Starting phenix.real_space_refine on Tue Feb 20 07:03:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vog_21263/02_2024/6vog_21263_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vog_21263/02_2024/6vog_21263.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vog_21263/02_2024/6vog_21263.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vog_21263/02_2024/6vog_21263.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vog_21263/02_2024/6vog_21263_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vog_21263/02_2024/6vog_21263_updated.pdb" } resolution = 4.35 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 14 5.49 5 S 98 5.16 5 C 17048 2.51 5 N 4689 2.21 5 O 5288 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 37": "OD1" <-> "OD2" Residue "A PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 263": "OD1" <-> "OD2" Residue "A GLU 321": "OE1" <-> "OE2" Residue "A ASP 348": "OD1" <-> "OD2" Residue "A PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 499": "OE1" <-> "OE2" Residue "A PHE 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 14": "NH1" <-> "NH2" Residue "B GLU 55": "OE1" <-> "OE2" Residue "B TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 230": "OD1" <-> "OD2" Residue "B TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 290": "OD1" <-> "OD2" Residue "B GLU 392": "OE1" <-> "OE2" Residue "B ASP 404": "OD1" <-> "OD2" Residue "B GLU 419": "OE1" <-> "OE2" Residue "B GLU 460": "OE1" <-> "OE2" Residue "C ASP 37": "OD1" <-> "OD2" Residue "C TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 165": "NH1" <-> "NH2" Residue "C GLU 215": "OE1" <-> "OE2" Residue "C TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 230": "OD1" <-> "OD2" Residue "C ARG 284": "NH1" <-> "NH2" Residue "C ASP 348": "OD1" <-> "OD2" Residue "C PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 450": "OE1" <-> "OE2" Residue "C GLU 484": "OE1" <-> "OE2" Residue "D ASP 83": "OD1" <-> "OD2" Residue "D PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 157": "OD1" <-> "OD2" Residue "D PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 211": "OD1" <-> "OD2" Residue "D GLU 241": "OE1" <-> "OE2" Residue "D PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 284": "OE1" <-> "OE2" Residue "D GLU 311": "OE1" <-> "OE2" Residue "D ASP 366": "OD1" <-> "OD2" Residue "D GLU 416": "OE1" <-> "OE2" Residue "D PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 204": "OE1" <-> "OE2" Residue "E GLU 208": "OE1" <-> "OE2" Residue "E TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 347": "OD1" <-> "OD2" Residue "E ASP 366": "OD1" <-> "OD2" Residue "E TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 403": "OD1" <-> "OD2" Residue "E PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 83": "OD1" <-> "OD2" Residue "F PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 265": "OE1" <-> "OE2" Residue "F PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 336": "OD1" <-> "OD2" Residue "F ASP 369": "OD1" <-> "OD2" Residue "F GLU 382": "OE1" <-> "OE2" Residue "F TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 130": "OD1" <-> "OD2" Residue "d GLU 160": "OE1" <-> "OE2" Residue "d TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 77": "OE1" <-> "OE2" Residue "g PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 126": "OD1" <-> "OD2" Residue "g GLU 142": "OE1" <-> "OE2" Residue "g ASP 224": "OD1" <-> "OD2" Residue "g PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 287": "OD1" <-> "OD2" Residue "g GLU 332": "OE1" <-> "OE2" Residue "e ASP 45": "OD1" <-> "OD2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 27137 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3796 Classifications: {'peptide': 496} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 477} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 3832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3832 Classifications: {'peptide': 501} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 483} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 3829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3829 Classifications: {'peptide': 501} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 481} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 16 Chain: "D" Number of atoms: 3589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3589 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 1, 'PTRANS': 25, 'TRANS': 451} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "E" Number of atoms: 3600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3600 Classifications: {'peptide': 479} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 451} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "F" Number of atoms: 3610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3610 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 451} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "d" Number of atoms: 1360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1360 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 173} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "g" Number of atoms: 2444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2444 Classifications: {'peptide': 321} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 308} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'PHE:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 28 Chain: "e" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 926 Classifications: {'peptide': 130} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 4, 'TRANS': 125} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 58 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: "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: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.07, per 1000 atoms: 0.48 Number of scatterers: 27137 At special positions: 0 Unit cell: (131.04, 151.84, 133.12, 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 98 16.00 P 14 15.00 O 5288 8.00 N 4689 7.00 C 17048 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS g 240 " - pdb=" SG CYS g 246 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.69 Conformation dependent library (CDL) restraints added in 5.2 seconds 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6546 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 124 helices and 29 sheets defined 41.2% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.36 Creating SS restraints... Processing helix chain 'A' and resid 11 through 24 Processing helix chain 'A' and resid 80 through 82 No H-bonds generated for 'chain 'A' and resid 80 through 82' Processing helix chain 'A' and resid 102 through 104 No H-bonds generated for 'chain 'A' and resid 102 through 104' Processing helix chain 'A' and resid 152 through 157 Processing helix chain 'A' and resid 176 through 189 removed outlier: 4.321A pdb=" N GLN A 188 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N GLY A 189 " --> pdb=" O LEU A 185 " (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 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 300 removed outlier: 3.750A pdb=" N PHE A 292 " --> pdb=" O GLY A 289 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 299 " --> pdb=" O SER A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 338 Processing helix chain 'A' and resid 347 through 351 Processing helix chain 'A' and resid 374 through 394 removed outlier: 4.422A pdb=" N LEU A 385 " --> pdb=" O GLY A 381 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N GLU A 386 " --> pdb=" O LYS A 382 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLU A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 421 removed outlier: 5.507A pdb=" N GLN A 410 " --> pdb=" O ALA A 406 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU A 411 " --> pdb=" O THR A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 443 Processing helix chain 'A' and resid 445 through 448 removed outlier: 3.763A pdb=" N SER A 448 " --> pdb=" O TYR A 445 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 445 through 448' Processing helix chain 'A' and resid 451 through 468 removed outlier: 3.868A pdb=" N ARG A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 478 removed outlier: 3.523A pdb=" N GLU A 474 " --> pdb=" O PRO A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 500 removed outlier: 3.529A pdb=" N GLN A 495 " --> pdb=" O LYS A 491 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ARG A 500 " --> pdb=" O GLU A 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 19 Processing helix chain 'B' and resid 57 through 59 No H-bonds generated for 'chain 'B' and resid 57 through 59' Processing helix chain 'B' and resid 102 through 104 No H-bonds generated for 'chain 'B' and resid 102 through 104' Processing helix chain 'B' and resid 152 through 157 Processing helix chain 'B' and resid 176 through 186 Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 218 through 221 Processing helix chain 'B' and resid 233 through 252 Proline residue: B 240 - end of helix Processing helix chain 'B' and resid 264 through 276 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 289 through 299 removed outlier: 4.005A pdb=" N PHE B 292 " --> pdb=" O GLY B 289 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU B 298 " --> pdb=" O HIS B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 338 Processing helix chain 'B' and resid 348 through 351 No H-bonds generated for 'chain 'B' and resid 348 through 351' Processing helix chain 'B' and resid 368 through 371 removed outlier: 3.541A pdb=" N ALA B 371 " --> pdb=" O GLY B 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 368 through 371' Processing helix chain 'B' and resid 374 through 397 removed outlier: 4.639A pdb=" N LYS B 382 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU B 383 " --> pdb=" O VAL B 379 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU B 385 " --> pdb=" O GLY B 381 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE B 396 " --> pdb=" O GLU B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 421 Processing helix chain 'B' and resid 431 through 442 Processing helix chain 'B' and resid 453 through 468 Processing helix chain 'B' and resid 470 through 479 Processing helix chain 'B' and resid 484 through 501 removed outlier: 3.788A pdb=" N GLN B 495 " --> pdb=" O LYS B 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 17 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 185 Processing helix chain 'C' and resid 203 through 216 Processing helix chain 'C' and resid 218 through 220 No H-bonds generated for 'chain 'C' and resid 218 through 220' Processing helix chain 'C' and resid 233 through 251 Proline residue: C 240 - end of helix removed outlier: 3.668A pdb=" N PHE C 250 " --> pdb=" O LEU C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 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 289 through 301 removed outlier: 3.652A pdb=" N PHE C 292 " --> pdb=" O GLY C 289 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS C 295 " --> pdb=" O PHE C 292 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU C 299 " --> pdb=" O SER C 296 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLU C 300 " --> pdb=" O ARG C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 325 No H-bonds generated for 'chain 'C' and resid 323 through 325' Processing helix chain 'C' and resid 330 through 337 removed outlier: 4.150A pdb=" N ILE C 336 " --> pdb=" O PRO C 332 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER C 337 " --> pdb=" O THR C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 351 Processing helix chain 'C' and resid 369 through 371 No H-bonds generated for 'chain 'C' and resid 369 through 371' Processing helix chain 'C' and resid 374 through 398 removed outlier: 7.358A pdb=" N LYS C 382 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LEU C 383 " --> pdb=" O VAL C 379 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N LYS C 384 " --> pdb=" O ALA C 380 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N LEU C 385 " --> pdb=" O GLY C 381 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLN C 398 " --> pdb=" O GLU C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 420 Processing helix chain 'C' and resid 431 through 442 Processing helix chain 'C' and resid 445 through 447 No H-bonds generated for 'chain 'C' and resid 445 through 447' Processing helix chain 'C' and resid 454 through 468 Processing helix chain 'C' and resid 471 through 479 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 158 Processing helix chain 'D' and resid 178 through 192 Processing helix chain 'D' and resid 206 through 218 Processing helix chain 'D' and resid 243 through 262 removed outlier: 5.250A pdb=" N GLY D 250 " --> pdb=" O ARG D 246 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LEU D 251 " --> pdb=" O MET D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 289 Processing helix chain 'D' and resid 302 through 312 removed outlier: 4.311A pdb=" N ARG D 312 " --> pdb=" O SER D 308 " (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 343 Processing helix chain 'D' and resid 354 through 359 Processing helix chain 'D' and resid 377 through 380 No H-bonds generated for 'chain 'D' and resid 377 through 380' Processing helix chain 'D' and resid 382 through 401 Processing helix chain 'D' and resid 405 through 408 No H-bonds generated for 'chain 'D' and resid 405 through 408' Processing helix chain 'D' and resid 415 through 430 Processing helix chain 'D' and resid 451 through 463 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 480 through 494 Processing helix chain 'E' and resid 104 through 