_start: 0.7596 (mtpt) cc_final: 0.7329 (mtmt) REVERT: B 419 GLU cc_start: 0.6757 (mm-30) cc_final: 0.6507 (mm-30) REVERT: B 450 GLU cc_start: 0.6607 (mp0) cc_final: 0.6320 (tp30) REVERT: B 489 LEU cc_start: 0.6122 (OUTLIER) cc_final: 0.5565 (pp) REVERT: B 498 MET cc_start: 0.6768 (tpt) cc_final: 0.4770 (tmm) REVERT: C 90 LYS cc_start: 0.8070 (ttpp) cc_final: 0.7577 (pptt) REVERT: C 402 ASP cc_start: 0.7473 (p0) cc_final: 0.7030 (p0) REVERT: C 456 LYS cc_start: 0.7993 (ttpt) cc_final: 0.7639 (pttp) REVERT: D 22 ARG cc_start: 0.7767 (mmt-90) cc_final: 0.7534 (mpt180) REVERT: D 134 ARG cc_start: 0.7599 (ptm-80) cc_final: 0.6880 (ptp-110) REVERT: D 218 GLU cc_start: 0.6732 (mp0) cc_final: 0.6455 (mp0) REVERT: D 306 MET cc_start: 0.7914 (tpp) cc_final: 0.7606 (tpp) REVERT: D 376 GLN cc_start: 0.8268 (mt0) cc_final: 0.8054 (mt0) REVERT: D 481 ASP cc_start: 0.7196 (p0) cc_final: 0.6976 (p0) REVERT: E 47 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8333 (pp) REVERT: E 397 ARG cc_start: 0.7502 (tpp80) cc_final: 0.7081 (tpp-160) REVERT: E 398 TYR cc_start: 0.8208 (t80) cc_final: 0.7861 (t80) REVERT: F 22 ARG cc_start: 0.7458 (mmt90) cc_final: 0.7205 (mmm-85) REVERT: F 32 ASP cc_start: 0.7496 (p0) cc_final: 0.7266 (p0) REVERT: F 71 ASN cc_start: 0.7124 (t0) cc_final: 0.6708 (t0) REVERT: F 183 MET cc_start: 0.7230 (mmt) cc_final: 0.7015 (mmt) REVERT: F 248 ARG cc_start: 0.7147 (mmt-90) cc_final: 0.6890 (mmt-90) REVERT: F 359 LYS cc_start: 0.8033 (ptpp) cc_final: 0.7799 (ptpp) REVERT: F 385 TYR cc_start: 0.8532 (t80) cc_final: 0.8243 (t80) REVERT: F 428 GLU cc_start: 0.7286 (tt0) cc_final: 0.6956 (tt0) REVERT: d 103 ILE cc_start: 0.6496 (OUTLIER) cc_final: 0.6205 (mt) REVERT: g 76 GLN cc_start: 0.6602 (tt0) cc_final: 0.6121 (tt0) REVERT: g 139 LYS cc_start: 0.7150 (ttmt) cc_final: 0.6793 (mtmt) REVERT: g 211 GLU cc_start: 0.6983 (pm20) cc_final: 0.6434 (pm20) REVERT: g 214 TYR cc_start: 0.8109 (p90) cc_final: 0.7158 (p90) REVERT: g 306 ARG cc_start: 0.7723 (tpp80) cc_final: 0.6800 (tpp-160) REVERT: g 353 ILE cc_start: 0.8726 (mt) cc_final: 0.8262 (pt) REVERT: e 12 ARG cc_start: 0.6058 (OUTLIER) cc_final: 0.5798 (ttp80) REVERT: e 104 ARG cc_start: 0.6577 (mmp-170) cc_final: 0.6355 (mmp-170) REVERT: e 110 ARG cc_start: 0.5717 (ptm-80) cc_final: 0.5489 (ptm-80) REVERT: e 125 ARG cc_start: 0.6920 (ttm170) cc_final: 0.6661 (ttp80) outliers start: 104 outliers final: 86 residues processed: 653 average time/residue: 0.4592 time to fit residues: 448.6614 Evaluate side-chains 676 residues out of total 2942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 584 time to evaluate : 3.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 77 MET Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 251 MET Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 452 ASP Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 193 HIS Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 305 GLU Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 428 GLU Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 467 ASP Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 59 MET Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 193 HIS Chi-restraints excluded: chain E residue 230 SER Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 414 SER Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 280 GLN Chi-restraints excluded: chain F residue 292 MET Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain F residue 488 MET Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain d residue 