Starting phenix.real_space_refine on Tue Apr 16 15:14:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8swk_40820/04_2024/8swk_40820_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8swk_40820/04_2024/8swk_40820.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8swk_40820/04_2024/8swk_40820.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8swk_40820/04_2024/8swk_40820.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8swk_40820/04_2024/8swk_40820_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8swk_40820/04_2024/8swk_40820_neut_updated.pdb" } resolution = 4.32 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= 0.005 sd= 0.039 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 18 5.49 5 S 342 5.16 5 C 25152 2.51 5 N 6672 2.21 5 O 7326 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 306": "OE1" <-> "OE2" Residue "A GLU 326": "OE1" <-> "OE2" Residue "A PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 581": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 632": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 729": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 918": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1009": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1010": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 306": "OE1" <-> "OE2" Residue "B GLU 326": "OE1" <-> "OE2" Residue "B PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 581": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 632": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 729": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 918": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1009": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1010": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 306": "OE1" <-> "OE2" Residue "C GLU 326": "OE1" <-> "OE2" Residue "C PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 581": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 632": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 918": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1009": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1010": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 306": "OE1" <-> "OE2" Residue "D GLU 326": "OE1" <-> "OE2" Residue "D PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 389": "OE1" <-> "OE2" Residue "D PHE 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 581": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 632": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 729": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 918": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1009": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1010": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 306": "OE1" <-> "OE2" Residue "E GLU 326": "OE1" <-> "OE2" Residue "E PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 581": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 632": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 729": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 918": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1009": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1010": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 306": "OE1" <-> "OE2" Residue "F GLU 326": "OE1" <-> "OE2" Residue "F PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 581": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 632": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 729": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 918": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 1010": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 39510 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 6526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 818, 6526 Classifications: {'peptide': 818} Link IDs: {'PTRANS': 23, 'TRANS': 794} Chain breaks: 4 Chain: "B" Number of atoms: 6526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 818, 6526 Classifications: {'peptide': 818} Link IDs: {'PTRANS': 23, 'TRANS': 794} Chain breaks: 4 Chain: "C" Number of atoms: 6526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 818, 6526 Classifications: {'peptide': 818} Link IDs: {'PTRANS': 23, 'TRANS': 794} Chain breaks: 4 Chain: "D" Number of atoms: 6526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 818, 6526 Classifications: {'peptide': 818} Link IDs: {'PTRANS': 23, 'TRANS': 794} Chain breaks: 4 Chain: "E" Number of atoms: 6526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 818, 6526 Classifications: {'peptide': 818} Link IDs: {'PTRANS': 23, 'TRANS': 794} Chain breaks: 4 Chain: "F" Number of atoms: 6526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 818, 6526 Classifications: {'peptide': 818} Link IDs: {'PTRANS': 23, 'TRANS': 794} Chain breaks: 4 Chain: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 59 Unusual residues: {'7YN': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 59 Unusual residues: {'7YN': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 59 Unusual residues: {'7YN': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 59 Unusual residues: {'7YN': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 59 Unusual residues: {'7YN': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 59 Unusual residues: {'7YN': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 20.24, per 1000 atoms: 0.51 Number of scatterers: 39510 At special positions: 0 Unit cell: (163.904, 157.248, 133.952, 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 342 16.00 P 18 15.00 O 7326 8.00 N 6672 7.00 C 25152 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.49 Conformation dependent library (CDL) restraints added in 6.8 seconds 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9312 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 222 helices and 18 sheets defined 44.7% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.96 Creating SS restraints... Processing helix chain 'A' and resid 136 through 147 Processing helix chain 'A' and resid 165 through 167 No H-bonds generated for 'chain 'A' and resid 165 through 167' Processing helix chain 'A' and resid 232 through 244 Processing helix chain 'A' and resid 261 through 263 No H-bonds generated for 'chain 'A' and resid 261 through 263' Processing helix chain 'A' and resid 273 through 277 removed outlier: 3.745A pdb=" N MET A 277 " --> pdb=" O ASP A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 292 No H-bonds generated for 'chain 'A' and resid 290 through 292' Processing helix chain 'A' and resid 304 through 306 No H-bonds generated for 'chain 'A' and resid 304 through 306' Processing helix chain 'A' and resid 328 through 336 Processing helix chain 'A' and resid 352 through 357 removed outlier: 4.163A pdb=" N GLU A 356 " --> pdb=" O VAL A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 362 No H-bonds generated for 'chain 'A' and resid 359 through 362' Processing helix chain 'A' and resid 375 through 385 Processing helix chain 'A' and resid 389 through 400 Processing helix chain 'A' and resid 403 through 410 removed outlier: 4.009A pdb=" N PHE A 410 " --> pdb=" O PHE A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 427 Processing helix chain 'A' and resid 439 through 452 Processing helix chain 'A' and resid 463 through 478 removed outlier: 4.945A pdb=" N TRP A 467 " --> pdb=" O ALA A 464 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER A 471 " --> pdb=" O GLY A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 492 removed outlier: 3.716A pdb=" N HIS