106 No H-bonds generated for 'chain 'E' and resid 104 through 106' Processing helix chain 'E' and resid 154 through 159 Processing helix chain 'E' and resid 178 through 189 Processing helix chain 'E' and resid 206 through 218 Processing helix chain 'E' and resid 243 through 262 removed outlier: 3.939A pdb=" N ARG E 248 " --> pdb=" O GLY E 244 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLY E 250 " --> pdb=" O ARG E 246 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N LEU E 251 " --> pdb=" O MET E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 288 removed outlier: 3.710A pdb=" N LEU E 288 " --> pdb=" O GLU E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 312 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 384 through 408 removed outlier: 4.831A pdb=" N ASP E 403 " --> pdb=" O LYS E 399 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N ILE E 404 " --> pdb=" O GLU E 400 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE E 407 " --> pdb=" O ASP E 403 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 431 removed outlier: 4.761A pdb=" N THR E 420 " --> pdb=" O GLU E 416 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA E 422 " --> pdb=" O ARG E 418 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG E 429 " --> pdb=" O ARG E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 442 Processing helix chain 'E' and resid 451 through 463 removed outlier: 3.660A pdb=" N SER E 463 " --> pdb=" O GLN E 459 " (cutoff:3.500A) Processing helix chain 'E' and resid 466 through 468 No H-bonds generated for 'chain 'E' and resid 466 through 468' Processing helix chain 'E' and resid 480 through 495 Processing helix chain 'F' and resid 103 through 106 Processing helix chain 'F' and resid 154 through 159 Processing helix chain 'F' and resid 179 through 189 Processing helix chain 'F' and resid 206 through 219 Processing helix chain 'F' and resid 243 through 262 removed outlier: 4.504A pdb=" N GLY F 250 " --> pdb=" O ARG F 246 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N LEU F 251 " --> pdb=" O MET F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 289 removed outlier: 3.894A pdb=" N LEU F 288 " --> pdb=" O GLU F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 311 Processing helix chain 'F' and resid 337 through 345 removed outlier: 3.867A pdb=" N THR F 342 " --> pdb=" O ALA F 338 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ALA F 344 " --> pdb=" O ALA F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 359 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 405 removed outlier: 3.904A pdb=" N THR F 394 " --> pdb=" O ARG F 390 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ILE F 404 " --> pdb=" O GLU F 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 431 Processing helix chain 'F' and resid 451 through 463 removed outlier: 4.223A pdb=" N PHE F 458 " --> pdb=" O THR F 454 " (cutoff:3.500A) Processing helix chain 'F' and resid 471 through 474 removed outlier: 3.965A pdb=" N PHE F 474 " --> pdb=" O GLU F 471 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 471 through 474' Processing helix chain 'F' and resid 480 through 492 Processing helix chain 'd' and resid 74 through 89 Processing helix chain 'd' and resid 92 through 106 Processing helix chain 'd' and resid 109 through 116 Processing helix chain 'd' and resid 122 through 136 Processing helix chain 'd' and resid 140 through 151 Processing helix chain 'd' and resid 154 through 172 removed outlier: 3.637A pdb=" N VAL d 158 " --> pdb=" O ILE d 155 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N LYS d 159 " --> pdb=" O ASN d 156 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN d 163 " --> pdb=" O GLU d 160 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU d 164 " --> pdb=" O ILE d 161 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLU d 166 " --> pdb=" O ASN d 163 " (cutoff:3.500A) Processing helix chain 'd' and resid 188 through 202 Processing helix chain 'd' and resid 238 through 248 removed outlier: 4.279A pdb=" N LEU d 248 " --> pdb=" O ILE d 244 " (cutoff:3.500A) Processing helix chain 'g' and resid 44 through 99 removed outlier: 3.505A pdb=" N ALA g 63 " --> pdb=" O LYS g 59 " (cutoff:3.500A) Proline residue: g 84 - end of helix Processing helix chain 'g' and resid 133 through 151 removed outlier: 4.681A pdb=" N LEU g 138 " --> pdb=" O ASN g 134 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU g 151 " --> pdb=" O GLU g 147 " (cutoff:3.500A) Processing helix chain 'g' and resid 162 through 169 Processing helix chain 'g' and resid 188 through 203 removed outlier: 4.342A pdb=" N ILE g 194 " --> pdb=" O GLU g 190 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASP g 197 " --> pdb=" O ALA g 193 " (cutoff:3.500A) Processing helix chain 'g' and resid 292 through 361 Proline residue: g 297 - end of helix removed outlier: 4.191A pdb=" N ASP g 328 " --> pdb=" O SER g 324 " (cutoff:3.500A) Processing helix chain 'e' and resid 93 through 103 removed outlier: 4.637A pdb=" N GLU e 100 " --> pdb=" O LEU e 96 " (cutoff:3.500A) Processing helix chain 'e' and resid 111 through 130 removed outlier: 4.041A pdb=" N ASN e 130 " --> pdb=" O VAL e 126 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 30 through 36 removed outlier: 3.564A pdb=" N LEU A 33 " --> pdb=" O ARG A 41 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ARG A 41 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N VAL A 35 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ILE A 39 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN A 66 " --> pdb=" O GLY A 73 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL A 75 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ALA A 64 " --> pdb=" O VAL A 75 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 97 through 100 removed outlier: 3.536A pdb=" N GLU A 126 " --> pdb=" O VAL A 100 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 225 through 227 removed outlier: 3.571A pdb=" N LEU A 258 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N SER A 313 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ILE A 259 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N THR A 315 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N TYR A 261 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 30 through 36 removed outlier: 6.470A pdb=" N ARG B 41 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N VAL B 35 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ILE B 39 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N VAL B 75 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ALA B 64 " --> pdb=" O VAL B 75 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 97 through 100 removed outlier: 4.165A pdb=" N GLU B 126 " --> pdb=" O VAL B 100 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 168 through 170 removed outlier: 3.546A pdb=" N VAL B 320 " --> pdb=" O ILE B 168 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 314 through 316 removed outlier: 6.960A pdb=" N THR B 257 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE B 193 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N ILE B 260 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL B 195 " --> pdb=" O ILE B 260 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL B 225 " --> pdb=" O ALA B 198 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N GLY B 200 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N GLU B 227 " --> pdb=" O GLY B 200 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'C' and resid 88 through 90 removed outlier: 3.521A pdb=" N LEU C 33 " --> pdb=" O ARG C 41 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ARG C 41 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL C 35 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE C 39 " --> pdb=" O VAL C 35 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 98 through 100 removed outlier: 3.685A pdb=" N VAL C 100 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLU C 126 " --> pdb=" O VAL C 100 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 167 through 170 Processing sheet with id= K, first strand: chain 'C' and resid 193 through 198 Processing sheet with id= L, first strand: chain 'C' and resid 64 through 67 removed outlier: 6.113A pdb=" N GLY C 73 " --> pdb=" O LEU C 65 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 23 through 27 removed outlier: 6.540A pdb=" N ASP D 32 " --> pdb=" O ALA D 24 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ILE D 26 " --> pdb=" O VAL D 30 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VAL D 30 " --> pdb=" O ILE D 26 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N VAL D 77 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N VAL D 65 " --> pdb=" O VAL D 77 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 99 through 101 Processing sheet with id= O, first strand: chain 'D' and resid 167 through 169 removed outlier: 8.318A pdb=" N ILE D 168 " --> pdb=" O ILE D 321 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N SER D 323 " --> pdb=" O ILE D 168 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 200 through 204 removed outlier: 7.614A pdb=" N VAL D 235 " --> pdb=" O GLY D 201 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N GLY D 203 " --> pdb=" O VAL D 235 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N GLY D 237 " --> pdb=" O GLY D 203 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'E' and resid 23 through 27 removed outlier: 6.548A pdb=" N ASP E 32 " --> pdb=" O ALA E 24 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ILE E 26 " --> pdb=" O VAL E 30 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL E 30 " --> pdb=" O ILE E 26 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLN E 67 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL E 77 " --> pdb=" O VAL E 65 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N VAL E 65 " --> pdb=" O VAL E 77 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 99 through 101 Processing sheet with id= S, first strand: chain 'E' and resid 348 through 351 removed outlier: 6.562A pdb=" N SER E 323 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N LEU E 170 " --> pdb=" O SER E 323 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N GLN E 325 " --> pdb=" O LEU E 170 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N GLY E 172 " --> pdb=" O GLN E 325 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL E 327 " --> pdb=" O GLY E 172 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 199 through 204 Processing sheet with id= U, first strand: chain 'F' and resid 20 through 22 Processing sheet with id= V, first strand: chain 'F' and resid 23 through 27 removed outlier: 6.636A pdb=" N ASP F 32 " --> pdb=" O ALA F 24 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ILE F 26 " --> pdb=" O VAL F 30 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL F 30 " --> pdb=" O ILE F 26 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N VAL F 77 " --> pdb=" O VAL F 65 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N VAL F 65 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL F 61 " --> pdb=" O VAL F 49 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 99 through 101 Processing sheet with id= X, first strand: chain 'F' and resid 348 through 350 removed outlier: 6.347A pdb=" N SER F 323 " --> pdb=" O ILE F 168 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N LEU F 170 " --> pdb=" O SER F 323 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLN F 325 " --> pdb=" O LEU F 170 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'F' and resid 200 through 204 removed outlier: 7.504A pdb=" N VAL F 235 " --> pdb=" O GLY F 201 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N GLY F 203 " --> pdb=" O VAL F 235 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N GLY F 237 " --> pdb=" O GLY F 203 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'g' and resid 226 through 228 removed outlier: 3.591A pdb=" N VAL g 226 " --> pdb=" O TYR g 214 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N TYR g 214 " --> pdb=" O VAL g 226 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N THR g 156 " --> pdb=" O LEU g 120 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N VAL g 122 " --> pdb=" O THR g 156 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ILE g 158 " --> pdb=" O VAL g 122 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ARG g 178 " --> pdb=" O SER g 159 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'g' and resid 253 through 258 removed outlier: 3.747A pdb=" N LEU g 254 " --> pdb=" O ASP g 269 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ASP g 269 " --> pdb=" O LEU g 254 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'e' and resid 5 through 8 removed outlier: 6.507A pdb=" N ILE e 74 " --> pdb=" O CYS e 6 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LEU e 8 " --> pdb=" O ILE e 74 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N ILE e 76 " --> pdb=" O LEU e 8 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR e 42 " --> pdb=" O ALA e 67 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'e' and resid 24 through 26 1049 hydrogen bonds defined for protein. 2997 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: 11.