103 ILE Chi-restraints excluded: chain d residue 142 THR Chi-restraints excluded: chain d residue 156 ASN Chi-restraints excluded: chain d residue 179 VAL Chi-restraints excluded: chain d residue 184 VAL Chi-restraints excluded: chain d residue 237 VAL Chi-restraints excluded: chain g residue 53 SER Chi-restraints excluded: chain g residue 129 LEU Chi-restraints excluded: chain g residue 135 ASN Chi-restraints excluded: chain g residue 181 ASP Chi-restraints excluded: chain e residue 5 LEU Chi-restraints excluded: chain e residue 9 THR Chi-restraints excluded: chain e residue 12 ARG Chi-restraints excluded: chain e residue 34 LEU Chi-restraints excluded: chain e residue 58 LEU Chi-restraints excluded: chain e residue 62 LEU Chi-restraints excluded: chain e residue 124 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 211 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 204 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 chunk 217 optimal weight: 0.9980 chunk 233 optimal weight: 0.0870 chunk 169 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 268 optimal weight: 1.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 GLN B 28 ASN ** D 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 389 GLN ** g 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 27936 Z= 0.244 Angle : 0.606 12.367 37865 Z= 0.306 Chirality : 0.044 0.254 4451 Planarity : 0.004 0.089 4918 Dihedral : 7.071 111.542 4054 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.93 % Favored : 93.93 % Rotamer: Outliers : 3.40 % Allowed : 20.22 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.14), residues: 3556 helix: 0.93 (0.14), residues: 1489 sheet: -0.89 (0.20), residues: 626 loop : -1.22 (0.16), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP e 15 HIS 0.004 0.001 HIS C 43 PHE 0.019 0.001 PHE E 441 TYR 0.015 0.001 TYR d 112 ARG 0.010 0.000 ARG e 104 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7112 Ramachandran restraints generated. 3556 Oldfield, 0 Emsley, 3556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7112 Ramachandran restraints generated. 3556 Oldfield, 0 Emsley, 3556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 691 residues out of total 2942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 591 time to evaluate : 3.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 LYS cc_start: 0.6690 (mttp) cc_final: 0.6389 (mttp) REVERT: A 330 TYR cc_start: 0.8237 (t80) cc_final: 0.7902 (t80) REVERT: A 382 LYS cc_start: 0.8228 (mttp) cc_final: 0.7815 (mttm) REVERT: B 37 ASP cc_start: 0.4877 (OUTLIER) cc_final: 0.4277 (p0) REVERT: B 68 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7497 (mt-10) REVERT: B 77 MET cc_start: 0.7803 (OUTLIER) cc_final: 0.7546 (mmp) REVERT: B 260 ILE cc_start: 0.8959 (mt) cc_final: 0.8653 (mp) REVERT: B 266 LYS cc_start: 0.7032 (tppt) cc_final: 0.6683 (tppt) REVERT: B 378 LYS cc_start: 0.7589 (mtpt) cc_final: 0.7317 (mtmt) REVERT: B 415 GLN cc_start: 0.7914 (mt0) cc_final: 0.7525 (mp10) REVERT: B 419 GLU cc_start: 0.6763 (mm-30) cc_final: 0.6521 (mm-30) REVERT: B 450 GLU cc_start: 0.6577 (mp0) cc_final: 0.6322 (tp30) REVERT: B 489 LEU cc_start: 0.6133 (OUTLIER) cc_final: 0.5580 (pp) REVERT: B 498 MET cc_start: 0.6770 (tpt) cc_final: 0.4770 (tmm) REVERT: C 90 LYS cc_start: 0.8066 (ttpp) cc_final: 0.7577 (pptt) REVERT: C 155 ASP cc_start: 0.8186 (m-30) cc_final: 0.7871 (m-30) REVERT: C 402 ASP cc_start: 0.7474 (p0) cc_final: 0.7037 (p0) REVERT: C 456 LYS cc_start: 0.7992 (ttpt) cc_final: 0.7647 (pttp) REVERT: D 22 ARG cc_start: 0.7771 (mmt-90) cc_final: 0.7536 (mpt180) REVERT: D 134 ARG cc_start: 0.7597 (ptm-80) cc_final: 0.6873 (ptp-110) REVERT: D 218 GLU cc_start: 0.6691 (mp0) cc_final: 0.6457 (mp0) REVERT: D 306 MET cc_start: 0.7911 (tpp) cc_final: 0.7603 (tpp) REVERT: D 376 GLN cc_start: 0.8264 (mt0) cc_final: 0.8060 (mt0) REVERT: D 481 ASP cc_start: 0.7205 (p0) cc_final: 0.6984 (p0) REVERT: E 47 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8330 (pp) REVERT: E 397 ARG cc_start: 0.7499 (tpp80) cc_final: 0.7075 (tpp-160) REVERT: E 398 TYR cc_start: 0.8200 (t80) cc_final: 0.7859 (t80) REVERT: F 22 ARG cc_start: 0.7466 (mmt90) cc_final: 0.7218 (mmm-85) REVERT: F 32 ASP cc_start: 0.7395 (p0) cc_final: 0.7135 (p0) REVERT: F 71 ASN cc_start: 0.7120 (t0) cc_final: 0.6685 (t0) REVERT: F 183 MET cc_start: 0.7176 (mmt) cc_final: 0.6955 (mmt) REVERT: F 204 GLU cc_start: 0.5884 (tp30) cc_final: 0.5617 (tp30) REVERT: F 248 ARG cc_start: 0.7146 (mmt-90) cc_final: 0.6887 (mmt-90) REVERT: F 385 TYR cc_start: 0.8527 (t80) cc_final: 0.8234 (t80) REVERT: F 428 GLU cc_start: 0.7256 (tt0) cc_final: 0.6924 (tt0) REVERT: d 164 GLU cc_start: 0.6289 (tm-30) cc_final: 0.5793 (tp30) REVERT: g 76 GLN cc_start: 0.6608 (tt0) cc_final: 0.6098 (tt0) REVERT: g 139 LYS cc_start: 0.7146 (ttmt) cc_final: 0.6788 (mtmt) REVERT: g 173 GLU cc_start: 0.6545 (mp0) cc_final: 0.6125 (pm20) REVERT: g 214 TYR cc_start: 0.8115 (p90) cc_final: 0.7131 (p90) REVERT: g 306 ARG cc_start: 0.7720 (tpp80) cc_final: 0.6791 (tpp-160) REVERT: g 353 ILE cc_start: 0.8727 (mt) cc_final: 0.8255 (pt) REVERT: e 12 ARG cc_start: 0.6054 (OUTLIER) cc_final: 0.5841 (ttp80) REVERT: e 110 ARG cc_start: 0.5634 (ptm-80) cc_final: 0.5411 (ptm-80) REVERT: e 125 ARG cc_start: 0.6952 (ttm170) cc_final: 0.6691 (ttp80) outliers start: 100 outliers final: 85 residues processed: 651 average time/residue: 0.4840 time to fit residues: 475.0083 Evaluate side-chains 666 residues out of total 2942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 576 time to evaluate : 3.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 77 MET Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 251 MET Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 452 ASP Chi-restraints excluded: chain C residue 495 GLN Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 193 HIS Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 305 GLU Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 428 GLU Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 467 ASP Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 59 MET Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 193 HIS Chi-restraints excluded: chain E residue 230 SER Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 414 SER Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 280 GLN Chi-restraints excluded: chain F residue 292 MET Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain F residue 488 MET Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain d residue 142 THR Chi-restraints excluded: chain d residue 156 ASN Chi-restraints excluded: chain d residue 179 VAL Chi-restraints excluded: chain d residue 184 VAL Chi-restraints excluded: chain d residue 237 VAL Chi-restraints excluded: chain g residue 53 SER Chi-restraints excluded: chain g residue 129 LEU Chi-restraints excluded: chain g residue 135 ASN Chi-restraints excluded: chain e residue 5 LEU Chi-restraints excluded: chain e residue 9 THR Chi-restraints excluded: chain e residue 12 ARG Chi-restraints excluded: chain e residue 