A 492 " --> pdb=" O ASP A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 504 Processing helix chain 'A' and resid 523 through 535 removed outlier: 3.609A pdb=" N TYR A 534 " --> pdb=" O ALA A 530 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU A 535 " --> pdb=" O ALA A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 563 Processing helix chain 'A' and resid 574 through 583 Processing helix chain 'A' and resid 593 through 595 No H-bonds generated for 'chain 'A' and resid 593 through 595' Processing helix chain 'A' and resid 598 through 616 Processing helix chain 'A' and resid 629 through 636 Processing helix chain 'A' and resid 640 through 649 removed outlier: 3.748A pdb=" N ASP A 648 " --> pdb=" O GLN A 644 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N TYR A 649 " --> pdb=" O ARG A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 672 removed outlier: 3.608A pdb=" N ASN A 672 " --> pdb=" O PHE A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 739 removed outlier: 4.294A pdb=" N GLY A 732 " --> pdb=" O PHE A 729 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N SER A 735 " --> pdb=" O GLY A 732 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER A 738 " --> pdb=" O SER A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 766 removed outlier: 3.632A pdb=" N GLN A 766 " --> pdb=" O CYS A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 794 Processing helix chain 'A' and resid 812 through 822 removed outlier: 3.835A pdb=" N VAL A 820 " --> pdb=" O ARG A 816 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLY A 821 " --> pdb=" O LEU A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 853 removed outlier: 3.862A pdb=" N ALA A 848 " --> pdb=" O GLN A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 879 removed outlier: 4.283A pdb=" N ILE A 874 " --> pdb=" O SER A 870 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS A 878 " --> pdb=" O ILE A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 908 removed outlier: 4.050A pdb=" N SER A 902 " --> pdb=" O VAL A 899 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER A 905 " --> pdb=" O SER A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 936 Processing helix chain 'A' and resid 955 through 967 removed outlier: 4.404A pdb=" N TRP A 959 " --> pdb=" O HIS A 956 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 961 " --> pdb=" O CYS A 958 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER A 962 " --> pdb=" O TRP A 959 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER A 967 " --> pdb=" O LEU A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 994 removed outlier: 3.599A pdb=" N VAL A 986 " --> pdb=" O GLY A 982 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS A 994 " --> pdb=" O CYS A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1024 Processing helix chain 'B' and resid 136 through 147 Processing helix chain 'B' and resid 165 through 167 No H-bonds generated for 'chain 'B' and resid 165 through 167' Processing helix chain 'B' and resid 232 through 244 Processing helix chain 'B' and resid 261 through 263 No H-bonds generated for 'chain 'B' and resid 261 through 263' Processing helix chain 'B' and resid 273 through 277 removed outlier: 3.755A pdb=" N MET B 277 " --> pdb=" O ASP B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 292 No H-bonds generated for 'chain 'B' and resid 290 through 292' Processing helix chain 'B' and resid 304 through 306 No H-bonds generated for 'chain 'B' and resid 304 through 306' Processing helix chain 'B' and resid 328 through 336 Processing helix chain 'B' and resid 352 through 357 removed outlier: 4.158A pdb=" N GLU B 356 " --> pdb=" O VAL B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 362 No H-bonds generated for 'chain 'B' and resid 359 through 362' Processing helix chain 'B' and resid 375 through 385 Processing helix chain 'B' and resid 389 through 400 Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.979A pdb=" N PHE B 410 " --> pdb=" O PHE B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 427 Processing helix chain 'B' and resid 439 through 452 Processing helix chain 'B' and resid 463 through 478 removed outlier: 4.953A pdb=" N TRP B 467 " --> pdb=" O ALA B 464 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER B 471 " --> pdb=" O GLY B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 492 removed outlier: 3.712A pdb=" N HIS B 492 " --> pdb=" O ASP B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 504 Processing helix chain 'B' and resid 523 through 535 removed outlier: 3.554A pdb=" N TYR B 534 " --> pdb=" O ALA B 530 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU B 535 " --> pdb=" O ALA B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 563 Processing helix chain 'B' and resid 574 through 583 Processing helix chain 'B' and resid 593 through 595 No H-bonds generated for 'chain 'B' and resid 593 through 595' Processing helix chain 'B' and resid 598 through 616 Processing helix chain 'B' and resid 629 through 636 Processing helix chain 'B' and resid 640 through 649 removed outlier: 3.685A pdb=" N ASP B 648 " --> pdb=" O GLN B 644 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N TYR B 649 " --> pdb=" O ARG B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 671 Processing helix chain 'B' and resid 728 through 739 removed outlier: 4.000A pdb=" N GLY B 732 " --> pdb=" O PHE B 729 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N SER B 735 " --> pdb=" O GLY B 732 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SER B 738 " --> pdb=" O SER B 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 766 removed outlier: 3.655A pdb=" N GLN B 766 " --> pdb=" O CYS B 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 794 removed outlier: 3.551A pdb=" N SER B 791 " --> pdb=" O PHE B 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 812 through 822 removed outlier: 3.873A pdb=" N VAL B 820 " --> pdb=" O ARG B 816 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLY B 821 " --> pdb=" O LEU B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 841 through 853 removed outlier: 3.876A pdb=" N ALA B 848 " --> pdb=" O GLN B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 869 through 879 removed outlier: 4.278A pdb=" N ILE B 874 " --> pdb=" O SER B 870 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS B 878 " --> pdb=" O ILE B 874 " (cutoff:3.500A) Processing helix chain 'B' and resid 898 through 908 removed outlier: 4.050A pdb=" N SER B 902 " --> pdb=" O VAL B 899 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER B 905 " --> pdb=" O SER B 902 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 936 Processing helix chain 'B' and resid 955 through 967 removed outlier: 4.392A pdb=" N TRP B 959 " --> pdb=" O HIS B 956 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU B 961 " --> pdb=" O CYS B 958 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER B 962 " --> pdb=" O TRP B 959 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER B 967 " --> pdb=" O LEU B 964 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 994 removed outlier: 3.619A pdb=" N VAL B 986 " --> pdb=" O GLY B 982 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS B 994 " --> pdb=" O CYS B 990 " (cutoff:3.500A) Processing helix chain 'B' and resid 1012 through 1024 Processing helix chain 'C' and resid 136 through 147 Processing helix chain 'C' and resid 165 through 167 No H-bonds generated for 'chain 'C' and resid 165 through 167' Processing helix chain 'C' and resid 232 through 244 Processing