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8222 1.33 - 1.45: 3776 1.45 - 1.57: 15307 1.57 - 1.69: 23 1.69 - 1.81: 185 Bond restraints: 27513 Sorted by residual: bond pdb=" C4 ATP A 601 " pdb=" C5 ATP A 601 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.61e+01 bond pdb=" C4 ATP C 601 " pdb=" C5 ATP C 601 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.52e+01 bond pdb=" C4 ATP F 601 " pdb=" C5 ATP F 601 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.34e+01 bond pdb=" C4 ATP B 601 " pdb=" C5 ATP B 601 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.75e+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 27508 not shown) Histogram of bond angle deviations from ideal: 98.45 - 106.17: 718 106.17 - 113.90: 16070 113.90 - 121.63: 14372 121.63 - 129.35: 6107 129.35 - 137.08: 60 Bond angle restraints: 37327 Sorted by residual: angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 118.43 21.44 1.00e+00 1.00e+00 4.60e+02 angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 119.32 20.55 1.00e+00 1.00e+00 4.22e+02 angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 119.78 20.09 1.00e+00 1.00e+00 4.04e+02 angle pdb=" PA ATP A 601 " pdb=" O3A ATP A 601 " pdb=" PB ATP A 601 " ideal model delta sigma weight residual 136.83 117.14 19.69 1.00e+00 1.00e+00 3.88e+02 angle pdb=" PB ATP F 601 " pdb=" O3B ATP F 601 " pdb=" PG ATP F 601 " ideal model delta sigma weight residual 139.87 120.88 18.99 1.00e+00 1.00e+00 3.61e+02 ... (remaining 37322 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.61: 15609 23.61 - 47.22: 1133 47.22 - 70.84: 125 70.84 - 94.45: 48 94.45 - 118.06: 3 Dihedral angle restraints: 16918 sinusoidal: 6718 harmonic: 10200 Sorted by residual: dihedral pdb=" CA TYR D 362 " pdb=" C TYR D 362 " pdb=" N PRO D 363 " pdb=" CA PRO D 363 " ideal model delta harmonic sigma weight residual 180.00 120.03 59.97 0 5.00e+00 4.00e-02 1.44e+02 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 -126.80 -53.20 0 5.00e+00 4.00e-02 1.13e+02 dihedral pdb=" CA ALA D 295 " pdb=" C ALA D 295 " pdb=" N VAL D 296 " pdb=" CA VAL D 296 " ideal model delta harmonic sigma weight residual -180.00 -127.78 -52.22 0 5.00e+00 4.00e-02 1.09e+02 ... (remaining 16915 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 3958 0.090 - 0.181: 438 0.181 - 0.271: 24 0.271 - 0.361: 4 0.361 - 0.452: 1 Chirality restraints: 4425 Sorted by residual: chirality pdb=" CB ILE B 331 " pdb=" CA ILE B 331 " pdb=" CG1 ILE B 331 " pdb=" CG2 ILE B 331 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.45 2.00e-01 2.50e+01 5.10e+00 chirality pdb=" CB ILE B 169 " pdb=" CA ILE B 169 " pdb=" CG1 ILE B 169 " pdb=" CG2 ILE B 169 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" CB ILE g 239 " pdb=" CA ILE g 239 " pdb=" CG1 ILE g 239 " pdb=" CG2 ILE g 239 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 3.06e+00 ... (remaining 4422 not shown) Planarity restraints: 4851 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR D 362 " -0.048 5.00e-02 4.00e+02 7.23e-02 8.37e+00 pdb=" N PRO D 363 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO D 363 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 363 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA F 338 " 0.047 5.00e-02 4.00e+02 7.09e-02 8.04e+00 pdb=" N PRO F 339 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO F 339 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO F 339 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 295 " 0.013 2.00e-02 2.50e+03 2.60e-02 6.75e+00 pdb=" C ALA D 295 " -0.045 2.00e-02 2.50e+03 pdb=" O ALA D 295 " 0.017 2.00e-02 2.50e+03 pdb=" N VAL D 296 " 0.015 2.00e-02 2.50e+03 ... (remaining 4848 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 6296 2.77 - 3.31: 29404 3.31 - 3.84: 50805 3.84 - 4.37: 58265 4.37 - 4.90: 93777 Nonbonded interactions: 238547 Sorted by model distance: nonbonded pdb=" OH TYR B 330 " pdb=" OE2 GLU D 284 " model vdw 2.242 2.440 nonbonded pdb=" O VAL D 102 " pdb=" OG1 THR D 128 " model vdw 2.243 2.440 nonbonded pdb=" O GLY F 450 " pdb=" OG1 THR F 454 " model vdw 2.252 2.440 nonbonded pdb=" OG1 THR A 228 " pdb=" OD1 ASP A 230 " model vdw 2.253 2.440 nonbonded pdb=" O ILE A 475 " pdb=" OG1 THR A 479 " model vdw 2.258 2.440 ... (remaining 238542 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 8 and (name N or name CA or name C or name O or name CB ) \ ) or resid 9 through 15 or (resid 16 and (name N or name CA or name C or name O \ or name CB )) or resid 17 through 23 or (resid 24 through 25 and (name N or name \ CA or name C or name O or name CB )) or resid 26 through 322 or (resid 323 thro \ ugh 324 and (name N or name CA or name C or name O or name CB )) or resid 325 th \ rough 398 or (resid 399 through 400 and (name N or name CA or name C or name O o \ r name CB )) or resid 401 through 471 or (resid 472 and (name N or name CA or na \ me C or name O or name CB )) or resid 473 through 503 or resid 601)) selection = (chain 'B' and (resid 8 through 15 or (resid 16 and (name N or name CA or name C \ or name O or name CB )) or resid 17 through 24 or (resid 25 and (name N or name \ CA or name C or name O or name CB )) or resid 26 through 393 or (resid 394 thro \ ugh 397 and (name N or name CA or name C or name O or name CB )) or resid 398 or \ (resid 399 through 400 and (name N or name CA or name C or name O or name CB )) \ or resid 401 through 432 or (resid 433 and (name N or name CA or name C or name \ O or name CB )) or resid 434 through 503 or resid 601)) selection = (chain 'C' and ((resid 8 and (name N or name CA or name C or name O or name CB ) \ ) or resid 9 through 23 or (resid 24 through 25 and (name N or name CA or name C \ or name O or name CB )) or resid 26 through 322 or (resid 323 through 324 and ( \ name N or name CA or name C or name O or name CB )) or resid 325 through 393 or \ (resid 394 through 397 and (name N or name CA or name C or name O or name CB )) \ or resid 398 through 432 or (resid 433 and (name N or name CA or name C or name \ O or name CB )) or resid 434 through 471 or (resid 472 and (name N or name CA or \ name C or name O or name CB )) or resid 473 through 503 or resid 601)) } ncs_group { reference = (chain 'D' and (resid 19 through 39 or (resid 40 and (name N or name CA or name \ C or name O or name CB )) or resid 41 through 52 or (resid 53 and (name N or nam \ e CA or name C or name O or name CB )) or resid 54 through 58 or (resid 59 and ( \ name N or name CA or name C or name O or name CB )) or resid 60 through 115 or ( \ resid 116 and (name N or name CA or name C or name O or name CB )) or resid 117 \ through 118 or (resid 119 and (name N or name CA or name C or name O or name CB \ )) or resid 120 through 260 or (resid 261 and (name N or name CA or name C or na \ me O or name CB )) or resid 262 through 310 or (resid 311 and (name N or name CA \ or name C or name O or name CB )) or resid 312 through 407 or (resid 408 and (n \ ame N or name CA or name C or name O or name CB )) or resid 409 through 416 or ( \ resid 417 and (name N or name CA or name C or name O or name CB )) or resid 418 \ through 494)) selection = (chain 'E' and (resid 19 through 56 or (resid 57 and (name N or name CA or name \ C or name O or name CB )) or resid 58 through 78 or (resid 79 and (name N or nam \ e CA or name C or name O or name CB )) or resid 80 through 260 or (resid 261 and \ (name N or name CA or name C or name O or name CB )) or resid 262 through 331 o \ r (resid 332 through 333 and (name N or name CA or name C or name O or name CB ) \ ) or resid 334 through 407 or (resid 408 and (name N or name CA or name C or nam \ e O or name CB )) or resid 409 through 414 or (resid 415 and (name N or name CA \ or name C or name O or name CB )) or resid 416 through 446 or (resid 447 and (na \ me N or name CA or name C or name O or name CB )) or resid 448 through 464 or (r \ esid 465 and (name N or name CA or name C or name O or name CB )) or resid 466 t \ hrough 494)) selection = (chain 'F' and (resid 19 through 39 or (resid 40 and (name N or name CA or name \ C or name O or name CB )) or resid 41 through 52 or (resid 53 and (name N or nam \ e CA or name C or name O or name CB )) or resid 54 through 56 or (resid 57 and ( \ name N or name CA or name C or name O or name CB )) or resid 58 or (resid 59 and \ (name N or name CA or name C or name O or name CB )) or resid 60 through 78 or \ (resid 79 and (name N or name CA or name C or name O or name CB )) or resid 80 t \ hrough 115 or (resid 116 and (name N or name CA or name C or name O or name CB ) \ ) or resid 117 through 118 or (resid 119 and (name N or name CA or name C or nam \ e O or name CB )) or resid 120 through 310 or (resid 311 and (name N or name CA \ or name C or name O or name CB )) or resid 312 through 317 or (resid 318 and (na \ me N or name CA or name C or name O or name CB )) or resid 319 through 331 or (r \ esid 332 through 333 and (name N or name CA or name C or name O or name CB )) or \ resid 334 through 414 or (resid 415 and (name N or name CA or name C or name O \ or name CB )) or resid 416 or (resid 417 and (name N or name CA or name C or nam \ e O or name CB )) or resid 418 through 446 or (resid 447 and (name N or name CA \ or name C or name O or name CB )) or resid 448 through 464 or (resid 465 and (na \ me N or name CA or name C or name O or name CB )) or resid 466 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.070 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: 10.120 Check model and map are aligned: 0.350 Set scattering table: 0.230 Process input model: 70.430 Find NCS groups from input model: 2.140 Set up NCS constraints: 0.160 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:3.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 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 : 0.007 0.081 27513 Z= 0.430 Angle : 1.078 21.440 37327 Z= 0.658 Chirality : 0.056 0.452 4425 Planarity : 0.007 0.072 4851 Dihedral : 16.400 118.062 10369 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.80 % Favored : 91.11 % Rotamer: Outliers : 0.49 % Allowed : 13.12 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.21 % Twisted Proline : 0.68 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.94 (0.12), residues: 3544 helix: -2.16 (0.10), residues: 1482 sheet: -3.57 (0.20), residues: 441 loop : -2.68 (0.13), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP e 15 HIS 0.009 0.002 HIS C 256 PHE 0.037 0.003 PHE F 343 TYR 0.024 0.003 TYR A 271 ARG 0.017 0.001 ARG B 107 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 964 residues out of total 2933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 950 time to evaluate : 3.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.7037 (tp30) cc_final: 0.6736 (tp30) REVERT: A 76 LEU cc_start: 0.9453 (mt) cc_final: 0.9224 (mt) REVERT: A 169 ILE cc_start: 0.8396 (tp) cc_final: 0.8183 (tp) REVERT: A 219 MET cc_start: 0.8268 (ppp) cc_final: 0.8001 (ppp) REVERT: A 230 ASP cc_start: 0.7896 (p0) cc_final: 0.7527 (p0) REVERT: A 251 MET cc_start: 0.8095 (tmm) cc_final: 0.7552 (ttp) REVERT: A 266 LYS cc_start: 0.8029 (mmtt) cc_final: 0.7569 (mmmm) REVERT: A 278 LEU cc_start: 0.7753 (mt) cc_final: 0.7481 (mt) REVERT: A 287 TYR cc_start: 0.7333 (m-80) cc_final: 0.7004 (m-80) REVERT: A 292 PHE cc_start: 0.8164 (t80) cc_final: 0.7617 (t80) REVERT: A 300 GLU cc_start: 0.8491 (tt0) cc_final: 0.8009 (mt-10) REVERT: A 309 LEU cc_start: 0.9223 (mm) cc_final: 0.8992 (tt) REVERT: A 314 MET cc_start: 0.7629 (ttm) cc_final: 0.7293 (ttp) REVERT: A 333 THR cc_start: 0.9105 (t) cc_final: 0.8714 (t) REVERT: A 349 LEU cc_start: 0.9243 (mt) cc_final: 0.9024 (mt) REVERT: A 376 MET cc_start: 0.7723 (tpp) cc_final: 0.7417 (tpp) REVERT: A 436 MET cc_start: 0.9145 (ppp) cc_final: 0.8670 (ppp) REVERT: A 464 TYR cc_start: 0.7360 (t80) cc_final: 0.7144 (t80) REVERT: B 15 GLU cc_start: 0.9137 (tt0) cc_final: 0.8546 (mm-30) REVERT: B 147 LEU cc_start: 0.8826 (tt) cc_final: 0.8554 (tt) REVERT: B 194 CYS cc_start: 0.8989 (m) cc_final: 0.8561 (m) REVERT: B 278 LEU cc_start: 0.9333 (mm) cc_final: 0.9105 (mm) REVERT: B 293 TYR cc_start: 0.7062 (t80) cc_final: 0.6038 (t80) REVERT: B 360 VAL cc_start: 0.8372 (m) cc_final: 0.8156 (t) REVERT: B 386 GLU cc_start: 0.7975 (tp30) cc_final: 0.7273 (tm-30) REVERT: B 449 LEU cc_start: 0.7171 (mm) cc_final: 0.6669 (mm) REVERT: B 453 GLN cc_start: 0.9216 (mm110) cc_final: 0.8987 (mp10) REVERT: B 480 LYS cc_start: 0.8719 (mtmt) cc_final: 0.8411 (mmtt) REVERT: C 14 ARG cc_start: 0.5918 (mmt90) cc_final: 0.5505 (mpt180) REVERT: C 49 MET cc_start: 0.7734 (tpt) cc_final: 0.6206 (tpt) REVERT: C 55 GLU cc_start: 0.8338 (tp30) cc_final: 0.8112 (tp30) REVERT: C 77 MET cc_start: 0.7670 (ppp) cc_final: 0.7435 (ppp) REVERT: C 108 VAL cc_start: 0.9053 (t) cc_final: 0.8658 (t) REVERT: C 194 CYS cc_start: 0.8645 (m) cc_final: 0.7560 (m) REVERT: C 219 MET cc_start: 0.8011 (ptm) cc_final: 0.7475 (ptm) REVERT: C 228 THR cc_start: 0.8442 (p) cc_final: 0.7960 (t) REVERT: C 251 MET cc_start: 0.8047 (ttp) cc_final: 0.6997 (ttp) REVERT: C 258 LEU cc_start: 0.9236 (tt) cc_final: 0.8991 (tt) REVERT: C 271 TYR cc_start: 0.8234 (t80) cc_final: 0.7957 (t80) REVERT: C 273 GLN cc_start: 0.8343 (tt0) cc_final: 0.7775 (tt0) REVERT: C 345 LEU cc_start: 0.7801 (mm) cc_final: 0.7004 (mp) REVERT: C 392 GLU cc_start: 0.8993 (tm-30) cc_final: 0.8715 (tm-30) REVERT: C 433 GLU cc_start: 0.6948 (tm-30) cc_final: 0.6703 (tp30) REVERT: C 434 GLN cc_start: 0.9076 (mt0) cc_final: 0.8529 (mt0) REVERT: C 436 MET cc_start: 0.8116 (mtt) cc_final: 0.7806 (mtt) REVERT: C 449 LEU cc_start: 0.8582 (mt) cc_final: 0.8150 (mt) REVERT: C 462 ARG cc_start: 0.8843 (ptm-80) cc_final: 0.8355 (ptm-80) REVERT: C 489 LEU cc_start: 0.9122 (mt) cc_final: 0.8365 (mt) REVERT: D 64 GLU cc_start: 0.7760 (mp0) cc_final: 0.7415 (mp0) REVERT: D 65 VAL cc_start: 0.7968 (t) cc_final: 0.7763 (t) REVERT: D 89 MET cc_start: 0.8012 (ttm) cc_final: 0.7669 (mtt) REVERT: D 182 ILE cc_start: 0.8629 (mt) cc_final: 0.8370 (mm) REVERT: D 199 PHE cc_start: 0.8957 (t80) cc_final: 0.8500 (t80) REVERT: D 204 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7554 (tm-30) REVERT: D 212 LEU cc_start: 0.9334 (tp) cc_final: 0.9077 (tt) REVERT: D 247 MET cc_start: 0.8862 (ttp) cc_final: 0.8326 (ttt) REVERT: D 335 THR cc_start: 0.8966 (t) cc_final: 0.8598 (m) REVERT: D 345 HIS cc_start: 0.7095 (t70) cc_final: 0.6093 (t70) REVERT: D 366 ASP cc_start: 0.8285 (t70) cc_final: 0.7973 (t0) REVERT: D 401 LEU cc_start: 0.8591 (mm) cc_final: 0.8343 (tt) REVERT: D 418 ARG cc_start: 0.8983 (ttp80) cc_final: 0.8570 (ttp80) REVERT: D 469 LEU cc_start: 0.8677 (mt) cc_final: 0.8470 (mt) REVERT: E 79 MET cc_start: 0.8198 (mpp) cc_final: 0.6688 (mpp) REVERT: E 102 VAL cc_start: 0.8652 (m) cc_final: 0.7999 (p) REVERT: E 251 LEU cc_start: 0.8052 (tp) cc_final: 0.7485 (tp) REVERT: E 264 ASN cc_start: 0.8133 (m110) cc_final: 0.7847 (t0) REVERT: E 328 TYR cc_start: 0.8422 (t80) cc_final: 0.8133 (t80) REVERT: E 386 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7954 (mm-30) REVERT: E 393 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7599 (tp30) REVERT: E 439 GLU cc_start: 0.8042 (pp20) cc_final: 0.7224 (pm20) REVERT: E 455 ILE cc_start: 0.9167 (pt) cc_final: 0.8801 (mm) REVERT: E 456 ARG cc_start: 0.8428 (tmt-80) cc_final: 0.8081 (tmm160) REVERT: F 168 ILE cc_start: 0.7662 (mm) cc_final: 0.7332 (mt) REVERT: F 213 TYR cc_start: 0.8482 (t80) cc_final: 0.8222 (t80) REVERT: F 214 MET cc_start: 0.8213 (mmp) cc_final: 0.7886 (tmm) REVERT: F 239 MET cc_start: 0.7905 (ttm) cc_final: 0.7424 (ttm) REVERT: F 306 MET cc_start: 0.8408 (tpp) cc_final: 0.7880 (tpt) REVERT: F 475 TYR cc_start: 0.7626 (t80) cc_final: 0.7392 (t80) REVERT: F 481 ASP cc_start: 0.8361 (m-30) cc_final: 0.8126 (m-30) REVERT: F 482 GLU cc_start: 0.8653 (tp30) cc_final: 0.8334 (tp30) REVERT: F 486 LYS cc_start: 0.8901 (tttp) cc_final: 0.8507 (tppp) REVERT: d 84 ASP cc_start: 0.8816 (t0) cc_final: 0.8551 (t0) REVERT: d 98 ASP cc_start: 0.8844 (t0) cc_final: 0.8543 (t0) REVERT: d 104 ARG cc_start: 0.8675 (tpt170) cc_final: 0.8327 (mmm-85) REVERT: d 112 TYR cc_start: 0.8711 (t80) cc_final: 0.8412 (t80) REVERT: d 114 PHE cc_start: 0.8966 (t80) cc_final: 0.8234 (t80) REVERT: d 125 LYS cc_start: 0.8275 (mtpt) cc_final: 0.7709 (mtpp) REVERT: d 164 GLU cc_start: 0.7664 (mm-30) cc_final: 0.6178 (tp30) REVERT: d 167 ASP cc_start: 0.8860 (t70) cc_final: 0.8588 (p0) REVERT: d 193 GLN cc_start: 0.8966 (tp-100) cc_final: 0.8514 (tt0) REVERT: d 235 MET cc_start: 0.7276 (ttp) cc_final: 0.7032 (ttp) REVERT: g 64 MET cc_start: 0.7920 (tpp) cc_final: 0.7420 (tpp) REVERT: g 96 MET cc_start: 0.8356 (mmp) cc_final: 0.7906 (mmm) REVERT: g 189 LYS cc_start: 0.8839 (mttp) cc_final: 0.8384 (mmmt) REVERT: g 287 ASP cc_start: 0.8787 (t70) cc_final: 0.8536 (m-30) REVERT: g 310 GLU cc_start: 0.8300 (tt0) cc_final: 0.7565 (tp30) REVERT: e 11 ASN cc_start: 0.8219 (p0) cc_final: 0.8014 (p0) REVERT: e 53 LEU cc_start: 0.6818 (tp) cc_final: 0.6614 (mt) REVERT: e 54 ASN cc_start: 0.8494 (m110) cc_final: 0.8211 (m-40) REVERT: e 124 THR cc_start: 0.8330 (m) cc_final: 0.7821 (m) REVERT: e 127 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7704 (mp0) outliers start: 14 outliers final: 5 residues processed: 958 average time/residue: 0.4029 time to fit residues: 595.8605 Evaluate side-chains 602 residues out of total 2933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 597 time to evaluate : 3.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 297 optimal weight: 2.9990 chunk 266 optimal weight: 0.9980 chunk 148 optimal weight: 8.9990 chunk 91 optimal weight: 8.9990 chunk 179 optimal weight: 1.9990 chunk 142 optimal weight: 0.6980 chunk 275 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 167 optimal weight: 7.9990 chunk 205 optimal weight: 5.9990 chunk 319 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS A 66 ASN A 201 GLN A 214 GLN A 342 GLN A 389 GLN ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 ASN B 256 HIS B 468 ASN ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN C 201 GLN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 ASN ** D 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 389 GLN D 433 GLN E 25 GLN ** E 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 376 GLN ** E 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 ASN F 141 GLN ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 240 ASN F 299 GLN ** F 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 489 ASN ** d 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 76 GLN g 243 ASN g 286 GLN ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 309 GLN g 342 ASN e 54 ASN e 56 GLN e 72 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 27513 Z= 0.259 Angle : 0.705 10.656 37327 Z= 0.363 Chirality : 0.046 0.230 4425 Planarity : 0.005 0.073 4851 Dihedral : 8.451 112.481 4002 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 22.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.90 % Favored : 92.04 % Rotamer: Outliers : 0.14 % Allowed : 6.81 % Favored : 93.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.21 % Twisted Proline : 0.68 % 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: -2.79 (0.13), residues: 3544 helix: -0.89 (0.12), residues: 1479 sheet: -3.39 (0.19), residues: 473 loop : -2.22 (0.15), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP e 15 HIS 0.008 0.001 HIS C 256 PHE 0.037 0.002 PHE F 343 TYR 0.031 0.002 TYR A 221 ARG 0.019 0.001 ARG D 22 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 757 residues out of total 2933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 753 time to evaluate : 3.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.8384 (tt0) cc_final: 0.7905 (tt0) REVERT: A 57 GLU cc_start: 0.7326 (tp30) cc_final: 0.6886 (tp30) REVERT: A 61 ILE cc_start: 0.8673 (pt) cc_final: 0.8097 (pt) REVERT: A 76 LEU cc_start: 0.9427 (mt) cc_final: 0.9189 (mt) REVERT: A 77 MET cc_start: 0.8020 (mtp) cc_final: 0.7593 (mtp) REVERT: A 141 ARG cc_start: 0.8446 (tpp80) cc_final: 0.7705 (ttp80) REVERT: A 197 VAL cc_start: 0.9095 (t) cc_final: 0.8797 (m) REVERT: A 251 MET cc_start: 0.8158 (tmm) cc_final: 0.7744 (ttp) REVERT: A 278 LEU cc_start: 0.7971 (mt) cc_final: 0.7652 (mt) REVERT: A 287 TYR cc_start: 0.7358 (m-80) cc_final: 0.7136 (m-80) REVERT: A 292 PHE cc_start: 0.7975 (t80) cc_final: 0.7544 (t80) REVERT: A 300 GLU cc_start: 0.8539 (tt0) cc_final: 0.7861 (mt-10) REVERT: A 333 THR cc_start: 0.8987 (t) cc_final: 0.8568 (t) REVERT: A 436 MET cc_start: 0.9118 (ppp) cc_final: 0.8699 (ppp) REVERT: A 498 MET cc_start: 0.8007 (mmm) cc_final: 0.7749 (tpp) REVERT: B 37 ASP cc_start: 0.7845 (m-30) cc_final: 0.6870 (m-30) REVERT: B 67 LEU cc_start: 0.6773 (pp) cc_final: 0.6558 (pp) REVERT: B 77 MET cc_start: 0.8921 (mtt) cc_final: 0.8626 (mtm) REVERT: B 145 GLU cc_start: 0.7094 (mm-30) cc_final: 0.6638 (tp30) REVERT: B 171 ASP cc_start: 0.7314 (t0) cc_final: 0.6879 (m-30) REVERT: B 194 CYS cc_start: 0.9001 (m) cc_final: 0.8637 (m) REVERT: B 274 MET cc_start: 0.8601 (ptm) cc_final: 0.8286 (tmm) REVERT: B 293 TYR cc_start: 0.7385 (t80) cc_final: 0.6546 (t80) REVERT: B 321 GLU cc_start: 0.7355 (pt0) cc_final: 0.7011 (pt0) REVERT: B 453 GLN cc_start: 0.9224 (mm110) cc_final: 0.8988 (mm-40) REVERT: B 480 LYS cc_start: 0.8708 (mtmt) cc_final: 0.8394 (mmtt) REVERT: B 482 PHE cc_start: 0.7668 (p90) cc_final: 0.7426 (p90) REVERT: B 498 MET cc_start: 0.8478 (ttm) cc_final: 0.8187 (mtt) REVERT: C 15 GLU cc_start: 0.8508 (tm-30) cc_final: 0.7637 (mm-30) REVERT: C 45 LEU cc_start: 0.8625 (tp) cc_final: 0.8218 (tt) REVERT: C 49 MET cc_start: 0.7763 (tpt) cc_final: 0.6289 (tpt) REVERT: C 105 LEU cc_start: 0.9267 (mp) cc_final: 0.9019 (mp) REVERT: C 108 VAL cc_start: 0.9123 (t) cc_final: 0.8884 (t) REVERT: C 165 ARG cc_start: 0.5662 (ptp90) cc_final: 0.5093 (ptp90) REVERT: C 219 MET cc_start: 0.8501 (ptm) cc_final: 0.8023 (ptm) REVERT: C 251 MET cc_start: 0.7845 (ttp) cc_final: 0.6946 (ttp) REVERT: C 273 GLN cc_start: 0.8552 (tt0) cc_final: 0.7566 (tt0) REVERT: C 365 SER cc_start: 0.8925 (p) cc_final: 0.8666 (p) REVERT: C 385 LEU cc_start: 0.8080 (mt) cc_final: 0.7767 (mt) REVERT: C 433 GLU cc_start: 0.7078 (tm-30) cc_final: 0.6707 (tp30) REVERT: C 434 GLN cc_start: 0.8898 (mt0) cc_final: 0.8696 (mt0) REVERT: C 436 MET cc_start: 0.8077 (mtt) cc_final: 0.7729 (mtt) REVERT: C 462 ARG cc_start: 0.8942 (ptm-80) cc_final: 0.8624 (ptm-80) REVERT: D 63 CYS cc_start: 0.8720 (m) cc_final: 0.8219 (m) REVERT: D 204 GLU cc_start: 0.7701 (tm-30) cc_final: 0.7456 (tm-30) REVERT: D 216 MET cc_start: 0.8925 (mtp) cc_final: 0.8624 (mtp) REVERT: D 239 MET cc_start: 0.8507 (mmm) cc_final: 0.8100 (mmm) REVERT: D 247 MET cc_start: 0.8684 (ttp) cc_final: 0.8415 (ttt) REVERT: D 292 MET cc_start: 0.8173 (ttm) cc_final: 0.7853 (ttm) REVERT: D 311 GLU cc_start: 0.8658 (tm-30) cc_final: 0.8218 (tm-30) REVERT: D 345 HIS cc_start: 0.7441 (t70) cc_final: 0.6947 (t70) REVERT: D 366 ASP cc_start: 0.8531 (t70) cc_final: 0.7891 (t0) REVERT: D 453 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8236 (mm-30) REVERT: D 461 ILE cc_start: 0.7808 (mt) cc_final: 0.7452 (mt) REVERT: D 466 LEU cc_start: 0.8256 (tp) cc_final: 0.7633 (pt) REVERT: E 63 CYS cc_start: 0.9066 (p) cc_final: 0.8508 (p) REVERT: E 79 MET cc_start: 0.8181 (mpp) cc_final: 0.7136 (mpp) REVERT: E 120 ASN cc_start: 0.7942 (m-40) cc_final: 0.7580 (m-40) REVERT: E 223 ASN cc_start: 0.8166 (t0) cc_final: 0.7735 (t0) REVERT: E 264 ASN cc_start: 0.8276 (m110) cc_final: 0.7842 (t0) REVERT: E 291 ARG cc_start: 0.8822 (ttp-110) cc_final: 0.7833 (ttm170) REVERT: E 375 LEU cc_start: 0.9312 (tp) cc_final: 0.9112 (tp) REVERT: E 393 GLU cc_start: 0.8493 (mt-10) cc_final: 0.8246 (tp30) REVERT: E 480 ILE cc_start: 0.8460 (tp) cc_final: 0.8186 (tp) REVERT: E 492 MET cc_start: 0.7150 (tpp) cc_final: 0.6923 (mmm) REVERT: F 72 ASN cc_start: 0.8740 (OUTLIER) cc_final: 0.8312 (p0) REVERT: F 145 LYS cc_start: 0.8286 (tptp) cc_final: 0.7624 (pttm) REVERT: F 168 ILE cc_start: 0.7573 (mm) cc_final: 0.7163 (mt) REVERT: F 184 GLU cc_start: 0.8391 (mm-30) cc_final: 0.8035 (tp30) REVERT: F 239 MET cc_start: 0.7782 (ttm) cc_final: 0.7329 (ttm) REVERT: F 276 PHE cc_start: 0.8605 (t80) cc_final: 0.8271 (t80) REVERT: F 306 MET cc_start: 0.8369 (tpp) cc_final: 0.8094 (tpt) REVERT: F 343 PHE cc_start: 0.7771 (p90) cc_final: 0.7488 (p90) REVERT: F 402 GLN cc_start: 0.8945 (tp40) cc_final: 0.8565 (tp40) REVERT: F 412 GLU cc_start: 0.5960 (mm-30) cc_final: 0.5383 (tp30) REVERT: F 481 ASP cc_start: 0.8408 (m-30) cc_final: 0.8131 (m-30) REVERT: F 482 GLU cc_start: 0.8667 (tp30) cc_final: 0.8434 (tp30) REVERT: F 486 LYS cc_start: 0.8915 (tttp) cc_final: 0.8581 (tppp) REVERT: d 77 ARG cc_start: 0.8571 (mtp180) cc_final: 0.8189 (mtp180) REVERT: d 104 ARG cc_start: 0.8572 (tpt170) cc_final: 0.8159 (mtm180) REVERT: d 112 TYR cc_start: 0.8523 (t80) cc_final: 0.8297 (t80) REVERT: d 138 LEU cc_start: 0.7574 (mt) cc_final: 0.7209 (mp) REVERT: d 139 GLN cc_start: 0.8471 (mm-40) cc_final: 0.7799 (mp10) REVERT: d 164 GLU cc_start: 0.7554 (mm-30) cc_final: 0.7146 (tp30) REVERT: d 193 GLN cc_start: 0.8896 (tp-100) cc_final: 0.8565 (tt0) REVERT: g 189 LYS cc_start: 0.8969 (mttp) cc_final: 0.8514 (mmmt) REVERT: g 260 LYS cc_start: 0.8332 (pttm) cc_final: 0.7809 (pttm) REVERT: g 320 MET cc_start: 0.6561 (ttm) cc_final: 0.6217 (tmm) REVERT: g 354 LEU cc_start: 0.8557 (tt) cc_final: 0.8264 (pp) REVERT: e 19 VAL cc_start: 0.8302 (t) cc_final: 0.7812 (t) REVERT: e 124 THR cc_start: 0.8212 (m) cc_final: 0.7752 (m) REVERT: e 127 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7712 (mp0) outliers start: 4 outliers final: 1 residues processed: 756 average time/residue: 0.3857 time to fit residues: 458.1034 Evaluate side-chains 537 residues out of total 2933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 535 time to evaluate : 3.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 177 optimal weight: 0.8980 chunk 99 optimal weight: 0.0270 chunk 266 optimal weight: 3.9990 chunk 217 optimal weight: 0.9990 chunk 88 optimal weight: 7.9990 chunk 320 optimal weight: 0.8980 chunk 345 optimal weight: 8.9990 chunk 285 optimal weight: 3.9990 chunk 317 optimal weight: 3.9990 chunk 109 optimal weight: 8.9990 chunk 256 optimal weight: 0.9980 overall best weight: 0.7640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 GLN ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 GLN B 186 ASN B 497 GLN ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 GLN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 ASN ** D 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 ASN ** E 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 19 ASN ** F 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 299 GLN ** F 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 472 GLN d 163 ASN g 58 GLN g 243 ASN ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 309 GLN e 56 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27513 Z= 0.191 Angle : 0.671 11.246 37327 Z= 0.335 Chirality : 0.044 0.205 4425 Planarity : 0.005 0.064 4851 Dihedral : 8.011 112.129 4002 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 20.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.08 % Favored : 92.89 % Rotamer: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.21 % Twisted Proline : 0.68 % 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: -2.20 (0.14), residues: 3544 helix: -0.27 (0.13), residues: 1477 sheet: -3.33 (0.19), residues: 486 loop : -1.92 (0.15), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP e 15 HIS 0.006 0.001 HIS D 345 PHE 0.028 0.002 PHE F 343 TYR 0.019 0.002 TYR E 298 ARG 0.011 0.001 ARG B 16 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 733 residues out of total 2933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 733 time to evaluate : 3.