34 LEU Chi-restraints excluded: chain e residue 58 LEU Chi-restraints excluded: chain e residue 62 LEU Chi-restraints excluded: chain e residue 124 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 311 optimal weight: 0.6980 chunk 327 optimal weight: 0.9990 chunk 299 optimal weight: 3.9990 chunk 318 optimal weight: 1.9990 chunk 191 optimal weight: 0.8980 chunk 138 optimal weight: 1.9990 chunk 250 optimal weight: 0.2980 chunk 97 optimal weight: 0.9980 chunk 288 optimal weight: 0.9980 chunk 301 optimal weight: 0.9980 chunk 317 optimal weight: 0.0980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 71 ASN A 201 GLN ** D 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 193 HIS F 389 GLN ** g 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27936 Z= 0.220 Angle : 0.602 12.543 37865 Z= 0.302 Chirality : 0.044 0.261 4451 Planarity : 0.004 0.092 4918 Dihedral : 6.982 111.075 4054 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.74 % Favored : 94.12 % Rotamer: Outliers : 3.06 % Allowed : 20.80 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.14), residues: 3556 helix: 1.03 (0.14), residues: 1488 sheet: -0.87 (0.20), residues: 638 loop : -1.18 (0.16), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP e 15 HIS 0.004 0.001 HIS C 43 PHE 0.019 0.001 PHE E 441 TYR 0.015 0.001 TYR E 385 ARG 0.014 0.000 ARG g 171 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7112 Ramachandran restraints generated. 3556 Oldfield, 0 Emsley, 3556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7112 Ramachandran restraints generated. 3556 Oldfield, 0 Emsley, 3556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 2942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 593 time to evaluate : 3.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 330 TYR cc_start: 0.8224 (t80) cc_final: 0.7984 (t80) REVERT: A 359 ASN cc_start: 0.8080 (t0) cc_final: 0.7868 (t0) REVERT: B 14 ARG cc_start: 0.5617 (ttp-170) cc_final: 0.4675 (ttt90) REVERT: B 37 ASP cc_start: 0.4878 (OUTLIER) cc_final: 0.4189 (p0) REVERT: B 68 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7368 (mt-10) REVERT: B 260 ILE cc_start: 0.8952 (mt) cc_final: 0.8641 (mp) REVERT: B 266 LYS cc_start: 0.6955 (tppt) cc_final: 0.6750 (tptp) REVERT: B 378 LYS cc_start: 0.7583 (mtpt) cc_final: 0.7244 (mttt) REVERT: B 386 GLU cc_start: 0.7289 (mt-10) cc_final: 0.7062 (mt-10) REVERT: B 387 LEU cc_start: 0.7979 (mt) cc_final: 0.7597 (pp) REVERT: B 415 GLN cc_start: 0.7936 (mt0) cc_final: 0.7578 (mp10) REVERT: B 489 LEU cc_start: 0.6148 (OUTLIER) cc_final: 0.5601 (pp) REVERT: B 495 GLN cc_start: 0.6661 (mt0) cc_final: 0.6421 (tm-30) REVERT: B 498 MET cc_start: 0.6767 (tpt) cc_final: 0.4799 (tmm) REVERT: C 90 LYS cc_start: 0.8059 (ttpp) cc_final: 0.7566 (pptt) REVERT: C 402 ASP cc_start: 0.7469 (p0) cc_final: 0.7039 (p0) REVERT: C 456 LYS cc_start: 0.7972 (ttpt) cc_final: 0.7698 (pttp) REVERT: D 22 ARG cc_start: 0.7777 (mmt-90) cc_final: 0.7538 (mpt180) REVERT: D 134 ARG cc_start: 0.7612 (ptm-80) cc_final: 0.6860 (ptp-110) REVERT: D 218 GLU cc_start: 0.6678 (mp0) cc_final: 0.6438 (mp0) REVERT: D 306 MET cc_start: 0.7909 (tpp) cc_final: 0.7592 (tpp) REVERT: E 47 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8295 (pp) REVERT: E 145 LYS cc_start: 0.7890 (tptt) cc_final: 0.7609 (tptt) REVERT: E 382 GLU cc_start: 0.7066 (tp30) cc_final: 0.6825 (tp30) REVERT: E 397 ARG cc_start: 0.7485 (tpp80) cc_final: 0.7067 (tpp-160) REVERT: E 398 TYR cc_start: 0.8196 (t80) cc_final: 0.7850 (t80) REVERT: F 22 ARG