helix chain 'C' and resid 261 through 263 No H-bonds generated for 'chain 'C' and resid 261 through 263' Processing helix chain 'C' and resid 273 through 277 removed outlier: 3.671A pdb=" N MET C 277 " --> pdb=" O ASP C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 292 No H-bonds generated for 'chain 'C' and resid 290 through 292' Processing helix chain 'C' and resid 304 through 306 No H-bonds generated for 'chain 'C' and resid 304 through 306' Processing helix chain 'C' and resid 328 through 336 Processing helix chain 'C' and resid 352 through 357 removed outlier: 4.139A pdb=" N GLU C 356 " --> pdb=" O VAL C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 362 No H-bonds generated for 'chain 'C' and resid 359 through 362' Processing helix chain 'C' and resid 375 through 385 Processing helix chain 'C' and resid 389 through 400 Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.930A pdb=" N PHE C 410 " --> pdb=" O PHE C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 427 Processing helix chain 'C' and resid 439 through 452 Processing helix chain 'C' and resid 463 through 478 removed outlier: 4.942A pdb=" N TRP C 467 " --> pdb=" O ALA C 464 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER C 471 " --> pdb=" O GLY C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 492 removed outlier: 3.715A pdb=" N HIS C 492 " --> pdb=" O ASP C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 504 Processing helix chain 'C' and resid 523 through 535 removed outlier: 3.555A pdb=" N TYR C 534 " --> pdb=" O ALA C 530 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU C 535 " --> pdb=" O ALA C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 563 Processing helix chain 'C' and resid 574 through 583 Processing helix chain 'C' and resid 593 through 595 No H-bonds generated for 'chain 'C' and resid 593 through 595' Processing helix chain 'C' and resid 598 through 616 Processing helix chain 'C' and resid 629 through 636 Processing helix chain 'C' and resid 640 through 649 removed outlier: 3.769A pdb=" N ASP C 648 " --> pdb=" O GLN C 644 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N TYR C 649 " --> pdb=" O ARG C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 660 through 672 removed outlier: 3.614A pdb=" N ASN C 672 " --> pdb=" O PHE C 668 " (cutoff:3.500A) Processing helix chain 'C' and resid 728 through 739 removed outlier: 4.921A pdb=" N SER C 735 " --> pdb=" O GLY C 732 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER C 738 " --> pdb=" O SER C 735 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 766 removed outlier: 3.649A pdb=" N GLN C 766 " --> pdb=" O CYS C 762 " (cutoff:3.500A) Processing helix chain 'C' and resid 784 through 794 removed outlier: 3.513A pdb=" N ILE C 790 " --> pdb=" O CYS C 787 " (cutoff:3.500A) Processing helix chain 'C' and resid 812 through 822 removed outlier: 3.992A pdb=" N VAL C 820 " --> pdb=" O ARG C 816 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLY C 821 " --> pdb=" O LEU C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 841 through 853 removed outlier: 3.863A pdb=" N ALA C 848 " --> pdb=" O GLN C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 869 through 879 removed outlier: 4.237A pdb=" N ILE C 874 " --> pdb=" O SER C 870 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS C 878 " --> pdb=" O ILE C 874 " (cutoff:3.500A) Processing helix chain 'C' and resid 898 through 908 removed outlier: 4.005A pdb=" N SER C 902 " --> pdb=" O VAL C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 925 through 936 Processing helix chain 'C' and resid 955 through 967 removed outlier: 4.420A pdb=" N TRP C 959 " --> pdb=" O HIS C 956 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU C 961 " --> pdb=" O CYS C 958 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER C 962 " --> pdb=" O TRP C 959 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER C 967 " --> pdb=" O LEU C 964 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 994 removed outlier: 3.603A pdb=" N VAL C 986 " --> pdb=" O GLY C 982 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS C 994 " --> pdb=" O CYS C 990 " (cutoff:3.500A) Processing helix chain 'C' and resid 1012 through 1024 Processing helix chain 'D' and resid 136 through 147 Processing helix chain 'D' and resid 165 through 167 No H-bonds generated for 'chain 'D' and resid 165 through 167' Processing helix chain 'D' and resid 232 through 244 Processing helix chain 'D' and resid 261 through 263 No H-bonds generated for 'chain 'D' and resid 261 through 263' Processing helix chain 'D' and resid 273 through 277 removed outlier: 3.772A pdb=" N MET D 277 " --> pdb=" O ASP D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 292 No H-bonds generated for 'chain 'D' and resid 290 through 292' Processing helix chain 'D' and resid 304 through 306 No H-bonds generated for 'chain 'D' and resid 304 through 306' Processing helix chain 'D' and resid 328 through 336 Processing helix chain 'D' and resid 352 through 357 removed outlier: 4.163A pdb=" N GLU D 356 " --> pdb=" O VAL D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 362 No H-bonds generated for 'chain 'D' and resid 359 through 362' Processing helix chain 'D' and resid 375 through 385 Processing helix chain 'D' and resid 389 through 400 Processing helix chain 'D' and resid 403 through 410 removed outlier: 3.512A pdb=" N PHE D 410 " --> pdb=" O PHE D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 427 Processing helix chain 'D' and resid 439 through 452 Processing helix chain 'D' and resid 463 through 478 removed outlier: 4.971A pdb=" N TRP D 467 " --> pdb=" O ALA D 464 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER D 471 " --> pdb=" O GLY D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 492 removed outlier: 3.732A pdb=" N HIS D 492 " --> pdb=" O ASP D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 504 Processing helix chain 'D' and resid 523 through 535 removed outlier: 3.567A pdb=" N TYR D 534 " --> pdb=" O ALA D 530 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU D 535 " --> pdb=" O ALA D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 558 through 563 Processing helix chain 'D' and resid 574 through 583 Processing helix chain 'D' and resid 593 through 595 No H-bonds generated for 'chain 'D' and resid 593 through 595' Processing helix chain 'D' and resid 598 through 616 Processing helix chain 'D' and resid 629 through 636 Processing helix chain 'D' and resid 640 through 649 removed outlier: 3.756A pdb=" N ASP D 648 " --> pdb=" O GLN D 644 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N TYR D 649 " --> pdb=" O ARG D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 660 through 672 removed outlier: 3.615A pdb=" N ASN D 672 " --> pdb=" O PHE D 668 " (cutoff:3.500A) Processing helix chain 'D' and resid 728 through 739 removed outlier: 4.335A pdb=" N GLY D 732 " --> pdb=" O PHE D 729 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N SER D 735 " --> pdb=" O GLY D 732 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER D 738 " --> pdb=" O SER D 735 " (cutoff:3.500A) Processing helix chain 'D' and resid 755 through 766 removed outlier: 3.659A pdb=" N GLN D 766 " --> pdb=" O CYS D 762 " (cutoff:3.500A) Processing helix chain 'D' and resid 784 through 794 removed outlier: 3.574A pdb=" N SER D 791 " --> pdb=" O PHE D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 812 through 822 removed outlier: 3.889A pdb=" N VAL D 820 " --> pdb=" O ARG D 816 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLY D 