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.8264 (tt0) cc_final: 0.7837 (tt0) REVERT: A 57 GLU cc_start: 0.7242 (tp30) cc_final: 0.6861 (tp30) REVERT: A 61 ILE cc_start: 0.8780 (pt) cc_final: 0.8181 (pt) REVERT: A 76 LEU cc_start: 0.9434 (mt) cc_final: 0.9211 (mt) REVERT: A 77 MET cc_start: 0.8081 (mtp) cc_final: 0.7848 (mtp) REVERT: A 251 MET cc_start: 0.8118 (tmm) cc_final: 0.7542 (ttp) REVERT: A 278 LEU cc_start: 0.8032 (mt) cc_final: 0.7762 (mt) REVERT: A 287 TYR cc_start: 0.7258 (m-80) cc_final: 0.6985 (m-10) REVERT: A 300 GLU cc_start: 0.8571 (tt0) cc_final: 0.7996 (mt-10) REVERT: A 314 MET cc_start: 0.7576 (ttm) cc_final: 0.7259 (ttp) REVERT: A 333 THR cc_start: 0.8936 (t) cc_final: 0.8563 (t) REVERT: A 436 MET cc_start: 0.9265 (ppp) cc_final: 0.8753 (ppp) REVERT: A 484 GLU cc_start: 0.8811 (mp0) cc_final: 0.7959 (tm-30) REVERT: A 498 MET cc_start: 0.7943 (mmm) cc_final: 0.7310 (tpp) REVERT: B 14 ARG cc_start: 0.8630 (mtp-110) cc_final: 0.8067 (mtp85) REVERT: B 77 MET cc_start: 0.8905 (mtt) cc_final: 0.8574 (mtm) REVERT: B 145 GLU cc_start: 0.7180 (mm-30) cc_final: 0.6628 (tp30) REVERT: B 194 CYS cc_start: 0.9027 (m) cc_final: 0.8667 (m) REVERT: B 274 MET cc_start: 0.8650 (ptm) cc_final: 0.8276 (tmm) REVERT: B 293 TYR cc_start: 0.7470 (t80) cc_final: 0.6667 (t80) REVERT: B 321 GLU cc_start: 0.7668 (pt0) cc_final: 0.7440 (pt0) REVERT: B 449 LEU cc_start: 0.7344 (mm) cc_final: 0.6887 (mm) REVERT: B 453 GLN cc_start: 0.9226 (mm110) cc_final: 0.8871 (tt0) REVERT: B 462 ARG cc_start: 0.8969 (mtm110) cc_final: 0.8763 (ptp90) REVERT: B 480 LYS cc_start: 0.8641 (mtmt) cc_final: 0.8253 (mmmt) REVERT: B 482 PHE cc_start: 0.7444 (p90) cc_final: 0.7230 (p90) REVERT: C 15 GLU cc_start: 0.8451 (tm-30) cc_final: 0.7593 (mm-30) REVERT: C 49 MET cc_start: 0.7194 (tpt) cc_final: 0.6268 (tpt) REVERT: C 165 ARG cc_start: 0.5387 (ptp90) cc_final: 0.4824 (ptp-170) REVERT: C 219 MET cc_start: 0.8473 (ptm) cc_final: 0.8015 (ptm) REVERT: C 251 MET cc_start: 0.7838 (ttp) cc_final: 0.6662 (ttp) REVERT: C 262 ASP cc_start: 0.7824 (t0) cc_final: 0.7475 (t0) REVERT: C 301 ARG cc_start: 0.7314 (ttm170) cc_final: 0.6861 (ttm170) REVERT: C 365 SER cc_start: 0.9017 (p) cc_final: 0.8723 (p) REVERT: C 385 LEU cc_start: 0.8061 (mt) cc_final: 0.7742 (mt) REVERT: C 409 ASN cc_start: 0.8906 (t0) cc_final: 0.8515 (m-40) REVERT: C 434 GLN cc_start: 0.8835 (mt0) cc_final: 0.8528 (mt0) REVERT: C 436 MET cc_start: 0.8050 (mtt) cc_final: 0.7754 (mtt) REVERT: C 462 ARG cc_start: 0.8907 (ptm-80) cc_final: 0.8588 (ptm-80) REVERT: D 26 ILE cc_start: 0.8062 (tt) cc_final: 0.7834 (tt) REVERT: D 63 CYS cc_start: 0.8771 (m) cc_final: 0.8168 (m) REVERT: D 64 GLU cc_start: 0.7297 (mp0) cc_final: 0.7010 (mp0) REVERT: D 109 ARG cc_start: 0.8371 (mmt-90) cc_final: 0.7873 (mmt90) REVERT: D 182 ILE cc_start: 0.8827 (mm) cc_final: 0.8242 (mm) REVERT: D 292 MET cc_start: 0.8113 (ttm) cc_final: 0.7756 (ttm) REVERT: D 311 GLU cc_start: 0.8630 (tm-30) cc_final: 0.8227 (tm-30) REVERT: D 335 THR cc_start: 0.8804 (t) cc_final: 0.8530 (m) REVERT: D 366 ASP cc_start: 0.8529 (t70) cc_final: 0.8300 (t0) REVERT: D 418 ARG cc_start: 0.8998 (ttp80) cc_final: 0.8655 (ttm110) REVERT: D 453 GLU cc_start: 0.8788 (mm-30) cc_final: 0.8214 (mm-30) REVERT: D 469 LEU cc_start: 0.8691 (mt) cc_final: 0.8396 (mt) REVERT: E 63 CYS cc_start: 0.9034 (p) cc_final: 0.8703 (p) REVERT: E 69 LEU cc_start: 0.8151 (mm) cc_final: 0.7840 (tp) REVERT: E 120 ASN cc_start: 0.7791 (m-40) cc_final: 0.7478 (m-40) REVERT: E 264 ASN cc_start: 0.8261 (m110) cc_final: 0.7805 (t0) REVERT: E 271 PHE cc_start: 0.8216 (m-80) cc_final: 0.7980 (m-80) REVERT: E 279 VAL cc_start: 0.9160 (t) cc_final: 0.8830 (t) REVERT: E 418 ARG cc_start: 0.7233 (ttp-110) cc_final: 0.6896 (ttm110) REVERT: F 145 LYS cc_start: 0.8470 (tptp) cc_final: 0.7875 (pttm) REVERT: F 216 MET cc_start: 0.8520 (tpp) cc_final: 0.8318 (tpp) REVERT: F 239 MET cc_start: 0.7756 (ttm) cc_final: 0.7417 (ttm) REVERT: F 247 MET cc_start: 0.8263 (tpp) cc_final: 0.7685 (tpt) REVERT: F 276 PHE cc_start: 0.8444 (t80) cc_final: 0.8236 (t80) REVERT: F 343 PHE cc_start: 0.7712 (p90) cc_final: 0.7378 (p90) REVERT: F 402 GLN cc_start: 0.8978 (tp40) cc_final: 0.8465 (tp40) REVERT: F 412 GLU cc_start: 0.5865 (mm-30) cc_final: 0.5379 (tp30) REVERT: F 481 ASP cc_start: 0.8366 (m-30) cc_final: 0.8072 (m-30) REVERT: F 482 GLU cc_start: 0.8612 (tp30) cc_final: 0.8339 (tp30) REVERT: F 486 LYS cc_start: 0.8943 (tttp) cc_final: 0.8538 (tppp) REVERT: d 84 ASP cc_start: 0.8932 (t0) cc_final: 0.8630 (t0) REVERT: d 104 ARG cc_start: 0.8603 (tpt170) cc_final: 0.8151 (mtm180) REVERT: d 114 PHE cc_start: 0.8716 (t80) cc_final: 0.8421 (t80) REVERT: d 125 LYS cc_start: 0.7934 (mtpp) cc_final: 0.7331 (mtpp) REVERT: d 154 ARG cc_start: 0.8068 (mmp80) cc_final: 0.7755 (mmp80) REVERT: d 160 GLU cc_start: 0.8886 (tp30) cc_final: 0.8499 (tp30) REVERT: d 164 GLU cc_start: 0.7538 (mm-30) cc_final: 0.7013 (tp30) REVERT: d 193 GLN cc_start: 0.8892 (tp-100) cc_final: 0.8512 (tt0) REVERT: g 45 ARG cc_start: 0.6208 (tpp-160) cc_final: 0.5833 (tpp-160) REVERT: g 81 ASN cc_start: 0.8233 (t0) cc_final: 0.8005 (t0) REVERT: g 189 LYS cc_start: 0.8975 (mttp) cc_final: 0.8521 (mmmt) REVERT: g 301 ASN cc_start: 0.8865 (t0) cc_final: 0.8655 (t0) REVERT: g 303 GLN cc_start: 0.8610 (tp40) cc_final: 0.8259 (tp40) REVERT: g 315 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7788 (tp30) REVERT: g 320 MET cc_start: 0.6560 (ttm) cc_final: 0.6165 (tmm) REVERT: e 11 ASN cc_start: 0.8530 (p0) cc_final: 0.8013 (p0) REVERT: e 18 GLU cc_start: 0.8385 (mt-10) cc_final: 0.7999 (mt-10) REVERT: e 19 VAL cc_start: 0.8456 (t) cc_final: 0.8059 (t) REVERT: e 124 THR cc_start: 0.8137 (m) cc_final: 0.7637 (m) REVERT: e 127 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7643 (mp0) outliers start: 0 outliers final: 0 residues processed: 733 average time/residue: 0.3893 time to fit residues: 448.5820 Evaluate side-chains 537 residues out of total 2933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 537 time to evaluate : 2.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 316 optimal weight: 4.9990 chunk 240 optimal weight: 1.9990 chunk 166 optimal weight: 7.9990 chunk 35 optimal weight: 0.9980 chunk 152 optimal weight: 9.9990 chunk 215 optimal weight: 9.9990 chunk 321 optimal weight: 0.1980 chunk 340 optimal weight: 10.0000 chunk 167 optimal weight: 9.9990 chunk 304 optimal weight: 20.0000 chunk 91 optimal weight: 0.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 ASN B 334 ASN B 342 GLN ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 GLN ** C 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 67 GLN ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 299 GLN ** F 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 247 GLN ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 56 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 27513 Z= 0.266 Angle : 0.693 10.561 37327 Z= 0.349 Chirality : 0.045 0.229 4425 Planarity : 0.005 0.061 4851 Dihedral : 7.962 111.393 4002 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 21.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.21 % Twisted Proline : 0.68 % 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: -1.91 (0.14), residues: 3544 helix: 0.03 (0.13), residues: 1485 sheet: -3.22 (0.20), residues: 479 loop : -1.83 (0.15), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP e 15 HIS 0.006 0.001 HIS D 345 PHE 0.025 0.002 PHE F 343 TYR 0.022 0.002 TYR E 398 ARG 0.009 0.001 ARG E 291 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 2933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 668 time to evaluate : 3.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.7465 (tp30) cc_final: 0.7102 (tp30) REVERT: A 61 ILE cc_start: 0.8680 (pt) cc_final: 0.8123 (pt) REVERT: A 76 LEU cc_start: 0.9427 (mt) cc_final: 0.9205 (mt) REVERT: A 77 MET cc_start: 0.7646 (mtp) cc_final: 0.7426 (mtp) REVERT: A 166 GLU cc_start: 0.7715 (tp30) cc_final: 0.7347 (tp30) REVERT: A 230 ASP cc_start: 0.7764 (p0) cc_final: 0.7449 (p0) REVERT: A 251 MET cc_start: 0.8051 (tmm) cc_final: 0.7709 (ttp) REVERT: A 285 GLU cc_start: 0.8268 (tt0) cc_final: 0.7866 (tt0) REVERT: A 436 MET cc_start: 0.9192 (ppp) cc_final: 0.8686 (ppp) REVERT: A 445 TYR cc_start: 0.6415 (t80) cc_final: 0.5949 (t80) REVERT: A 484 GLU cc_start: 0.8861 (mp0) cc_final: 0.7853 (tm-30) REVERT: A 498 MET cc_start: 0.8405 (tpt) cc_final: 0.7935 (tpt) REVERT: B 76 LEU cc_start: 0.9513 (mp) cc_final: 0.9297 (mm) REVERT: B 77 MET cc_start: 0.8925 (mtt) cc_final: 0.8543 (mtm) REVERT: B 152 ILE cc_start: 0.8914 (tp) cc_final: 0.8614 (pt) REVERT: B 194 CYS cc_start: 0.8959 (m) cc_final: 0.8623 (m) REVERT: B 293 TYR cc_start: 0.7639 (t80) cc_final: 0.7330 (t80) REVERT: B 453 GLN cc_start: 0.9205 (mm110) cc_final: 0.8996 (tt0) REVERT: B 480 LYS cc_start: 0.8734 (mtmt) cc_final: 0.8382 (mmtt) REVERT: C 15 GLU cc_start: 0.8496 (tm-30) cc_final: 0.7614 (mm-30) REVERT: C 49 MET cc_start: 0.7213 (tpt) cc_final: 0.6302 (tpt) REVERT: C 155 ASP cc_start: 0.8055 (t0) cc_final: 0.7822 (t0) REVERT: C 219 MET cc_start: 0.8540 (ptm) cc_final: 0.8064 (ptm) REVERT: C 228 THR cc_start: 0.8147 (p) cc_final: 0.7561 (t) REVERT: C 251 MET cc_start: 0.7498 (ttp) cc_final: 0.6561 (ttp) REVERT: C 266 LYS cc_start: 0.8457 (mmpt) cc_final: 0.8216 (mmmt) REVERT: C 271 TYR cc_start: 0.8488 (t80) cc_final: 0.8282 (t80) REVERT: C 301 ARG cc_start: 0.7351 (ttm170) cc_final: 0.6848 (ttm170) REVERT: C 314 MET cc_start: 0.7623 (ttm) cc_final: 0.7018 (ttm) REVERT: C 365 SER cc_start: 0.8889 (p) cc_final: 0.8601 (p) REVERT: D 40 MET cc_start: 0.8131 (mmm) cc_final: 0.7839 (mmm) REVERT: D 63 CYS cc_start: 0.8802 (m) cc_final: 0.8141 (m) REVERT: D 64 GLU cc_start: 0.7461 (mp0) cc_final: 0.7232 (mp0) REVERT: D 89 MET cc_start: 0.8808 (mtp) cc_final: 0.8517 (mtp) REVERT: D 182 ILE cc_start: 0.8984 (mm) cc_final: 0.8735 (mm) REVERT: D 292 MET cc_start: 0.8111 (ttm) cc_final: 0.7657 (ttm) REVERT: D 305 GLU cc_start: 0.8213 (tt0) cc_final: 0.7955 (tt0) REVERT: D 311 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8149 (tm-30) REVERT: D 345 HIS cc_start: 0.7214 (t-170) cc_final: 0.6887 (t-170) REVERT: D 366 ASP cc_start: 0.8584 (t70) cc_final: 0.7675 (t0) REVERT: D 418 ARG cc_start: 0.8978 (ttp80) cc_final: 0.8647 (ttm110) REVERT: D 453 GLU cc_start: 0.8810 (mm-30) cc_final: 0.8265 (mm-30) REVERT: D 466 LEU cc_start: 0.8436 (tp) cc_final: 0.8211 (tp) REVERT: E 69 LEU cc_start: 0.8162 (mm) cc_final: 0.7831 (tp) REVERT: E 120 ASN cc_start: 0.7738 (m-40) cc_final: 0.7391 (m-40) REVERT: E 336 ASP cc_start: 0.7071 (t0) cc_final: 0.6811 (t0) REVERT: E 375 LEU cc_start: 0.9295 (tp) cc_final: 0.9071 (tp) REVERT: E 393 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8202 (tp30) REVERT: E 396 GLN cc_start: 0.9138 (tp40) cc_final: 0.8698 (tp40) REVERT: E 435 PHE cc_start: 0.7607 (m-80) cc_final: 0.7370 (m-80) REVERT: E 471 GLU cc_start: 0.8664 (pt0) cc_final: 0.8266 (pt0) REVERT: F 145 LYS cc_start: 0.8475 (tptp) cc_final: 0.8066 (pttm) REVERT: F 239 MET cc_start: 0.7741 (ttm) cc_final: 0.7194 (ttm) REVERT: F 311 GLU cc_start: 0.8482 (tp30) cc_final: 0.7989 (tp30) REVERT: F 343 PHE cc_start: 0.7899 (p90) cc_final: 0.7586 (p90) REVERT: F 412 GLU cc_start: 0.6103 (mm-30) cc_final: 0.5683 (tp30) REVERT: F 481 ASP cc_start: 0.8400 (m-30) cc_final: 0.8134 (m-30) REVERT: F 486 LYS cc_start: 0.8880 (tttp) cc_final: 0.8545 (tppp) REVERT: d 104 ARG cc_start: 0.8638 (tpt170) cc_final: 0.8165 (mtm180) REVERT: d 114 PHE cc_start: 0.8963 (t80) cc_final: 0.8631 (t80) REVERT: d 139 GLN cc_start: 0.8617 (mm-40) cc_final: 0.8201 (mp10) REVERT: d 154 ARG cc_start: 0.8224 (mmp80) cc_final: 0.7788 (mmp80) REVERT: d 162 LEU cc_start: 0.8875 (mt) cc_final: 0.8441 (tt) REVERT: d 164 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7424 (mm-30) REVERT: d 193 GLN cc_start: 0.8933 (tp-100) cc_final: 0.8574 (tt0) REVERT: g 81 ASN cc_start: 0.8307 (t0) cc_final: 0.8022 (t0) REVERT: g 189 LYS cc_start: 0.9029 (mttp) cc_final: 0.8594 (mmmt) REVERT: g 232 PRO cc_start: 0.6808 (Cg_endo) cc_final: 0.6518 (Cg_exo) REVERT: g 301 ASN cc_start: 0.8775 (t0) cc_final: 0.8437 (t0) REVERT: g 354 LEU cc_start: 0.8517 (tt) cc_final: 0.8232 (pp) REVERT: e 11 ASN cc_start: 0.8626 (p0) cc_final: 0.7917 (p0) REVERT: e 19 VAL cc_start: 0.8391 (t) cc_final: 0.8111 (t) REVERT: e 80 ASP cc_start: 0.7493 (t0) cc_final: 0.6769 (t0) outliers start: 0 outliers final: 0 residues processed: 668 average time/residue: 0.3883 time to fit residues: 412.5708 Evaluate side-chains 496 residues out of total 2933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 496 time to evaluate : 3.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 283 optimal weight: 0.8980 chunk 193 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 253 optimal weight: 5.9990 chunk 140 optimal weight: 0.9980 chunk 290 optimal weight: 8.9990 chunk 235 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 173 optimal weight: 0.9980 chunk 305 optimal weight: 0.9980 chunk 85 optimal weight: 10.0000 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 ASN B 342 GLN ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 497 GLN D 19 ASN ** D 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 238 GLN ** E 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 67 GLN F 299 GLN ** F 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 58 GLN ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 309 GLN g 331 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 27513 Z= 0.242 Angle : 0.676 11.174 37327 Z= 0.340 Chirality : 0.045 0.250 4425 Planarity : 0.005 0.062 4851 Dihedral : 7.858 112.489 4002 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 22.