cc_start: 0.7453 (mmt90) cc_final: 0.7205 (mmm-85) REVERT: F 32 ASP cc_start: 0.7350 (p0) cc_final: 0.7084 (p0) REVERT: F 71 ASN cc_start: 0.7116 (t0) cc_final: 0.6679 (t0) REVERT: F 183 MET cc_start: 0.7174 (mmt) cc_final: 0.6940 (mmt) REVERT: F 248 ARG cc_start: 0.7136 (mmt-90) cc_final: 0.6868 (mmt-90) REVERT: F 385 TYR cc_start: 0.8514 (t80) cc_final: 0.8220 (t80) REVERT: F 428 GLU cc_start: 0.7206 (tt0) cc_final: 0.6882 (tt0) REVERT: d 164 GLU cc_start: 0.6361 (tm-30) cc_final: 0.5716 (tp30) REVERT: d 176 GLU cc_start: 0.5724 (mm-30) cc_final: 0.5276 (mp0) REVERT: g 55 LYS cc_start: 0.7656 (mttt) cc_final: 0.7352 (mptt) REVERT: g 76 GLN cc_start: 0.6490 (tt0) cc_final: 0.6024 (tt0) REVERT: g 121 MET cc_start: 0.6507 (ptm) cc_final: 0.5642 (ppp) REVERT: g 139 LYS cc_start: 0.7077 (ttmt) cc_final: 0.6699 (mtmt) REVERT: g 173 GLU cc_start: 0.6548 (mp0) cc_final: 0.6128 (pm20) REVERT: g 214 TYR cc_start: 0.8066 (p90) cc_final: 0.7015 (p90) REVERT: g 286 GLN cc_start: 0.5576 (OUTLIER) cc_final: 0.3858 (tm-30) REVERT: g 306 ARG cc_start: 0.7736 (tpp80) cc_final: 0.6760 (tpp-160) REVERT: g 353 ILE cc_start: 0.8721 (mt) cc_final: 0.8243 (pt) REVERT: e 110 ARG cc_start: 0.5603 (ptm-80) cc_final: 0.5383 (ptm-80) REVERT: e 117 LEU cc_start: 0.6911 (tp) cc_final: 0.6682 (tp) REVERT: e 125 ARG cc_start: 0.6951 (ttm170) cc_final: 0.6692 (ttp80) outliers start: 90 outliers final: 77 residues processed: 649 average time/residue: 0.4563 time to fit residues: 442.5286 Evaluate side-chains 667 residues out of total 2942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 586 time to evaluate : 3.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 251 MET Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 452 ASP Chi-restraints excluded: chain C residue 495 GLN Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 193 HIS Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 305 GLU Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 428 GLU Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 467 ASP Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 59 MET Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 230 SER Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 414 SER Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 280 GLN Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain d residue 156 ASN Chi-restraints excluded: chain d residue 179 VAL Chi-restraints excluded: chain d residue 181 THR Chi-restraints excluded: chain d residue 184 VAL Chi-restraints excluded: chain d residue 237 VAL Chi-restraints excluded: chain g residue 53 SER Chi-restraints excluded: chain g residue 135 ASN Chi-restraints excluded: chain g residue 286 GLN Chi-restraints excluded: chain e residue 5 LEU Chi-restraints excluded: chain e residue 9 THR Chi-restraints excluded: chain e residue 19 VAL Chi-restraints excluded: chain e residue 34 LEU Chi-restraints excluded: chain e residue 58 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 209 optimal weight: 0.0670 chunk 337 optimal weight: 0.9980 chunk 205 optimal weight: 0.9980 chunk 159 optimal weight: 0.8980 chunk 234 optimal weight: 0.5980 chunk 353 optimal weight: 0.9990 chunk 325 optimal weight: 0.7980 chunk 281 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 217 optimal weight: 0.9990 chunk 172 optimal weight: 0.6980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 GLN ** C 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 472 GLN F 389 GLN ** g 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27936 Z= 0.216 