821 " --> pdb=" O LEU D 817 " (cutoff:3.500A) Processing helix chain 'D' and resid 841 through 853 removed outlier: 3.500A pdb=" N LEU D 847 " --> pdb=" O CYS D 844 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA D 848 " --> pdb=" O GLN D 845 " (cutoff:3.500A) Processing helix chain 'D' and resid 869 through 879 removed outlier: 4.286A pdb=" N ILE D 874 " --> pdb=" O SER D 870 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS D 878 " --> pdb=" O ILE D 874 " (cutoff:3.500A) Processing helix chain 'D' and resid 898 through 908 removed outlier: 4.042A pdb=" N SER D 902 " --> pdb=" O VAL D 899 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER D 905 " --> pdb=" O SER D 902 " (cutoff:3.500A) Processing helix chain 'D' and resid 925 through 936 Processing helix chain 'D' and resid 955 through 967 removed outlier: 4.382A pdb=" N TRP D 959 " --> pdb=" O HIS D 956 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU D 961 " --> pdb=" O CYS D 958 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER D 962 " --> pdb=" O TRP D 959 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER D 967 " --> pdb=" O LEU D 964 " (cutoff:3.500A) Processing helix chain 'D' and resid 982 through 994 removed outlier: 3.615A pdb=" N VAL D 986 " --> pdb=" O GLY D 982 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS D 994 " --> pdb=" O CYS D 990 " (cutoff:3.500A) Processing helix chain 'D' and resid 1012 through 1024 Processing helix chain 'E' and resid 136 through 147 Processing helix chain 'E' and resid 165 through 167 No H-bonds generated for 'chain 'E' and resid 165 through 167' Processing helix chain 'E' and resid 232 through 244 Processing helix chain 'E' and resid 261 through 263 No H-bonds generated for 'chain 'E' and resid 261 through 263' Processing helix chain 'E' and resid 273 through 277 removed outlier: 3.640A pdb=" N MET E 277 " --> pdb=" O ASP E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 290 through 292 No H-bonds generated for 'chain 'E' and resid 290 through 292' Processing helix chain 'E' and resid 304 through 306 No H-bonds generated for 'chain 'E' and resid 304 through 306' Processing helix chain 'E' and resid 328 through 336 Processing helix chain 'E' and resid 352 through 357 removed outlier: 4.143A pdb=" N GLU E 356 " --> pdb=" O VAL E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 362 No H-bonds generated for 'chain 'E' and resid 359 through 362' Processing helix chain 'E' and resid 375 through 385 Processing helix chain 'E' and resid 389 through 400 Processing helix chain 'E' and resid 403 through 410 removed outlier: 3.547A pdb=" N PHE E 410 " --> pdb=" O PHE E 406 " (cutoff:3.500A) Processing helix chain 'E' and resid 412 through 427 Processing helix chain 'E' and resid 439 through 452 Processing helix chain 'E' and resid 463 through 478 removed outlier: 4.944A pdb=" N TRP E 467 " --> pdb=" O ALA E 464 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER E 471 " --> pdb=" O GLY E 468 " (cutoff:3.500A) Processing helix chain 'E' and resid 486 through 492 removed outlier: 3.711A pdb=" N HIS E 492 " --> pdb=" O ASP E 488 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 504 Processing helix chain 'E' and resid 523 through 535 removed outlier: 3.545A pdb=" N TYR E 534 " --> pdb=" O ALA E 530 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU E 535 " --> pdb=" O ALA E 531 " (cutoff:3.500A) Processing helix chain 'E' and resid 558 through 563 Processing helix chain 'E' and resid 574 through 583 Processing helix chain 'E' and resid 593 through 595 No H-bonds generated for 'chain 'E' and resid 593 through 595' Processing helix chain 'E' and resid 598 through 616 Processing helix chain 'E' and resid 629 through 636 Processing helix chain 'E' and resid 640 through 649 removed outlier: 3.744A pdb=" N ASP E 648 " --> pdb=" O GLN E 644 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N TYR E 649 " --> pdb=" O ARG E 645 " (cutoff:3.500A) Processing helix chain 'E' and resid 660 through 672 removed outlier: 3.613A pdb=" N ASN E 672 " --> pdb=" O PHE E 668 " (cutoff:3.500A) Processing helix chain 'E' and resid 728 through 739 removed outlier: 4.021A pdb=" N GLY E 732 " --> pdb=" O PHE E 729 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N SER E 735 " --> pdb=" O GLY E 732 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N SER E 738 " --> pdb=" O SER E 735 " (cutoff:3.500A) Processing helix chain 'E' and resid 755 through 766 removed outlier: 3.679A pdb=" N GLN E 766 " --> pdb=" O CYS E 762 " (cutoff:3.500A) Processing helix chain 'E' and resid 784 through 794 removed outlier: 3.583A pdb=" N SER E 791 " --> pdb=" O PHE E 788 " (cutoff:3.500A) Processing helix chain 'E' and resid 812 through 822 removed outlier: 3.838A pdb=" N VAL E 820 " --> pdb=" O ARG E 816 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY E 821 " --> pdb=" O LEU E 817 " (cutoff:3.500A) Processing helix chain 'E' and resid 841 through 853 removed outlier: 3.746A pdb=" N ALA E 848 " --> pdb=" O GLN E 845 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU E 851 " --> pdb=" O ALA E 848 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER E 852 " --> pdb=" O SER E 849 " (cutoff:3.500A) Processing helix chain 'E' and resid 869 through 879 removed outlier: 4.208A pdb=" N ILE E 874 " --> pdb=" O SER E 870 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS E 878 " --> pdb=" O ILE E 874 " (cutoff:3.500A) Processing helix chain 'E' and resid 898 through 908 removed outlier: 4.001A pdb=" N SER E 902 " --> pdb=" O VAL E 899 " (cutoff:3.500A) Processing helix chain 'E' and resid 925 through 936 Processing helix chain 'E' and resid 955 through 967 removed outlier: 4.383A pdb=" N TRP E 959 " --> pdb=" O HIS E 956 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU E 961 " --> pdb=" O CYS E 958 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER E 962 " --> pdb=" O TRP E 959 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER E 967 " --> pdb=" O LEU E 964 " (cutoff:3.500A) Processing helix chain 'E' and resid 982 through 994 removed outlier: 3.613A pdb=" N VAL E 986 " --> pdb=" O GLY E 982 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS E 994 " --> pdb=" O CYS E 990 " (cutoff:3.500A) Processing helix chain 'E' and resid 1012 through 1024 Processing helix chain 'F' and resid 136 through 147 Processing helix chain 'F' and resid 165 through 167 No H-bonds generated for 'chain 'F' and resid 165 through 167' Processing helix chain 'F' and resid 232 through 244 Processing helix chain 'F' and resid 261 through 263 No H-bonds generated for 'chain 'F' and resid 261 through 263' Processing helix chain 'F' and resid 273 through 277 removed outlier: 3.640A pdb=" N MET F 277 " --> pdb=" O ASP F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 290 through 292 No H-bonds generated for 'chain 'F' and resid 290 through 292' Processing helix chain 'F' and resid 304 through 306 No H-bonds generated for 'chain 'F' and resid 304 through 306' Processing helix chain 'F' and resid 328 through 336 Processing helix chain 'F' and resid 352 through 357 removed outlier: 4.145A pdb=" N GLU F 356 " --> pdb=" O VAL F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 362 No H-bonds generated for 'chain 'F' and resid 359 through 362' Processing helix chain 'F' and resid 375 through 385 Processing helix chain 'F' and resid 389 through 400 Processing helix chain 'F' and resid 403 through 410 removed outlier: 3.553A pdb=" N PHE F 410 " --> pdb=" O PHE F 406 " (cutoff:3.500A) Processing helix chain 'F' and resid 