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 0.03 % Allowed : 3.49 % Favored : 96.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.21 % Twisted Proline : 0.68 % 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: -1.71 (0.14), residues: 3544 helix: 0.18 (0.13), residues: 1472 sheet: -3.08 (0.21), residues: 475 loop : -1.71 (0.15), residues: 1597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP e 15 HIS 0.006 0.001 HIS E 384 PHE 0.022 0.002 PHE F 343 TYR 0.024 0.002 TYR E 298 ARG 0.006 0.001 ARG E 291 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 2933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 666 time to evaluate : 2.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.7461 (tp30) cc_final: 0.7133 (tp30) REVERT: A 76 LEU cc_start: 0.9425 (mt) cc_final: 0.9218 (mt) REVERT: A 77 MET cc_start: 0.7662 (mtp) cc_final: 0.7442 (mtp) REVERT: A 219 MET cc_start: 0.8309 (ppp) cc_final: 0.8078 (ppp) REVERT: A 230 ASP cc_start: 0.7725 (p0) cc_final: 0.7414 (p0) REVERT: A 251 MET cc_start: 0.8051 (tmm) cc_final: 0.7715 (ttp) REVERT: A 285 GLU cc_start: 0.8237 (tt0) cc_final: 0.8012 (tt0) REVERT: A 287 TYR cc_start: 0.7437 (m-80) cc_final: 0.7190 (m-10) REVERT: A 300 GLU cc_start: 0.8747 (mt-10) cc_final: 0.7976 (mt-10) REVERT: A 436 MET cc_start: 0.9263 (ppp) cc_final: 0.8824 (ppp) REVERT: A 445 TYR cc_start: 0.6453 (t80) cc_final: 0.5991 (t80) REVERT: A 460 GLU cc_start: 0.9099 (mp0) cc_final: 0.8676 (mp0) REVERT: A 484 GLU cc_start: 0.8810 (mp0) cc_final: 0.7795 (tm-30) REVERT: A 498 MET cc_start: 0.8350 (tpt) cc_final: 0.7825 (tpt) REVERT: B 75 VAL cc_start: 0.9211 (m) cc_final: 0.8881 (p) REVERT: B 76 LEU cc_start: 0.9495 (mp) cc_final: 0.9288 (mm) REVERT: B 152 ILE cc_start: 0.8958 (tp) cc_final: 0.8655 (pt) REVERT: B 194 CYS cc_start: 0.8974 (m) cc_final: 0.8555 (m) REVERT: B 237 TYR cc_start: 0.8691 (t80) cc_final: 0.8398 (t80) REVERT: B 274 MET cc_start: 0.8732 (ptm) cc_final: 0.8315 (tmm) REVERT: B 293 TYR cc_start: 0.8033 (t80) cc_final: 0.7448 (t80) REVERT: B 462 ARG cc_start: 0.8944 (mtm110) cc_final: 0.8690 (ptp90) REVERT: B 480 LYS cc_start: 0.8752 (mtmt) cc_final: 0.8368 (mmtt) REVERT: C 15 GLU cc_start: 0.8459 (tm-30) cc_final: 0.7515 (mm-30) REVERT: C 49 MET cc_start: 0.7302 (tpt) cc_final: 0.6296 (tpt) REVERT: C 105 LEU cc_start: 0.9089 (mp) cc_final: 0.8882 (mp) REVERT: C 157 MET cc_start: 0.7895 (ptp) cc_final: 0.7652 (ptp) REVERT: C 165 ARG cc_start: 0.5362 (ptp-170) cc_final: 0.4033 (ptp-170) REVERT: C 219 MET cc_start: 0.8552 (ptm) cc_final: 0.8106 (ptm) REVERT: C 228 THR cc_start: 0.8470 (p) cc_final: 0.7792 (t) REVERT: C 251 MET cc_start: 0.7504 (ttp) cc_final: 0.6647 (ttp) REVERT: C 274 MET cc_start: 0.8544 (mmm) cc_final: 0.8258 (mmm) REVERT: C 301 ARG cc_start: 0.7478 (ttm170) cc_final: 0.7188 (ttm170) REVERT: C 314 MET cc_start: 0.7637 (ttm) cc_final: 0.7359 (ttm) REVERT: C 365 SER cc_start: 0.8793 (p) cc_final: 0.8474 (p) REVERT: C 385 LEU cc_start: 0.8221 (mt) cc_final: 0.7965 (mt) REVERT: D 63 CYS cc_start: 0.8826 (m) cc_final: 0.8147 (m) REVERT: D 64 GLU cc_start: 0.7614 (mp0) cc_final: 0.7396 (mp0) REVERT: D 89 MET cc_start: 0.8821 (mtp) cc_final: 0.8585 (mtp) REVERT: D 292 MET cc_start: 0.8083 (ttm) cc_final: 0.7610 (ttm) REVERT: D 311 GLU cc_start: 0.8731 (tm-30) cc_final: 0.8155 (tm-30) REVERT: D 366 ASP cc_start: 0.8583 (t70) cc_final: 0.8234 (t0) REVERT: D 418 ARG cc_start: 0.8974 (ttp80) cc_final: 0.8653 (ttm110) REVERT: D 453 GLU cc_start: 0.8780 (mm-30) cc_final: 0.8251 (mm-30) REVERT: E 64 GLU cc_start: 0.8061 (pm20) cc_final: 0.7242 (pm20) REVERT: E 69 LEU cc_start: 0.8205 (mm) cc_final: 0.7859 (tp) REVERT: E 79 MET cc_start: 0.8193 (mmp) cc_final: 0.7907 (mmm) REVERT: E 89 MET cc_start: 0.7371 (mtp) cc_final: 0.6962 (mtp) REVERT: E 120 ASN cc_start: 0.7719 (m-40) cc_final: 0.7420 (m-40) REVERT: E 248 ARG cc_start: 0.6886 (mmt180) cc_final: 0.6628 (mmt180) REVERT: E 385 TYR cc_start: 0.9076 (t80) cc_final: 0.8749 (t80) REVERT: E 393 GLU cc_start: 0.8334 (mt-10) cc_final: 0.8096 (mt-10) REVERT: E 396 GLN cc_start: 0.9152 (tp40) cc_final: 0.8693 (tp40) REVERT: F 40 MET cc_start: 0.8110 (tpp) cc_final: 0.7863 (mmm) REVERT: F 145 LYS cc_start: 0.8440 (tptp) cc_final: 0.8071 (pttm) REVERT: F 247 MET cc_start: 0.8175 (tpp) cc_final: 0.7754 (tpt) REVERT: F 486 LYS cc_start: 0.8922 (tttp) cc_final: 0.8612 (tppp) REVERT: d 104 ARG cc_start: 0.8611 (tpt170) cc_final: 0.8173 (mtm180) REVERT: d 113 TYR cc_start: 0.8822 (t80) cc_final: 0.8595 (t80) REVERT: d 139 GLN cc_start: 0.8558 (mm-40) cc_final: 0.8194 (mp10) REVERT: d 162 LEU cc_start: 0.8874 (mt) cc_final: 0.8418 (tt) REVERT: d 193 GLN cc_start: 0.8956 (tp-100) cc_final: 0.8603 (tt0) REVERT: g 81 ASN cc_start: 0.8320 (t0) cc_final: 0.8063 (t0) REVERT: g 189 LYS cc_start: 0.9008 (mttp) cc_final: 0.8541 (mmmt) REVERT: g 232 PRO cc_start: 0.6705 (Cg_endo) cc_final: 0.6486 (Cg_exo) REVERT: g 303 GLN cc_start: 0.8593 (tp40) cc_final: 0.8171 (tp40) REVERT: g 354 LEU cc_start: 0.8490 (tt) cc_final: 0.8185 (pp) REVERT: e 11 ASN cc_start: 0.8653 (p0) cc_final: 0.7978 (p0) REVERT: e 19 VAL cc_start: 0.8458 (t) cc_final: 0.8163 (t) REVERT: e 124 THR cc_start: 0.8374 (m) cc_final: 0.7924 (m) outliers start: 1 outliers final: 0 residues processed: 666 average time/residue: 0.3867 time to fit residues: 409.7053 Evaluate side-chains 507 residues out of total 2933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 507 time to evaluate : 3.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 114 optimal weight: 6.9990 chunk 306 optimal weight: 10.0000 chunk 67 optimal weight: 0.0870 chunk 199 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 340 optimal weight: 0.8980 chunk 282 optimal weight: 1.9990 chunk 157 optimal weight: 6.9990 chunk 28 optimal weight: 8.9990 chunk 112 optimal weight: 2.9990 chunk 178 optimal weight: 0.7980 overall best weight: 1.3562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 212 ASN ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 ASN ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 497 GLN ** D 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 ASN ** D 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 299 GLN ** F 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 141 HIS g 58 GLN ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 56 GLN e 72 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 27513 Z= 0.224 Angle : 0.673 11.894 37327 Z= 0.336 Chirality : 0.045 0.271 4425 Planarity : 0.004 0.063 4851 Dihedral : 7.768 111.300 4002 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 21.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 0.10 % Allowed : 3.53 % Favored : 96.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.21 % Twisted Proline : 0.68 % 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: -1.58 (0.14), residues: 3544 helix: 0.29 (0.13), residues: 1482 sheet: -3.04 (0.21), residues: 487 loop : -1.62 (0.16), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP e 15 HIS 0.006 0.001 HIS E 384 PHE 0.032 0.002 PHE E 278 TYR 0.026 0.002 TYR E 298 ARG 0.008 0.001 ARG F 87 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 673 residues out of total 2933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 670 time to evaluate : 3.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.7444 (tp30) cc_final: 0.7037 (tp30) REVERT: A 76 LEU cc_start: 0.9408 (mt) cc_final: 0.9170 (mt) REVERT: A 77 MET cc_start: 0.7678 (mtp) cc_final: 0.7466 (mtp) REVERT: A 157 MET cc_start: 0.8521 (ttm) cc_final: 0.8313 (ttm) REVERT: A 219 MET cc_start: 0.8311 (ppp) cc_final: 0.8069 (ppp) REVERT: A 230 ASP cc_start: 0.7801 (p0) cc_final: 0.7233 (p0) REVERT: A 251 MET cc_start: 0.8157 (tmm) cc_final: 0.7533 (tmm) REVERT: A 285 GLU cc_start: 0.8154 (tt0) cc_final: 0.7899 (tt0) REVERT: A 287 TYR cc_start: 0.7487 (m-80) cc_final: 0.7211 (m-10) REVERT: A 360 VAL cc_start: 0.8371 (m) cc_final: 0.8138 (m) REVERT: A 436 MET cc_start: 0.9219 (ppp) cc_final: 0.8794 (ppp) REVERT: A 445 TYR cc_start: 0.6465 (t80) cc_final: 0.5995 (t80) REVERT: A 460 GLU cc_start: 0.9071 (mp0) cc_final: 0.8709 (mp0) REVERT: A 484 GLU cc_start: 0.8832 (mp0) cc_final: 0.7714 (tm-30) REVERT: A 498 MET cc_start: 0.8336 (tpt) cc_final: 0.7828 (tpt) REVERT: B 75 VAL cc_start: 0.9248 (m) cc_final: 0.8894 (p) REVERT: B 194 CYS cc_start: 0.8915 (m) cc_final: 0.8429 (m) REVERT: B 237 TYR cc_start: 0.8637 (t80) cc_final: 0.8331 (t80) REVERT: B 274 MET cc_start: 0.8762 (ptm) cc_final: 0.8321 (tmm) REVERT: B 293 TYR cc_start: 0.8053 (t80) cc_final: 0.7594 (t80) REVERT: B 453 GLN cc_start: 0.8532 (tt0) cc_final: 0.8215 (tt0) REVERT: B 480 LYS cc_start: 0.8703 (mtmt) cc_final: 0.8252 (mmtt) REVERT: C 15 GLU cc_start: 0.8449 (tm-30) cc_final: 0.7477 (mm-30) REVERT: C 49 MET cc_start: 0.7368 (tpt) cc_final: 0.6321 (tpt) REVERT: C 165 ARG cc_start: 0.5269 (ptp-170) cc_final: 0.4167 (ptp-170) REVERT: C 219 MET cc_start: 0.8523 (ptm) cc_final: 0.7962 (ptm) REVERT: C 251 MET cc_start: 0.7453 (ttp) cc_final: 0.6517 (ttp) REVERT: C 263 ASP cc_start: 0.7467 (p0) cc_final: 0.7216 (p0) REVERT: C 266 LYS cc_start: 0.8611 (mmpt) cc_final: 0.8062 (mmmt) REVERT: C 274 MET cc_start: 0.8570 (mmm) cc_final: 0.8261 (mmm) REVERT: C 301 ARG cc_start: 0.7550 (ttm170) cc_final: 0.7112 (ttm170) REVERT: C 314 MET cc_start: 0.7627 (ttm) cc_final: 0.7055 (ttm) REVERT: C 385 LEU cc_start: 0.8207 (mt) cc_final: 0.7935 (mt) REVERT: D 63 CYS cc_start: 0.8804 (m) cc_final: 0.8104 (m) REVERT: D 292 MET cc_start: 0.8094 (ttm) cc_final: 0.7600 (ttm) REVERT: D 311 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8089 (tm-30) REVERT: D 366 ASP cc_start: 0.8594 (t70) cc_final: 0.7720 (t0) REVERT: D 418 ARG cc_start: 0.8988 (ttp80) cc_final: 0.8673 (ttm110) REVERT: D 426 LYS cc_start: 0.8431 (mttm) cc_final: 0.7688 (ptpt) REVERT: D 453 GLU cc_start: 0.8753 (mm-30) cc_final: 0.8248 (mm-30) REVERT: D 466 LEU cc_start: 0.8513 (tp) cc_final: 0.8298 (tp) REVERT: E 63 CYS cc_start: 0.9153 (p) cc_final: 0.8953 (p) REVERT: E 64 GLU cc_start: 0.7935 (pm20) cc_final: 0.7184 (pm20) REVERT: E 69 LEU cc_start: 0.8190 (mm) cc_final: 0.7902 (tp) REVERT: E 79 MET cc_start: 0.8297 (mmp) cc_final: 0.7960 (mmm) REVERT: E 89 MET cc_start: 0.7448 (mtp) cc_final: 0.6961 (mtp) REVERT: E 120 ASN cc_start: 0.7635 (m-40) cc_final: 0.7267 (m-40) REVERT: E 278 PHE cc_start: 0.9048 (t80) cc_final: 0.8793 (t80) REVERT: E 396 GLN cc_start: 0.9137 (tp40) cc_final: 0.8649 (tp40) REVERT: E 398 TYR cc_start: 0.7862 (t80) cc_final: 0.7567 (t80) REVERT: E 475 TYR cc_start: 0.8100 (t80) cc_final: 0.7804 (t80) REVERT: F 145 LYS cc_start: 0.8517 (tptp) cc_final: 0.8195 (pttm) REVERT: F 184 GLU cc_start: 0.8449 (tp30) cc_final: 0.8152 (mm-30) REVERT: F 247 MET cc_start: 0.8203 (tpp) cc_final: 0.7694 (tpt) REVERT: F 343 PHE cc_start: 0.8018 (p90) cc_final: 0.7807 (p90) REVERT: F 362 TYR cc_start: 0.7940 (m-80) cc_final: 0.7729 (m-80) REVERT: F 486 LYS cc_start: 0.8910 (tttp) cc_final: 0.8596 (tppp) REVERT: d 104 ARG cc_start: 0.8604 (tpt170) cc_final: 0.8202 (mtm180) REVERT: d 139 GLN cc_start: 0.8510 (mm-40) cc_final: 0.8166 (mp10) REVERT: d 162 LEU cc_start: 0.8868 (mt) cc_final: 0.8412 (tt) REVERT: d 193 GLN cc_start: 0.8965 (tp-100) cc_final: 0.8608 (tt0) REVERT: g 81 ASN cc_start: 0.8323 (t0) cc_final: 0.8073 (t0) REVERT: g 189 LYS cc_start: 0.8990 (mttp) cc_final: 0.8555 (mmmt) REVERT: g 232 PRO cc_start: 0.6673 (Cg_endo) cc_final: 0.6413 (Cg_exo) REVERT: g 303 GLN cc_start: 0.8647 (tp40) cc_final: 0.8291 (tp40) REVERT: g 354 LEU cc_start: 0.8439 (tt) cc_final: 0.8143 (pp) REVERT: e 11 ASN cc_start: 0.8668 (p0) cc_final: 0.8014 (p0) REVERT: e 19 VAL cc_start: 0.8518 (t) cc_final: 0.8245 (t) REVERT: e 124 THR cc_start: 0.8282 (m) cc_final: 0.7814 (m) outliers start: 3 outliers final: 0 residues processed: 671 average time/residue: 0.3708 time to fit residues: 395.7151 Evaluate side-chains 502 residues out of total 2933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 502 time to evaluate : 2.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 328 optimal weight: 6.9990 chunk 38 optimal weight: 0.7980 chunk 194 optimal weight: 3.9990 chunk 248 optimal weight: 0.9990 chunk 192 optimal weight: 2.9990 chunk 286 optimal weight: 0.6980 chunk 190 optimal weight: 0.8980 chunk 339 optimal weight: 8.9990 chunk 212 optimal weight: 5.9990 chunk 206 optimal weight: 0.0070 chunk 156 optimal weight: 0.6980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 ASN B 342 GLN ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 273 GLN ** C 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 497 GLN ** D 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 ASN ** D 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 299 GLN ** F 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 141 HIS ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 56 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.4556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27513 Z= 0.181 Angle : 0.673 11.773 37327 Z= 0.332 Chirality : 0.045 0.279 4425 Planarity : 0.004 0.060 4851 Dihedral : 7.600 111.994 4002 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 20.