Angle : 0.603 12.773 37865 Z= 0.302 Chirality : 0.044 0.279 4451 Planarity : 0.004 0.091 4918 Dihedral : 6.922 111.242 4054 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.76 % Favored : 94.09 % Rotamer: Outliers : 2.92 % Allowed : 21.38 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.14), residues: 3556 helix: 1.11 (0.14), residues: 1482 sheet: -0.79 (0.21), residues: 620 loop : -1.14 (0.16), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP e 15 HIS 0.004 0.001 HIS C 43 PHE 0.019 0.001 PHE E 441 TYR 0.017 0.001 TYR d 225 ARG 0.013 0.000 ARG g 171 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7112 Ramachandran restraints generated. 3556 Oldfield, 0 Emsley, 3556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7112 Ramachandran restraints generated. 3556 Oldfield, 0 Emsley, 3556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 2942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 588 time to evaluate : 3.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 ARG cc_start: 0.7614 (mtp85) cc_final: 0.7393 (mtp85) REVERT: A 330 TYR cc_start: 0.8220 (t80) cc_final: 0.7986 (t80) REVERT: B 14 ARG cc_start: 0.5602 (ttp-170) cc_final: 0.4666 (ttt90) REVERT: B 37 ASP cc_start: 0.4831 (OUTLIER) cc_final: 0.4159 (p0) REVERT: B 68 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7406 (mt-10) REVERT: B 260 ILE cc_start: 0.8947 (mt) cc_final: 0.8642 (mp) REVERT: B 266 LYS cc_start: 0.7000 (tppt) cc_final: 0.6760 (tptp) REVERT: B 378 LYS cc_start: 0.7576 (mtpt) cc_final: 0.7251 (mtmt) REVERT: B 415 GLN cc_start: 0.7898 (mt0) cc_final: 0.7609 (mp10) REVERT: B 489 LEU cc_start: 0.6151 (OUTLIER) cc_final: 0.5601 (pp) REVERT: B 495 GLN cc_start: 0.6645 (mt0) cc_final: 0.6409 (tm-30) REVERT: B 498 MET cc_start: 0.6681 (tpt) cc_final: 0.4825 (tmm) REVERT: C 90 LYS cc_start: 0.8056 (ttpp) cc_final: 0.7552 (pptt) REVERT: C 155 ASP cc_start: 0.8105 (m-30) cc_final: 0.7832 (m-30) REVERT: C 402 ASP cc_start: 0.7464 (p0) cc_final: 0.7044 (p0) REVERT: C 456 LYS cc_start: 0.7960 (ttpt) cc_final: 0.7692 (pttp) REVERT: D 22 ARG cc_start: 0.7757 (mmt-90) cc_final: 0.7524 (mpt180) REVERT: D 134 ARG cc_start: 0.7593 (ptm-80) cc_final: 0.7380 (ptt90) REVERT: D 218 GLU cc_start: 0.6712 (mp0) cc_final: 0.6494 (mp0) REVERT: D 306 MET cc_start: 0.7908 (tpp) cc_final: 0.7589 (tpp) REVERT: D 401 LEU cc_start: 0.8016 (pp) cc_final: 0.7300 (mt) REVERT: E 47 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8261 (pp) REVERT: E 382 GLU cc_start: 0.7034 (tp30) cc_final: 0.6804 (tp30) REVERT: E 397 ARG cc_start: 0.7500 (tpp80) cc_final: 0.7074 (tpp-160) REVERT: E 398 TYR cc_start: 0.8195 (t80) cc_final: 0.7853 (t80) REVERT: F 22 ARG cc_start: 0.7464 (mmt90) cc_final: 0.7205 (mmm-85) REVERT: F 32 ASP cc_start: 0.7321 (p0) cc_final: 0.7058 (p0) REVERT: F 71 ASN cc_start: 0.7070 (t0) cc_final: 0.6653 (t0) REVERT: F 204 GLU cc_start: 0.5909 (tp30) cc_final: 0.5675 (tp30) REVERT: F 248 ARG cc_start: 0.7134 (mmt-90) cc_final: 0.6854 (mmt-90) REVERT: F 385 TYR cc_start: 0.8508 (t80) cc_final: 0.8223 (t80) REVERT: F 428 GLU cc_start: 0.7200 (tt0) cc_final: 0.6870 (tt0) REVERT: d 164 GLU cc_start: 0.6347 (tm-30) cc_final: 0.5714 (tp30) REVERT: d 176 GLU cc_start: 0.5678 (mm-30) cc_final: 0.5332 (mp0) REVERT: g 130 CYS cc_start: 0.5525 (m) cc_final: 0.4559 (p) REVERT: g 139 LYS cc_start: 0.7063 (ttmt) cc_final: 0.6691 (mtmt) REVERT: g 173 GLU cc_start: 0.6556 (mp0) cc_final: 0.6123 (pm20) REVERT: g 214 TYR cc_start: 0.8022 (p90) cc_final: 0.6970 (p90) REVERT: g 286 GLN