412 through 427 Processing helix chain 'F' and resid 439 through 452 Processing helix chain 'F' and resid 463 through 478 removed outlier: 4.960A pdb=" N TRP F 467 " --> pdb=" O ALA F 464 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER F 471 " --> pdb=" O GLY F 468 " (cutoff:3.500A) Processing helix chain 'F' and resid 486 through 492 removed outlier: 3.725A pdb=" N HIS F 492 " --> pdb=" O ASP F 488 " (cutoff:3.500A) Processing helix chain 'F' and resid 498 through 504 Processing helix chain 'F' and resid 523 through 535 removed outlier: 3.586A pdb=" N TYR F 534 " --> pdb=" O ALA F 530 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU F 535 " --> pdb=" O ALA F 531 " (cutoff:3.500A) Processing helix chain 'F' and resid 558 through 563 Processing helix chain 'F' and resid 574 through 583 Processing helix chain 'F' and resid 593 through 595 No H-bonds generated for 'chain 'F' and resid 593 through 595' Processing helix chain 'F' and resid 598 through 616 Processing helix chain 'F' and resid 629 through 636 Processing helix chain 'F' and resid 640 through 649 removed outlier: 3.741A pdb=" N ASP F 648 " --> pdb=" O GLN F 644 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N TYR F 649 " --> pdb=" O ARG F 645 " (cutoff:3.500A) Processing helix chain 'F' and resid 660 through 672 removed outlier: 3.614A pdb=" N ASN F 672 " --> pdb=" O PHE F 668 " (cutoff:3.500A) Processing helix chain 'F' and resid 728 through 739 removed outlier: 4.226A pdb=" N GLY F 732 " --> pdb=" O PHE F 729 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N SER F 735 " --> pdb=" O GLY F 732 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER F 738 " --> pdb=" O SER F 735 " (cutoff:3.500A) Processing helix chain 'F' and resid 755 through 766 removed outlier: 3.629A pdb=" N GLN F 766 " --> pdb=" O CYS F 762 " (cutoff:3.500A) Processing helix chain 'F' and resid 784 through 794 Processing helix chain 'F' and resid 812 through 822 removed outlier: 3.833A pdb=" N VAL F 820 " --> pdb=" O ARG F 816 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY F 821 " --> pdb=" O LEU F 817 " (cutoff:3.500A) Processing helix chain 'F' and resid 841 through 853 removed outlier: 3.878A pdb=" N ALA F 848 " --> pdb=" O GLN F 845 " (cutoff:3.500A) Processing helix chain 'F' and resid 869 through 879 removed outlier: 4.236A pdb=" N ILE F 874 " --> pdb=" O SER F 870 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS F 878 " --> pdb=" O ILE F 874 " (cutoff:3.500A) Processing helix chain 'F' and resid 898 through 908 removed outlier: 4.003A pdb=" N SER F 902 " --> pdb=" O VAL F 899 " (cutoff:3.500A) Processing helix chain 'F' and resid 925 through 936 Processing helix chain 'F' and resid 955 through 967 removed outlier: 4.405A pdb=" N TRP F 959 " --> pdb=" O HIS F 956 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU F 961 " --> pdb=" O CYS F 958 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER F 962 " --> pdb=" O TRP F 959 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER F 967 " --> pdb=" O LEU F 964 " (cutoff:3.500A) Processing helix chain 'F' and resid 982 through 994 removed outlier: 3.622A pdb=" N VAL F 986 " --> pdb=" O GLY F 982 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS F 994 " --> pdb=" O CYS F 990 " (cutoff:3.500A) Processing helix chain 'F' and resid 1012 through 1024 Processing sheet with id= A, first strand: chain 'A' and resid 172 through 175 removed outlier: 3.752A pdb=" N ARG A 172 " --> pdb=" O LEU A 371 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU A 346 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N PHE A 224 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE A 348 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N GLY A 226 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N THR A 350 " --> pdb=" O GLY A 226 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N TYR A 255 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N LEU A 300 " --> pdb=" O TYR A 255 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N PHE A 257 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ASP A 302 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ILE A 259 " --> pdb=" O ASP A 302 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 652 through 657 removed outlier: 6.769A pdb=" N SER A 678 " --> pdb=" O ILE A 653 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N ILE A 655 " --> pdb=" O SER A 678 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N SER A 680 " --> pdb=" O ILE A 655 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N LEU A 657 " --> pdb=" O SER A 680 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLY A 682 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLU A 745 " --> pdb=" O LEU A 679 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N LEU A 681 " --> pdb=" O GLU A 745 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASP A 747 " --> pdb=" O LEU A 681 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N PHE A 683 " --> pdb=" O ASP A 747 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ARG A 774 " --> pdb=" O LEU A 746 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N LEU A 748 " --> pdb=" O ARG A 774 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N TRP A 776 " --> pdb=" O LEU A 748 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLU A 802 " --> pdb=" O LEU A 775 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N LEU A 777 " --> pdb=" O GLU A 802 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ASP A 804 " --> pdb=" O LEU A 777 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LYS A 831 " --> pdb=" O LEU A 803 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ARG A 859 " --> pdb=" O LEU A 832 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LYS A 888 " --> pdb=" O LEU A 860 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 916 through 918 removed outlier: 6.709A pdb=" N VAL A 945 " --> pdb=" O LEU A 917 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LYS A 973 " --> pdb=" O LEU A 946 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N LEU A 948 " --> pdb=" O LYS A 973 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N SER A 975 " --> pdb=" O LEU A 948 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 172 through 175 removed outlier: 3.784A pdb=" N ARG B 172 " --> pdb=" O LEU B 371 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU B 346 " --> pdb=" O VAL B 222 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N PHE B 224 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE B 348 " --> pdb=" O PHE B 224 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N GLY B 226 " --> pdb=" O ILE B 348 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N THR B 350 " --> pdb=" O GLY B 226 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N TYR B 255 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N LEU B 300 " --> pdb=" O TYR B 255 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N PHE B 257 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ASP B 302 " --> pdb=" O PHE B 257 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ILE B 259 " --> pdb=" O ASP B 302 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 652 through 657 removed outlier: 6.831A pdb=" N SER B 678 " --> pdb=" O ILE B 653 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N ILE B 655 " --> pdb=" O SER B 678 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N SER B 680 " --> pdb=" O ILE B 655 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N LEU B 657 " --> pdb=" O SER B 680 