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 0.03 % Allowed : 2.06 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.21 % Twisted Proline : 0.68 % 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: -1.46 (0.14), residues: 3544 helix: 0.33 (0.14), residues: 1477 sheet: -2.91 (0.21), residues: 487 loop : -1.51 (0.16), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP e 15 HIS 0.005 0.001 HIS g 228 PHE 0.031 0.002 PHE A 292 TYR 0.031 0.002 TYR E 385 ARG 0.005 0.000 ARG D 22 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 2933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 691 time to evaluate : 3.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.7457 (tp30) cc_final: 0.7060 (tp30) REVERT: A 76 LEU cc_start: 0.9434 (mt) cc_final: 0.9213 (mt) REVERT: A 157 MET cc_start: 0.8527 (ttm) cc_final: 0.8305 (ttm) REVERT: A 219 MET cc_start: 0.8264 (ppp) cc_final: 0.7986 (ppp) REVERT: A 230 ASP cc_start: 0.7790 (p0) cc_final: 0.7431 (p0) REVERT: A 251 MET cc_start: 0.7995 (tmm) cc_final: 0.7565 (tmm) REVERT: A 285 GLU cc_start: 0.8218 (tt0) cc_final: 0.7931 (tt0) REVERT: A 287 TYR cc_start: 0.7365 (m-80) cc_final: 0.7058 (m-10) REVERT: A 333 THR cc_start: 0.9122 (t) cc_final: 0.8739 (t) REVERT: A 360 VAL cc_start: 0.8251 (m) cc_final: 0.7973 (m) REVERT: A 436 MET cc_start: 0.9211 (ppp) cc_final: 0.8762 (ppp) REVERT: A 460 GLU cc_start: 0.9160 (mp0) cc_final: 0.8821 (mp0) REVERT: A 484 GLU cc_start: 0.8824 (mp0) cc_final: 0.7544 (tm-30) REVERT: B 34 GLN cc_start: 0.7556 (tp-100) cc_final: 0.6861 (tt0) REVERT: B 75 VAL cc_start: 0.9313 (m) cc_final: 0.9008 (p) REVERT: B 76 LEU cc_start: 0.9476 (mp) cc_final: 0.9273 (mm) REVERT: B 152 ILE cc_start: 0.8882 (tp) cc_final: 0.8651 (pt) REVERT: B 194 CYS cc_start: 0.8809 (m) cc_final: 0.8360 (m) REVERT: B 202 LYS cc_start: 0.8182 (mppt) cc_final: 0.7950 (mptt) REVERT: B 274 MET cc_start: 0.8777 (ptm) cc_final: 0.8343 (tmm) REVERT: B 293 TYR cc_start: 0.8044 (t80) cc_final: 0.7584 (t80) REVERT: B 453 GLN cc_start: 0.8510 (tt0) cc_final: 0.8193 (tt0) REVERT: B 480 LYS cc_start: 0.8670 (mtmt) cc_final: 0.8201 (mmmt) REVERT: C 15 GLU cc_start: 0.8374 (tm-30) cc_final: 0.7552 (mm-30) REVERT: C 49 MET cc_start: 0.7422 (tpt) cc_final: 0.6390 (tpt) REVERT: C 77 MET cc_start: 0.7490 (ppp) cc_final: 0.7264 (ppp) REVERT: C 105 LEU cc_start: 0.9163 (mp) cc_final: 0.8924 (mp) REVERT: C 219 MET cc_start: 0.8455 (ptm) cc_final: 0.7768 (ptm) REVERT: C 251 MET cc_start: 0.7428 (ttp) cc_final: 0.6811 (ttp) REVERT: C 266 LYS cc_start: 0.8538 (mmpt) cc_final: 0.8321 (mmmt) REVERT: C 274 MET cc_start: 0.8544 (mmm) cc_final: 0.8249 (mmm) REVERT: C 301 ARG cc_start: 0.7501 (ttm170) cc_final: 0.7134 (ttm170) REVERT: C 314 MET cc_start: 0.7565 (ttm) cc_final: 0.7057 (ttm) REVERT: C 365 SER cc_start: 0.8789 (p) cc_final: 0.8540 (p) REVERT: C 385 LEU cc_start: 0.8118 (mt) cc_final: 0.7790 (mt) REVERT: C 484 GLU cc_start: 0.8879 (tp30) cc_final: 0.8634 (tp30) REVERT: D 63 CYS cc_start: 0.8698 (m) cc_final: 0.8169 (m) REVERT: D 89 MET cc_start: 0.8820 (mtp) cc_final: 0.8600 (mtp) REVERT: D 182 ILE cc_start: 0.8789 (mm) cc_final: 0.8435 (mm) REVERT: D 247 MET cc_start: 0.8707 (ttt) cc_final: 0.8207 (ttm) REVERT: D 292 MET cc_start: 0.8040 (ttm) cc_final: 0.7517 (ttm) REVERT: D 305 GLU cc_start: 0.8151 (tt0) cc_final: 0.7855 (tp30) REVERT: D 311 GLU cc_start: 0.8663 (tm-30) cc_final: 0.8121 (tm-30) REVERT: D 361 ILE cc_start: 0.8306 (pt) cc_final: 0.7756 (mp) REVERT: D 366 ASP cc_start: 0.8540 (t70) cc_final: 0.7710 (t0) REVERT: D 418 ARG cc_start: 0.8968 (ttp80) cc_final: 0.8663 (ttm110) REVERT: D 426 LYS cc_start: 0.8429 (mttm) cc_final: 0.7651 (ptpt) REVERT: D 453 GLU cc_start: 0.8725 (mm-30) cc_final: 0.8102 (mm-30) REVERT: D 467 ASP cc_start: 0.8493 (p0) cc_final: 0.8259 (p0) REVERT: E 64 GLU cc_start: 0.7921 (pm20) cc_final: 0.7345 (pm20) REVERT: E 89 MET cc_start: 0.7477 (mtp) cc_final: 0.7185 (mtp) REVERT: E 120 ASN cc_start: 0.7703 (m-40) cc_final: 0.7285 (m-40) REVERT: E 396 GLN cc_start: 0.9157 (tp40) cc_final: 0.8682 (tp40) REVERT: E 401 LEU cc_start: 0.7432 (tp) cc_final: 0.7083 (tp) REVERT: F 145 LYS cc_start: 0.8552 (tptp) cc_final: 0.8242 (pttm) REVERT: F 184 GLU cc_start: 0.8498 (tp30) cc_final: 0.8234 (mm-30) REVERT: F 204 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7542 (mm-30) REVERT: F 216 MET cc_start: 0.8480 (tpp) cc_final: 0.8040 (tpp) REVERT: F 247 MET cc_start: 0.8033 (tpp) cc_final: 0.7617 (tpt) REVERT: F 362 TYR cc_start: 0.7738 (m-80) cc_final: 0.7533 (m-80) REVERT: F 486 LYS cc_start: 0.8891 (tttp) cc_final: 0.8565 (tppp) REVERT: d 104 ARG cc_start: 0.8633 (tpt170) cc_final: 0.8248 (mtm180) REVERT: d 139 GLN cc_start: 0.8537 (mm-40) cc_final: 0.8076 (mt0) REVERT: d 151 ASP cc_start: 0.7854 (m-30) cc_final: 0.7451 (m-30) REVERT: d 154 ARG cc_start: 0.8509 (mmp80) cc_final: 0.8265 (mmp80) REVERT: d 189 ASP cc_start: 0.9087 (m-30) cc_final: 0.8501 (t0) REVERT: d 193 GLN cc_start: 0.8962 (tp-100) cc_final: 0.8612 (tt0) REVERT: g 81 ASN cc_start: 0.8252 (t0) cc_final: 0.8007 (t0) REVERT: g 189 LYS cc_start: 0.8741 (mttp) cc_final: 0.8444 (mmmt) REVERT: g 232 PRO cc_start: 0.6389 (Cg_endo) cc_final: 0.6186 (Cg_exo) REVERT: e 11 ASN cc_start: 0.8614 (p0) cc_final: 0.8021 (p0) REVERT: e 19 VAL cc_start: 0.8533 (t) cc_final: 0.8225 (t) REVERT: e 57 TRP cc_start: 0.7595 (m100) cc_final: 0.7110 (m100) REVERT: e 124 THR cc_start: 0.7892 (m) cc_final: 0.7568 (m) outliers start: 1 outliers final: 0 residues processed: 691 average time/residue: 0.3811 time to fit residues: 421.5204 Evaluate side-chains 509 residues out of total 2933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 509 time to evaluate : 3.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 209 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 chunk 202 optimal weight: 1.9990 chunk 102 optimal weight: 0.4980 chunk 66 optimal weight: 0.4980 chunk 65 optimal weight: 0.9990 chunk 215 optimal weight: 0.7980 chunk 231 optimal weight: 2.9990 chunk 167 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 266 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 273 GLN ** C 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 497 GLN ** D 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 ASN ** D 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 299 GLN ** F 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.4761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27513 Z= 0.202 Angle : 0.689 12.507 37327 Z= 0.340 Chirality : 0.045 0.295 4425 Planarity : 0.005 0.122 4851 Dihedral : 7.542 110.518 4002 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 21.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 0.03 % Allowed : 1.92 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.21 % Twisted Proline : 0.68 % 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: -1.40 (0.14), residues: 3544 helix: 0.37 (0.14), residues: 1471 sheet: -2.82 (0.22), residues: 492 loop : -1.47 (0.16), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP e 15 HIS 0.005 0.001 HIS g 228 PHE 0.024 0.002 PHE D 474 TYR 0.029 0.002 TYR E 385 ARG 0.009 0.000 ARG F 277 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 2933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 665 time to evaluate : 3.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.7505 (tp30) cc_final: 0.7119 (tp30) REVERT: A 76 LEU cc_start: 0.9365 (mt) cc_final: 0.9138 (mt) REVERT: A 77 MET cc_start: 0.7867 (mtp) cc_final: 0.7563 (mtp) REVERT: A 138 MET cc_start: 0.7560 (mmt) cc_final: 0.7089 (mmt) REVERT: A 157 MET cc_start: 0.8543 (ttm) cc_final: 0.8306 (ttm) REVERT: A 219 MET cc_start: 0.8321 (ppp) cc_final: 0.8046 (ppp) REVERT: A 251 MET cc_start: 0.8043 (tmm) cc_final: 0.7776 (ttp) REVERT: A 285 GLU cc_start: 0.8250 (tt0) cc_final: 0.7746 (tt0) REVERT: A 300 GLU cc_start: 0.8916 (mt-10) cc_final: 0.8365 (mt-10) REVERT: A 360 VAL cc_start: 0.8261 (m) cc_final: 0.7963 (m) REVERT: A 436 MET cc_start: 0.9198 (ppp) cc_final: 0.8767 (ppp) REVERT: A 460 GLU cc_start: 0.9158 (mp0) cc_final: 0.8710 (mp0) REVERT: A 484 GLU cc_start: 0.8999 (mp0) cc_final: 0.8145 (tp30) REVERT: B 34 GLN cc_start: 0.7481 (tp-100) cc_final: 0.6960 (tt0) REVERT: B 75 VAL cc_start: 0.9285 (m) cc_final: 0.8915 (p) REVERT: B 152 ILE cc_start: 0.8887 (tp) cc_final: 0.8670 (pt) REVERT: B 171 ASP cc_start: 0.7968 (t0) cc_final: 0.7454 (t0) REVERT: B 194 CYS cc_start: 0.8765 (m) cc_final: 0.8285 (m) REVERT: B 264 LEU cc_start: 0.9259 (tp) cc_final: 0.8987 (tp) REVERT: B 274 MET cc_start: 0.8793 (ptm) cc_final: 0.8328 (tmm) REVERT: B 293 TYR cc_start: 0.8085 (t80) cc_final: 0.7675 (t80) REVERT: B 453 GLN cc_start: 0.8531 (tt0) cc_final: 0.8199 (tt0) REVERT: B 480 LYS cc_start: 0.8707 (mtmt) cc_final: 0.8192 (mmmt) REVERT: B 498 MET cc_start: 0.7634 (mmt) cc_final: 0.7164 (tpp) REVERT: C 15 GLU cc_start: 0.8387 (tm-30) cc_final: 0.7466 (mm-30) REVERT: C 77 MET cc_start: 0.7503 (ppp) cc_final: 0.7294 (ppp) REVERT: C 219 MET cc_start: 0.8475 (ptm) cc_final: 0.7781 (ptm) REVERT: C 274 MET cc_start: 0.8611 (mmm) cc_final: 0.8247 (mmm) REVERT: C 301 ARG cc_start: 0.7565 (ttm170) cc_final: 0.7211 (ttm170) REVERT: C 313 SER cc_start: 0.7388 (p) cc_final: 0.6905 (p) REVERT: C 314 MET cc_start: 0.7855 (ttm) cc_final: 0.7019 (ttm) REVERT: C 365 SER cc_start: 0.8834 (p) cc_final: 0.8539 (p) REVERT: C 385 LEU cc_start: 0.8121 (mt) cc_final: 0.7807 (mt) REVERT: C 436 MET cc_start: 0.7759 (mtt) cc_final: 0.7474 (mtt) REVERT: C 484 GLU cc_start: 0.9069 (tp30) cc_final: 0.8629 (tp30) REVERT: D 63 CYS cc_start: 0.8717 (m) cc_final: 0.8010 (m) REVERT: D 64 GLU cc_start: 0.7399 (mp0) cc_final: 0.7176 (mp0) REVERT: D 89 MET cc_start: 0.8803 (mtp) cc_final: 0.8590 (mtp) REVERT: D 247 MET cc_start: 0.8659 (ttt) cc_final: 0.8172 (ttm) REVERT: D 292 MET cc_start: 0.8023 (ttm) cc_final: 0.7549 (ttm) REVERT: D 305 GLU cc_start: 0.8125 (tt0) cc_final: 0.7827 (tp30) REVERT: D 311 GLU cc_start: 0.8639 (tm-30) cc_final: 0.8125 (tt0) REVERT: D 366 ASP cc_start: 0.8549 (t70) cc_final: 0.7708 (t0) REVERT: D 418 ARG cc_start: 0.8949 (ttp80) cc_final: 0.8668 (ttm110) REVERT: D 426 LYS cc_start: 0.8470 (mttm) cc_final: 0.7730 (ptpt) REVERT: D 453 GLU cc_start: 0.8757 (mm-30) cc_final: 0.8161 (mm-30) REVERT: E 64 GLU cc_start: 0.7971 (pm20) cc_final: 0.7279 (pm20) REVERT: E 79 MET cc_start: 0.8360 (mmp) cc_final: 0.8057 (mmm) REVERT: E 89 MET cc_start: 0.7348 (mtp) cc_final: 0.7040 (mtp) REVERT: E 120 ASN cc_start: 0.7717 (m-40) cc_final: 0.7298 (m-40) REVERT: E 207 ARG cc_start: 0.8324 (mmt180) cc_final: 0.8064 (mmt180) REVERT: E 396 GLN cc_start: 0.9179 (tp40) cc_final: 0.8725 (tp40) REVERT: E 418 ARG cc_start: 0.7380 (ttp-110) cc_final: 0.7090 (mtm110) REVERT: F 79 MET cc_start: 0.8622 (mmt) cc_final: 0.8125 (mmm) REVERT: F 145 LYS cc_start: 0.8535 (tptp) cc_final: 0.8194 (pttm) REVERT: F 204 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7581 (mm-30) REVERT: F 256 MET cc_start: 0.8566 (mmp) cc_final: 0.8323 (mmt) REVERT: F 362 TYR cc_start: 0.7772 (m-80) cc_final: 0.7558 (m-80) REVERT: F 486 LYS cc_start: 0.8897 (tttp) cc_final: 0.8572 (tppp) REVERT: d 104 ARG cc_start: 0.8748 (tpt170) cc_final: 0.8295 (mtm180) REVERT: d 139 GLN cc_start: 0.8590 (mm-40) cc_final: 0.8114 (mt0) REVERT: d 151 ASP cc_start: 0.7819 (m-30) cc_final: 0.7434 (m-30) REVERT: d 154 ARG cc_start: 0.8412 (mmp80) cc_final: 0.8130 (mmp80) REVERT: d 189 ASP cc_start: 0.9082 (m-30) cc_final: 0.8506 (t0) REVERT: d 193 GLN cc_start: 0.8965 (tp-100) cc_final: 0.8612 (tt0) REVERT: g 81 ASN cc_start: 0.8284 (t0) cc_final: 0.8046 (t0) REVERT: g 189 LYS cc_start: 0.8679 (mttp) cc_final: 0.8446 (mmmt) REVERT: g 232 PRO cc_start: 0.6365 (Cg_endo) cc_final: 0.6132 (Cg_exo) REVERT: g 354 LEU cc_start: 0.8416 (tt) cc_final: 0.8142 (pp) REVERT: e 11 ASN cc_start: 0.8649 (p0) cc_final: 0.8067 (p0) REVERT: e 19 VAL cc_start: 0.8549 (t) cc_final: 0.8242 (t) REVERT: e 57 TRP cc_start: 0.7555 (m100) cc_final: 0.7295 (m100) outliers start: 1 outliers final: 0 residues processed: 665 average time/residue: 0.3738 time to fit residues: 398.1474 Evaluate side-chains 498 residues out of total 2933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 498 time to evaluate : 3.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 308 optimal weight: 0.0470 chunk 325 optimal weight: 4.9990 chunk 296 optimal weight: 2.9990 chunk 316 optimal weight: 0.9990 chunk 324 optimal weight: 2.9990 chunk 190 optimal weight: 0.9990 chunk 137 optimal weight: 0.5980 chunk 248 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 285 optimal weight: 0.2980 chunk 299 optimal weight: 5.9990 overall best weight: 0.5880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 342 GLN ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 273 GLN ** C 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 497 GLN ** D 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 238 GLN ** E 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 299 GLN ** F 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 141 HIS g 58 GLN ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.4932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 27513 Z= 0.186 Angle : 0.699 12.821 37327 Z= 0.340 Chirality : 0.045 0.304 4425 Planarity : 0.005 0.109 4851 Dihedral : 7.428 112.077 4002 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 20.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 0.03 % Allowed : 0.87 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.21 % Twisted Proline : 0.68 % 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: -1.36 (0.14), residues: 3544 helix: 0.41 (0.14), residues: 1476 sheet: -2.80 (0.21), residues: 504 loop : -1.45 (0.16), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP e 15 HIS 0.015 0.001 HIS D 345 PHE 0.022 0.002 PHE E 199 TYR 0.028 0.002 TYR E 298 ARG 0.006 0.000 ARG C 165 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 2933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 671 time to evaluate : 3.