cc_start: 0.5552 (OUTLIER) cc_final: 0.3863 (tm-30) REVERT: g 306 ARG cc_start: 0.7725 (tpp80) cc_final: 0.7427 (tpp-160) REVERT: g 353 ILE cc_start: 0.8735 (mt) cc_final: 0.8254 (pt) REVERT: e 24 LEU cc_start: 0.6433 (tp) cc_final: 0.6192 (pp) REVERT: e 110 ARG cc_start: 0.5694 (ptm-80) cc_final: 0.5473 (ptm-80) REVERT: e 125 ARG cc_start: 0.6949 (ttm170) cc_final: 0.6693 (ttp80) outliers start: 86 outliers final: 77 residues processed: 643 average time/residue: 0.4526 time to fit residues: 433.2685 Evaluate side-chains 662 residues out of total 2942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 581 time to evaluate : 2.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 251 MET Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 452 ASP Chi-restraints excluded: chain C residue 495 GLN Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 193 HIS Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 305 GLU Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 428 GLU Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 467 ASP Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 59 MET Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 230 SER Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 414 SER Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 280 GLN Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain d residue 142 THR Chi-restraints excluded: chain d residue 156 ASN Chi-restraints excluded: chain d residue 179 VAL Chi-restraints excluded: chain d residue 181 THR Chi-restraints excluded: chain d residue 184 VAL Chi-restraints excluded: chain d residue 237 VAL Chi-restraints excluded: chain g residue 53 SER Chi-restraints excluded: chain g residue 135 ASN Chi-restraints excluded: chain g residue 286 GLN Chi-restraints excluded: chain e residue 5 LEU Chi-restraints excluded: chain e residue 9 THR Chi-restraints excluded: chain e residue 19 VAL Chi-restraints excluded: chain e residue 34 LEU Chi-restraints excluded: chain e residue 58 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 223 optimal weight: 0.6980 chunk 300 optimal weight: 0.7980 chunk 86 optimal weight: 0.0370 chunk 259 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 78 optimal weight: 0.1980 chunk 282 optimal weight: 0.6980 chunk 118 optimal weight: 0.6980 chunk 289 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 GLN C 97 GLN ** C 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 504 GLN ** D 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 472 GLN F 389 GLN g 76 GLN ** g 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.157459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.130533 restraints weight = 35452.905| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.65 r_work: 0.3394 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27936 Z= 0.192 Angle : 0.601 12.647 37865 Z= 0.299 Chirality : 0.043 0.270 4451 Planarity : 0.004 0.085 4918 Dihedral : 6.797 111.278 4054 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.65 % Favored : 94.21 % Rotamer: Outliers : 2.72 % Allowed : 21.62 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.14), residues: 3556 helix: 1.17 (0.14), residues: 1483 sheet: -0.79 (0.20), residues: 636 loop : -1.09 (0.16), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP e 15 HIS 0.004 0.001 HIS C 43 PHE 0.019 0.001 PHE E 441 TYR 0.020 0.001 TYR B 457 ARG 0.012 0.000 ARG g 171 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8509.54 seconds wall clock time: 153 minutes 10.84 seconds (9190.84 seconds total)