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLY B 682 " --> pdb=" O LEU B 657 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLU B 745 " --> pdb=" O LEU B 679 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N LEU B 681 " --> pdb=" O GLU B 745 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ASP B 747 " --> pdb=" O LEU B 681 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N PHE B 683 " --> pdb=" O ASP B 747 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ARG B 774 " --> pdb=" O LEU B 746 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N LEU B 748 " --> pdb=" O ARG B 774 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N TRP B 776 " --> pdb=" O LEU B 748 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N GLU B 802 " --> pdb=" O LEU B 775 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N LEU B 777 " --> pdb=" O GLU B 802 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ASP B 804 " --> pdb=" O LEU B 777 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LYS B 831 " --> pdb=" O LEU B 803 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ARG B 859 " --> pdb=" O LEU B 832 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LYS B 888 " --> pdb=" O LEU B 860 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 916 through 918 removed outlier: 6.719A pdb=" N VAL B 945 " --> pdb=" O LEU B 917 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LYS B 973 " --> pdb=" O LEU B 946 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N LEU B 948 " --> pdb=" O LYS B 973 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N SER B 975 " --> pdb=" O LEU B 948 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'C' and resid 172 through 175 removed outlier: 3.791A pdb=" N ARG C 172 " --> pdb=" O LEU C 371 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU C 346 " --> pdb=" O VAL C 222 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N PHE C 224 " --> pdb=" O LEU C 346 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE C 348 " --> pdb=" O PHE C 224 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N GLY C 226 " --> pdb=" O ILE C 348 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR C 350 " --> pdb=" O GLY C 226 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N TYR C 255 " --> pdb=" O LEU C 298 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N LEU C 300 " --> pdb=" O TYR C 255 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N PHE C 257 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ASP C 302 " --> pdb=" O PHE C 257 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ILE C 259 " --> pdb=" O ASP C 302 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 652 through 657 removed outlier: 6.848A pdb=" N SER C 678 " --> pdb=" O ILE C 653 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N ILE C 655 " --> pdb=" O SER C 678 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N SER C 680 " --> pdb=" O ILE C 655 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N LEU C 657 " --> pdb=" O SER C 680 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLY C 682 " --> pdb=" O LEU C 657 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLU C 745 " --> pdb=" O LEU C 679 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N LEU C 681 " --> pdb=" O GLU C 745 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ASP C 747 " --> pdb=" O LEU C 681 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N PHE C 683 " --> pdb=" O ASP C 747 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ARG C 774 " --> pdb=" O LEU C 746 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N LEU C 748 " --> pdb=" O ARG C 774 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N TRP C 776 " --> pdb=" O LEU C 748 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N GLU C 802 " --> pdb=" O LEU C 775 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N LEU C 777 " --> pdb=" O GLU C 802 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ASP C 804 " --> pdb=" O LEU C 777 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LYS C 831 " --> pdb=" O LEU C 803 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ARG C 859 " --> pdb=" O LEU C 832 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LYS C 888 " --> pdb=" O LEU C 860 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'C' and resid 916 through 918 removed outlier: 6.729A pdb=" N VAL C 945 " --> pdb=" O LEU C 917 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LYS C 973 " --> pdb=" O LEU C 946 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N LEU C 948 " --> pdb=" O LYS C 973 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N SER C 975 " --> pdb=" O LEU C 948 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'D' and resid 172 through 175 removed outlier: 3.906A pdb=" N ARG D 172 " --> pdb=" O LEU D 371 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU D 346 " --> pdb=" O VAL D 222 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N PHE D 224 " --> pdb=" O LEU D 346 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE D 348 " --> pdb=" O PHE D 224 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N GLY D 226 " --> pdb=" O ILE D 348 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N THR D 350 " --> pdb=" O GLY D 226 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TYR D 255 " --> pdb=" O LEU D 298 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N LEU D 300 " --> pdb=" O TYR D 255 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N PHE D 257 " --> pdb=" O LEU D 300 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ASP D 302 " --> pdb=" O PHE D 257 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ILE D 259 " --> pdb=" O ASP D 302 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 652 through 657 removed outlier: 6.712A pdb=" N SER D 678 " --> pdb=" O ILE D 653 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N ILE D 655 " --> pdb=" O SER D 678 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N SER D 680 " --> pdb=" O ILE D 655 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N LEU D 657 " --> pdb=" O SER D 680 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLY D 682 " --> pdb=" O LEU D 657 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N GLU D 745 " --> pdb=" O LEU D 679 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N LEU D 681 " --> pdb=" O GLU D 745 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASP D 747 " --> pdb=" O LEU D 681 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N PHE D 683 " --> pdb=" O ASP D 747 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ARG D 774 " --> pdb=" O LEU D 746 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N LEU D 748 " --> pdb=" O ARG D 774 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N TRP D 776 " --> pdb=" O LEU D 748 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLU D 802 " --> pdb=" O LEU D 775 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N LEU D 777 " --> pdb=" O GLU D 802 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ASP D 804 " --> pdb=" O LEU D 777 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LYS D 831 " --> pdb=" O LEU D 803 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARG D 859 " --> pdb=" O LEU D 832 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LYS D 888 " --> pdb=" O LEU D 860 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'D' and resid 916 through 918 removed outlier: 6.696A pdb=" N VAL D 945 " --> pdb=" O LEU D 917 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LYS D 973 " --> pdb=" O LEU D 946 