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.7478 (tp30) cc_final: 0.7093 (tp30) REVERT: A 63 ILE cc_start: 0.9392 (mm) cc_final: 0.8698 (mm) REVERT: A 76 LEU cc_start: 0.9424 (mt) cc_final: 0.9184 (mt) REVERT: A 77 MET cc_start: 0.7803 (mtp) cc_final: 0.7095 (mtp) REVERT: A 79 ASP cc_start: 0.8416 (p0) cc_final: 0.8107 (t0) REVERT: A 138 MET cc_start: 0.7529 (mmt) cc_final: 0.7067 (mmt) REVERT: A 157 MET cc_start: 0.8456 (ttm) cc_final: 0.8197 (ttm) REVERT: A 219 MET cc_start: 0.8296 (ppp) cc_final: 0.8014 (ppp) REVERT: A 251 MET cc_start: 0.8135 (tmm) cc_final: 0.7700 (tmm) REVERT: A 285 GLU cc_start: 0.8276 (tt0) cc_final: 0.7766 (tt0) REVERT: A 360 VAL cc_start: 0.8241 (m) cc_final: 0.7948 (m) REVERT: A 362 ILE cc_start: 0.8540 (tp) cc_final: 0.8172 (pt) REVERT: A 436 MET cc_start: 0.9162 (ppp) cc_final: 0.8709 (ppp) REVERT: A 460 GLU cc_start: 0.9150 (mp0) cc_final: 0.8703 (mp0) REVERT: A 484 GLU cc_start: 0.9128 (mp0) cc_final: 0.8412 (tp30) REVERT: A 498 MET cc_start: 0.8718 (tpp) cc_final: 0.7766 (ptt) REVERT: B 34 GLN cc_start: 0.7485 (tp-100) cc_final: 0.7174 (tt0) REVERT: B 75 VAL cc_start: 0.9219 (m) cc_final: 0.8869 (p) REVERT: B 171 ASP cc_start: 0.7947 (t0) cc_final: 0.7381 (t0) REVERT: B 264 LEU cc_start: 0.9184 (tp) cc_final: 0.8953 (tp) REVERT: B 274 MET cc_start: 0.8752 (ptm) cc_final: 0.8340 (tmm) REVERT: B 293 TYR cc_start: 0.8155 (t80) cc_final: 0.7715 (t80) REVERT: B 453 GLN cc_start: 0.8533 (tt0) cc_final: 0.8199 (tt0) REVERT: B 480 LYS cc_start: 0.8681 (mtmt) cc_final: 0.8183 (mmmt) REVERT: B 498 MET cc_start: 0.7755 (mmt) cc_final: 0.7363 (tpp) REVERT: C 15 GLU cc_start: 0.8360 (tm-30) cc_final: 0.7456 (mm-30) REVERT: C 77 MET cc_start: 0.7436 (ppp) cc_final: 0.7234 (ppp) REVERT: C 105 LEU cc_start: 0.9038 (mp) cc_final: 0.8567 (mp) REVERT: C 251 MET cc_start: 0.7795 (ttp) cc_final: 0.6960 (ttp) REVERT: C 266 LYS cc_start: 0.8610 (mmmt) cc_final: 0.8327 (mmmt) REVERT: C 274 MET cc_start: 0.8551 (mmm) cc_final: 0.8222 (mmm) REVERT: C 301 ARG cc_start: 0.7593 (ttm170) cc_final: 0.7215 (ttm170) REVERT: C 365 SER cc_start: 0.8852 (p) cc_final: 0.8581 (p) REVERT: C 436 MET cc_start: 0.7709 (mtt) cc_final: 0.7449 (mtt) REVERT: C 484 GLU cc_start: 0.9046 (tp30) cc_final: 0.8638 (tp30) REVERT: D 63 CYS cc_start: 0.8714 (m) cc_final: 0.8012 (m) REVERT: D 64 GLU cc_start: 0.7378 (mp0) cc_final: 0.7146 (mp0) REVERT: D 214 MET cc_start: 0.8538 (mtt) cc_final: 0.8216 (mtm) REVERT: D 292 MET cc_start: 0.8028 (ttm) cc_final: 0.7539 (ttm) REVERT: D 311 GLU cc_start: 0.8663 (tm-30) cc_final: 0.8099 (tt0) REVERT: D 366 ASP cc_start: 0.8496 (t70) cc_final: 0.7662 (t0) REVERT: D 418 ARG cc_start: 0.8913 (ttp80) cc_final: 0.8652 (ttm110) REVERT: D 426 LYS cc_start: 0.8483 (mttm) cc_final: 0.7762 (ptpt) REVERT: D 453 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8128 (mm-30) REVERT: E 32 ASP cc_start: 0.8268 (t70) cc_final: 0.7656 (t70) REVERT: E 64 GLU cc_start: 0.7921 (pm20) cc_final: 0.7397 (pm20) REVERT: E 79 MET cc_start: 0.8326 (mmp) cc_final: 0.8044 (mmm) REVERT: E 120 ASN cc_start: 0.7724 (m-40) cc_final: 0.7319 (m-40) REVERT: E 396 GLN cc_start: 0.9194 (tp40) cc_final: 0.8745 (tp40) REVERT: E 418 ARG cc_start: 0.7382 (ttp-110) cc_final: 0.7147 (mtm180) REVERT: E 429 ARG cc_start: 0.8815 (mtm110) cc_final: 0.8554 (mtm-85) REVERT: F 145 LYS cc_start: 0.8543 (tptp) cc_final: 0.8202 (pttm) REVERT: F 204 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7399 (mm-30) REVERT: F 216 MET cc_start: 0.8305 (tpp) cc_final: 0.7939 (tpp) REVERT: F 256 MET cc_start: 0.8567 (mmp) cc_final: 0.8348 (mmt) REVERT: F 486 LYS cc_start: 0.8884 (tttp) cc_final: 0.8557 (tppp) REVERT: d 98 ASP cc_start: 0.8592 (t0) cc_final: 0.6999 (t0) REVERT: d 104 ARG cc_start: 0.8788 (tpt170) cc_final: 0.8381 (mtm180) REVERT: d 112 TYR cc_start: 0.8099 (t80) cc_final: 0.7880 (t80) REVERT: d 139 GLN cc_start: 0.8563 (mm-40) cc_final: 0.7876 (mt0) REVERT: d 151 ASP cc_start: 0.7678 (m-30) cc_final: 0.7325 (m-30) REVERT: d 154 ARG cc_start: 0.8433 (mmp80) cc_final: 0.8182 (mmp80) REVERT: d 189 ASP cc_start: 0.9032 (m-30) cc_final: 0.8417 (t0) REVERT: d 193 GLN cc_start: 0.8963 (tp-100) cc_final: 0.8604 (tt0) REVERT: g 81 ASN cc_start: 0.8206 (t0) cc_final: 0.8000 (t0) REVERT: g 189 LYS cc_start: 0.8532 (mttp) cc_final: 0.8165 (mmmt) REVERT: g 232 PRO cc_start: 0.6101 (Cg_endo) cc_final: 0.5859 (Cg_exo) REVERT: g 283 GLU cc_start: 0.8188 (pm20) cc_final: 0.7598 (mm-30) REVERT: g 308 LEU cc_start: 0.8943 (mm) cc_final: 0.8687 (mm) REVERT: g 354 LEU cc_start: 0.8467 (tt) cc_final: 0.8214 (pp) REVERT: e 11 ASN cc_start: 0.8702 (p0) cc_final: 0.7907 (p0) REVERT: e 19 VAL cc_start: 0.8622 (t) cc_final: 0.8369 (t) REVERT: e 57 TRP cc_start: 0.7540 (m100) cc_final: 0.7237 (m100) outliers start: 1 outliers final: 0 residues processed: 671 average time/residue: 0.3868 time to fit residues: 419.6983 Evaluate side-chains 506 residues out of total 2933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 506 time to evaluate : 3.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 315 optimal weight: 10.0000 chunk 207 optimal weight: 9.9990 chunk 334 optimal weight: 1.9990 chunk 204 optimal weight: 0.0170 chunk 158 optimal weight: 0.9980 chunk 232 optimal weight: 1.9990 chunk 350 optimal weight: 0.8980 chunk 322 optimal weight: 0.9990 chunk 279 optimal weight: 0.6980 chunk 28 optimal weight: 10.0000 chunk 215 optimal weight: 10.0000 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 342 GLN ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 273 GLN C 295 HIS ** C 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 238 GLN ** E 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 299 GLN ** F 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.5056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27513 Z= 0.196 Angle : 0.696 12.737 37327 Z= 0.341 Chirality : 0.045 0.309 4425 Planarity : 0.005 0.113 4851 Dihedral : 7.396 110.998 4002 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 20.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.21 % Twisted Proline : 0.68 % 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: -1.34 (0.14), residues: 3544 helix: 0.42 (0.14), residues: 1477 sheet: -2.79 (0.21), residues: 503 loop : -1.44 (0.16), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP e 15 HIS 0.004 0.001 HIS F 193 PHE 0.024 0.002 PHE F 343 TYR 0.029 0.002 TYR E 475 ARG 0.006 0.000 ARG C 165 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 2933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 669 time to evaluate : 3.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.7441 (tp30) cc_final: 0.7086 (tp30) REVERT: A 63 ILE cc_start: 0.9460 (mm) cc_final: 0.8778 (mm) REVERT: A 76 LEU cc_start: 0.9403 (mt) cc_final: 0.9174 (mt) REVERT: A 77 MET cc_start: 0.7839 (mtp) cc_final: 0.7145 (mtp) REVERT: A 138 MET cc_start: 0.7563 (mmt) cc_final: 0.7087 (mmt) REVERT: A 157 MET cc_start: 0.8445 (ttm) cc_final: 0.8176 (ttm) REVERT: A 219 MET cc_start: 0.8307 (ppp) cc_final: 0.8046 (ppp) REVERT: A 251 MET cc_start: 0.8102 (tmm) cc_final: 0.7617 (tmm) REVERT: A 285 GLU cc_start: 0.8290 (tt0) cc_final: 0.7781 (tt0) REVERT: A 360 VAL cc_start: 0.8194 (m) cc_final: 0.7903 (m) REVERT: A 362 ILE cc_start: 0.8533 (tp) cc_final: 0.8180 (pt) REVERT: A 436 MET cc_start: 0.9124 (ppp) cc_final: 0.8741 (ppp) REVERT: A 460 GLU cc_start: 0.9164 (mp0) cc_final: 0.8694 (mp0) REVERT: A 484 GLU cc_start: 0.9118 (mp0) cc_final: 0.8440 (tp30) REVERT: A 498 MET cc_start: 0.8698 (tpp) cc_final: 0.7736 (ptt) REVERT: B 34 GLN cc_start: 0.7503 (tp-100) cc_final: 0.7214 (tt0) REVERT: B 75 VAL cc_start: 0.9218 (m) cc_final: 0.8858 (p) REVERT: B 171 ASP cc_start: 0.7993 (t0) cc_final: 0.7401 (t0) REVERT: B 194 CYS cc_start: 0.8660 (m) cc_final: 0.8199 (m) REVERT: B 264 LEU cc_start: 0.9201 (tp) cc_final: 0.8996 (tp) REVERT: B 274 MET cc_start: 0.8769 (ptm) cc_final: 0.8351 (tmm) REVERT: B 293 TYR cc_start: 0.8129 (t80) cc_final: 0.7664 (t80) REVERT: B 453 GLN cc_start: 0.8534 (tt0) cc_final: 0.8214 (tt0) REVERT: B 480 LYS cc_start: 0.8748 (mtmt) cc_final: 0.8253 (mmmt) REVERT: B 498 MET cc_start: 0.7735 (mmt) cc_final: 0.7353 (tpp) REVERT: C 15 GLU cc_start: 0.8340 (tm-30) cc_final: 0.7411 (mm-30) REVERT: C 20 TYR cc_start: 0.6003 (p90) cc_final: 0.5314 (p90) REVERT: C 77 MET cc_start: 0.7400 (ppp) cc_final: 0.7189 (ppp) REVERT: C 105 LEU cc_start: 0.9037 (mp) cc_final: 0.8798 (mp) REVERT: C 133 PRO cc_start: 0.8703 (Cg_exo) cc_final: 0.8462 (Cg_endo) REVERT: C 251 MET cc_start: 0.7757 (ttp) cc_final: 0.7001 (ttp) REVERT: C 266 LYS cc_start: 0.8577 (mmmt) cc_final: 0.8242 (mmmt) REVERT: C 274 MET cc_start: 0.8586 (mmm) cc_final: 0.8240 (mmm) REVERT: C 365 SER cc_start: 0.8890 (p) cc_final: 0.8623 (p) REVERT: C 484 GLU cc_start: 0.9086 (tp30) cc_final: 0.8652 (tp30) REVERT: D 63 CYS cc_start: 0.8756 (m) cc_final: 0.7925 (m) REVERT: D 64 GLU cc_start: 0.7373 (mp0) cc_final: 0.6947 (mp0) REVERT: D 98 LEU cc_start: 0.8870 (mt) cc_final: 0.8653 (mt) REVERT: D 292 MET cc_start: 0.8062 (ttm) cc_final: 0.7564 (ttm) REVERT: D 311 GLU cc_start: 0.8643 (tm-30) cc_final: 0.8350 (tm-30) REVERT: D 366 ASP cc_start: 0.8427 (t70) cc_final: 0.7643 (t0) REVERT: D 418 ARG cc_start: 0.8908 (ttp80) cc_final: 0.8646 (ttm110) REVERT: D 426 LYS cc_start: 0.8491 (mttm) cc_final: 0.7737 (ptpt) REVERT: D 453 GLU cc_start: 0.8726 (mm-30) cc_final: 0.8090 (mm-30) REVERT: E 32 ASP cc_start: 0.8244 (t70) cc_final: 0.7630 (t70) REVERT: E 64 GLU cc_start: 0.7864 (pm20) cc_final: 0.7274 (pm20) REVERT: E 79 MET cc_start: 0.8314 (mmp) cc_final: 0.8041 (mmm) REVERT: E 120 ASN cc_start: 0.7710 (m-40) cc_final: 0.7310 (m-40) REVERT: E 214 MET cc_start: 0.7887 (mmp) cc_final: 0.7529 (mmm) REVERT: E 269 LEU cc_start: 0.8259 (mm) cc_final: 0.7988 (mm) REVERT: E 336 ASP cc_start: 0.7143 (t0) cc_final: 0.6881 (t0) REVERT: E 418 ARG cc_start: 0.7344 (ttp-110) cc_final: 0.7012 (mtm110) REVERT: F 79 MET cc_start: 0.8817 (mmt) cc_final: 0.7874 (mmm) REVERT: F 145 LYS cc_start: 0.8520 (tptp) cc_final: 0.8248 (pttm) REVERT: F 216 MET cc_start: 0.8126 (tpp) cc_final: 0.7815 (tpp) REVERT: F 342 THR cc_start: 0.8390 (m) cc_final: 0.8188 (m) REVERT: F 486 LYS cc_start: 0.8884 (tttp) cc_final: 0.8559 (tppp) REVERT: d 98 ASP cc_start: 0.8580 (t0) cc_final: 0.6990 (t0) REVERT: d 104 ARG cc_start: 0.8817 (tpt170) cc_final: 0.8390 (mtm180) REVERT: d 139 GLN cc_start: 0.8584 (mm-40) cc_final: 0.7889 (mt0) REVERT: d 154 ARG cc_start: 0.8409 (mmp80) cc_final: 0.8040 (mmp80) REVERT: d 189 ASP cc_start: 0.9016 (m-30) cc_final: 0.8390 (t0) REVERT: d 193 GLN cc_start: 0.8964 (tp-100) cc_final: 0.8679 (tt0) REVERT: g 121 MET cc_start: 0.7765 (tmm) cc_final: 0.7563 (tmm) REVERT: g 189 LYS cc_start: 0.8482 (mttp) cc_final: 0.8149 (mmmt) REVERT: g 232 PRO cc_start: 0.6026 (Cg_endo) cc_final: 0.5774 (Cg_exo) REVERT: g 283 GLU cc_start: 0.8177 (pm20) cc_final: 0.7546 (mm-30) REVERT: g 303 GLN cc_start: 0.8597 (tp40) cc_final: 0.8263 (tp40) REVERT: g 308 LEU cc_start: 0.8946 (mm) cc_final: 0.8682 (mm) REVERT: g 354 LEU cc_start: 0.8489 (tt) cc_final: 0.8233 (pp) REVERT: e 11 ASN cc_start: 0.8725 (p0) cc_final: 0.7957 (p0) REVERT: e 19 VAL cc_start: 0.8588 (t) cc_final: 0.8308 (t) REVERT: e 57 TRP cc_start: 0.7545 (m100) cc_final: 0.7162 (m100) outliers start: 0 outliers final: 0 residues processed: 669 average time/residue: 0.3952 time to fit residues: 427.3461 Evaluate side-chains 504 residues out of total 2933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 504 time to evaluate : 3.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 171 optimal weight: 0.9990 chunk 221 optimal weight: 3.9990 chunk 297 optimal weight: 8.9990 chunk 85 optimal weight: 3.9990 chunk 257 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 279 optimal weight: 0.0570 chunk 117 optimal weight: 5.9990 chunk 287 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 overall best weight: 0.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 342 GLN B 389 GLN ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 273 GLN ** C 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 ASN ** D 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 299 GLN ** F 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 141 HIS d 199 GLN ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.090325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.077595 restraints weight = 86150.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.079826 restraints weight = 49078.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.081323 restraints weight = 31575.875| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.5165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27513 Z= 0.209 Angle : 0.708 12.609 37327 Z= 0.346 Chirality : 0.046 0.312 4425 Planarity : 0.005 0.076 4851 Dihedral : 7.404 111.690 4002 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 21.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 0.07 % Allowed : 0.63 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.21 % Twisted Proline : 0.68 % 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: -1.32 (0.14), residues: 3544 helix: 0.42 (0.14), residues: 1468 sheet: -2.80 (0.21), residues: 497 loop : -1.40 (0.16), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP e 15 HIS 0.004 0.001 HIS C 256 PHE 0.026 0.002 PHE D 343 TYR 0.028 0.002 TYR E 475 ARG 0.006 0.000 ARG D 246 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7349.68 seconds wall clock time: 133 minutes 21.20 seconds (8001.20 seconds total)