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N LEU D 948 " --> pdb=" O LYS D 973 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N SER D 975 " --> pdb=" O LEU D 948 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'E' and resid 172 through 175 removed outlier: 3.894A pdb=" N ARG E 172 " --> pdb=" O LEU E 371 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU E 346 " --> pdb=" O VAL E 222 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N PHE E 224 " --> pdb=" O LEU E 346 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE E 348 " --> pdb=" O PHE E 224 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N GLY E 226 " --> pdb=" O ILE E 348 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N THR E 350 " --> pdb=" O GLY E 226 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N TYR E 255 " --> pdb=" O LEU E 298 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N LEU E 300 " --> pdb=" O TYR E 255 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N PHE E 257 " --> pdb=" O LEU E 300 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N ASP E 302 " --> pdb=" O PHE E 257 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ILE E 259 " --> pdb=" O ASP E 302 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 652 through 657 removed outlier: 6.834A pdb=" N SER E 678 " --> pdb=" O ILE E 653 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N ILE E 655 " --> pdb=" O SER E 678 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N SER E 680 " --> pdb=" O ILE E 655 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N LEU E 657 " --> pdb=" O SER E 680 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLY E 682 " --> pdb=" O LEU E 657 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLU E 745 " --> pdb=" O LEU E 679 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N LEU E 681 " --> pdb=" O GLU E 745 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ASP E 747 " --> pdb=" O LEU E 681 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N PHE E 683 " --> pdb=" O ASP E 747 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ARG E 774 " --> pdb=" O LEU E 746 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N LEU E 748 " --> pdb=" O ARG E 774 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N TRP E 776 " --> pdb=" O LEU E 748 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLU E 802 " --> pdb=" O LEU E 775 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N LEU E 777 " --> pdb=" O GLU E 802 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ASP E 804 " --> pdb=" O LEU E 777 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LYS E 831 " --> pdb=" O LEU E 803 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ARG E 859 " --> pdb=" O LEU E 832 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LYS E 888 " --> pdb=" O LEU E 860 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'E' and resid 916 through 918 removed outlier: 6.718A pdb=" N VAL E 945 " --> pdb=" O LEU E 917 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LYS E 973 " --> pdb=" O LEU E 946 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N LEU E 948 " --> pdb=" O LYS E 973 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N SER E 975 " --> pdb=" O LEU E 948 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'F' and resid 172 through 175 removed outlier: 3.915A pdb=" N ARG F 172 " --> pdb=" O LEU F 371 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU F 346 " --> pdb=" O VAL F 222 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N PHE F 224 " --> pdb=" O LEU F 346 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE F 348 " --> pdb=" O PHE F 224 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N GLY F 226 " --> pdb=" O ILE F 348 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N THR F 350 " --> pdb=" O GLY F 226 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N TYR F 255 " --> pdb=" O LEU F 298 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N LEU F 300 " --> pdb=" O TYR F 255 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N PHE F 257 " --> pdb=" O LEU F 300 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ASP F 302 " --> pdb=" O PHE F 257 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ILE F 259 " --> pdb=" O ASP F 302 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 652 through 657 removed outlier: 6.857A pdb=" N SER F 678 " --> pdb=" O ILE F 653 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N ILE F 655 " --> pdb=" O SER F 678 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N SER F 680 " --> pdb=" O ILE F 655 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N LEU F 657 " --> pdb=" O SER F 680 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N GLY F 682 " --> pdb=" O LEU F 657 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLU F 745 " --> pdb=" O LEU F 679 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N LEU F 681 " --> pdb=" O GLU F 745 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ASP F 747 " --> pdb=" O LEU F 681 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N PHE F 683 " --> pdb=" O ASP F 747 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ARG F 774 " --> pdb=" O LEU F 746 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N LEU F 748 " --> pdb=" O ARG F 774 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N TRP F 776 " --> pdb=" O LEU F 748 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N GLU F 802 " --> pdb=" O LEU F 775 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N LEU F 777 " --> pdb=" O GLU F 802 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ASP F 804 " --> pdb=" O LEU F 777 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LYS F 831 " --> pdb=" O LEU F 803 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ARG F 859 " --> pdb=" O LEU F 832 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LYS F 888 " --> pdb=" O LEU F 860 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'F' and resid 916 through 918 removed outlier: 6.721A pdb=" N VAL F 945 " --> pdb=" O LEU F 917 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LYS F 973 " --> pdb=" O LEU F 946 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N LEU F 948 " --> pdb=" O LYS F 973 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N SER F 975 " --> pdb=" O LEU F 948 " (cutoff:3.500A) No H-bonds generated for sheet with id= R 1293 hydrogen bonds defined for protein. 2970 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: 13.92 Time building geometry restraints manager: 16.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 6451 1.30 - 1.43: 10263 1.43 - 1.57: 23015 1.57 - 1.70: 84 1.70 - 1.84: 453 Bond restraints: 40266 Sorted by residual: bond pdb=" C08 7YN B1101 " pdb=" C09 7YN B1101 " ideal model delta sigma weight residual 1.340 1.519 -0.179 2.00e-02 2.50e+03 8.00e+01 bond pdb=" C08 7YN D1101 " pdb=" C09 7YN D1101 " ideal model delta sigma weight residual 1.340 1.518 -0.178 2.00e-02 2.50e+03 7.90e+01 bond pdb=" C08 7YN C1101 " pdb=" C09 7YN C1101 " ideal model delta sigma weight residual 1.340 1.518 -0.178 2.00e-02 2.50e+03 7.90e+01 bond pdb=" C08 7YN A1101 " pdb=" C09 7YN A1101 " ideal model delta sigma weight residual 1.340 1.516 -0.176 2.00e-02 2.50e+03 7.78e+01 bond pdb=" C08 7YN E1101 " pdb=" C09 7YN E1101 " ideal model delta sigma weight residual 1.340 1.515 -0.175 2.00e-02 2.50e+03 7.69e+01 ... (remaining 40261 not shown) Histogram of bond angle deviations from ideal: 97.21 - 104.90: 581 104.90 - 112.60: 21099 112.60 - 120.29: 15710 120.29 - 127.98: 16708 127.98 - 135.68: 274 Bond angle restraints: 54372 Sorted by residual: angle pdb=" PB ATP F1102 " pdb=" O3B ATP F1102 " pdb=" PG ATP F1102 " ideal model delta sigma weight residual 139.87 110.94 28.93 1.00e+00 1.00e+00 8.37e+02 angle pdb=" PB ATP D1102 " pdb=" O3B ATP D1102 " pdb=" PG ATP D1102 " ideal model delta sigma weight residual 139.87 110.95 28.92 1.00e+00 1.00e+00 8.36e+02 angle pdb=" PB ATP A1102 " pdb=" O3B ATP A1102 " pdb=" PG ATP A1102 " ideal model delta sigma weight residual 139.87 111.00 28.87 1.00e+00 1.00e+00 8.34e+02 angle pdb=" PB ATP B1102 " pdb=" O3B ATP B1102 " pdb=" PG ATP B1102 " ideal model delta sigma weight residual 139.87 111.01 28.86 1.00e+00 1.00e+00 8.33e+02 angle pdb=" PB ATP C1102 " pdb=" O3B ATP C1102 " pdb=" PG ATP C1102 " ideal model delta sigma weight residual 139.87 111.02 28.85 1.00e+00 1.00e+00 8.32e+02 ... (remaining 54367 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.92: 24127 33.92 - 67.84: 293 67.84 - 101.76: 85 101.76 - 135.68: 8 135.68 - 169.60: 3 Dihedral angle restraints: 24516 sinusoidal: 10188 harmonic: 14328 Sorted by residual: dihedral pdb=" C14 7YN F1101 " pdb=" N15 7YN F1101 " pdb=" S17 7YN F1101 " pdb=" O18 7YN F1101 " ideal model delta sinusoidal sigma weight residual 196.22 26.62 169.60 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C14 7YN D1101 " pdb=" N15 7YN D1101 " pdb=" S17 7YN D1101 " pdb=" O18 7YN D1101 " ideal model delta sinusoidal sigma weight residual 196.22 59.03 137.19 1 3.00e+01 1.11e-03 1.85e+01 dihedral pdb=" C14 7YN A1101 " pdb=" N15 7YN A1101 " pdb=" S17 7YN A1101 " pdb=" O18 7YN A1101 " ideal model delta sinusoidal sigma weight residual 196.22 60.36 135.86 1 3.00e+01 1.11e-03 1.83e+01 ... (remaining 24513 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 3592 0.049 - 0.098: 1560 0.098 - 0.147: 655 0.147 - 0.195: 305 0.195 - 0.244: 44 Chirality restraints: 6156 Sorted by residual: chirality pdb=" CG LEU B 971 " pdb=" CB LEU B 971 " pdb=" CD1 LEU B 971 " pdb=" CD2 LEU B 971 " both_signs ideal model delta sigma weight residual False -2.59 -2.83 0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CG LEU A 971 " pdb=" CB LEU A 971 " pdb=" CD1 LEU A 971 " pdb=" CD2 LEU A 971 " both_signs ideal model delta sigma weight residual False -2.59 -2.83 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CG LEU E 971 " pdb=" CB LEU E 971 " pdb=" CD1 LEU E 971 " pdb=" CD2 LEU E 971 " both_signs ideal model delta sigma weight residual False -2.59 -2.83 0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 6153 not shown) Planarity restraints: 6810 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C01 7YN B1101 " -0.072 2.00e-02 2.50e+03 2.00e-01 1.30e+03 pdb=" C02 7YN B1101 " -0.082 2.00e-02 2.50e+03 pdb=" C03 7YN B1101 " -0.097 2.00e-02 2.50e+03 pdb=" C04 7YN B1101 " -0.071 2.00e-02 2.50e+03 pdb=" C05 7YN B1101 " -0.115 2.00e-02 2.50e+03 pdb=" C06 7YN B1101 " -0.097 2.00e-02 2.50e+03 pdb=" C07 7YN B1101 " -0.075 2.00e-02 2.50e+03 pdb=" C08 7YN B1101 " 0.462 2.00e-02 2.50e+03 pdb=" C09 7YN B1101 " -0.100 2.00e-02 2.50e+03 pdb=" C10 7YN B1101 " -0.076 2.00e-02 2.50e+03 pdb=" C11 7YN B1101 " 0.473 2.00e-02 2.50e+03 pdb=" C12 7YN B1101 " -0.108 2.00e-02 2.50e+03 pdb=" N13 7YN B1101 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C01 7YN D1101 " -0.073 2.00e-02 2.50e+03 1.97e-01 1.26e+03 pdb=" C02 7YN D1101 " -0.060 2.00e-02 2.50e+03 pdb=" C03 7YN D1101 " -0.103 2.00e-02 2.50e+03 pdb=" C04 7YN D1101 " -0.102 2.00e-02 2.50e+03 pdb=" C05 7YN D1101 " -0.114 2.00e-02 2.50e+03 pdb=" C06 7YN D1101 " -0.076 2.00e-02 2.50e+03 pdb=" C07 7YN D1101 " -0.061 2.00e-02 2.50e+03 pdb=" C08 7YN D1101 " 0.452 2.00e-02 2.50e+03 pdb=" C09 7YN D1101 " -0.100 2.00e-02 2.50e+03 pdb=" C10 7YN D1101 " -0.069 2.00e-02 2.50e+03 pdb=" C11 7YN D1101 " 0.468 2.00e-02 2.50e+03 pdb=" C12 7YN D1101 " -0.112 2.00e-02 2.50e+03 pdb=" N13 7YN D1101 " -0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C01 7YN C1101 " 0.062 2.00e-02 2.50e+03 1.95e-01 1.23e+03 pdb=" C02 7YN C1101 " 0.074 2.00e-02 2.50e+03 pdb=" C03 7YN C1101 " 0.109 2.00e-02 2.50e+03 pdb=" C04 7YN C1101 " 0.089 2.00e-02 2.50e+03 pdb=" C05 7YN C1101 " 0.106 2.00e-02 2.50e+03 pdb=" C06 7YN C1101 " 0.085 2.00e-02 2.50e+03 pdb=" C07 7YN C1101 " 0.061 2.00e-02 2.50e+03 pdb=" C08 7YN C1101 " -0.454 2.00e-02 2.50e+03 pdb=" C09 7YN C1101 " 0.107 2.00e-02 2.50e+03 pdb=" C10 7YN C1101 " 0.069 2.00e-02 2.50e+03 pdb=" C11 7YN C1101 " -0.455 2.00e-02 2.50e+03 pdb=" C12 7YN C1101 " 0.100 2.00e-02 2.50e+03 pdb=" N13 7YN C1101 " 0.046 2.00e-02 2.50e+03 ... (remaining 6807 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.89: 14754 2.89 - 3.39: 38792 3.39 - 3.89: 67319 3.89 - 4.40: 79978 4.40 - 4.90: 127216 Nonbonded interactions: 328059 Sorted by model distance: nonbonded pdb=" OG1 THR B 221 " pdb=" NZ LYS B 338 " model vdw 2.383 2.520 nonbonded pdb=" OG1 THR A 221 " pdb=" NZ LYS A 338 " model vdw 2.385 2.520 nonbonded pdb=" OG1 THR C 221 " pdb=" NZ LYS C 338 " model vdw 2.388 2.520 nonbonded pdb=" OG1 THR D 221 " pdb=" NZ LYS D 338 " model vdw 2.395 2.520 nonbonded pdb=" OG1 THR D 233 " pdb=" O2G ATP D1102 " model vdw 2.404 2.440 ... (remaining 328054 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 2.030 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: 0.030 Extract box with map and model: 11.870 Check model and map are aligned: 0.520 Set scattering table: 0.320 Process input model: 100.030 Find NCS groups from input model: 3.000 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 120.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 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 : 0.012 0.179 40266 Z= 0.765 Angle : 1.277 28.927 54372 Z= 0.913 Chirality : 0.069 0.244 6156 Planarity : 0.007 0.200 6810 Dihedral : 12.464 169.596 15204 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 1.05 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.63 % Favored : 95.85 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.12), residues: 4848 helix: -0.31 (0.10), residues: 2298 sheet: 0.07 (0.22), residues: 588 loop : -0.54 (0.14), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.004 TRP E 611 HIS 0.005 0.001 HIS E 916 PHE 0.019 0.003 PHE C 406 TYR 0.024 0.003 TYR D 249 ARG 0.004 0.000 ARG E 605 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1604 residues out of total 4452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1604 time to evaluate : 4.599 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: 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 142 LYS cc_start: 0.9369 (mttt) cc_final: 0.9054 (pttm) REVERT: A 220 HIS cc_start: 0.8264 (m90) cc_final: 0.7676 (p-80) REVERT: A 238 LYS cc_start: 0.8744 (tptp) cc_final: 0.8470 (tttt) REVERT: A 240 MET cc_start: 0.8608 (mtm) cc_final: 0.7870 (mmt) REVERT: A 253 PHE cc_start: 0.7651 (m-80) cc_final: 0.4650 (m-10) REVERT: A 304 PHE cc_start: 0.8913 (t80) cc_final: 0.8507 (t80) REVERT: A 368 VAL cc_start: 0.9514 (t) cc_final: 0.9172 (t) REVERT: A 381 TYR cc_start: 0.8340 (t80) cc_final: 0.7870 (t80) REVERT: A 403 GLU cc_start: 0.8735 (tt0) cc_final: 0.7991 (tp30) REVERT: A 408 MET cc_start: 0.8679 (mtm) cc_final: 0.8085 (mtm) REVERT: A 415 CYS cc_start: 0.8306 (p) cc_final: 0.7773 (p) REVERT: A 419 CYS cc_start: 0.7713 (m) cc_final: 0.7316 (p) REVERT: A 517 PHE cc_start: 0.7322 (p90) cc_final: 0.6721 (p90) REVERT: A 521 ILE cc_start: 0.8704 (tt) cc_final: 0.8287 (tt) REVERT: A 527 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8608 (tt0) REVERT: A 535 LEU cc_start: 0.9495 (mt) cc_final: 0.9210 (mm) REVERT: A 669 CYS cc_start: 0.8666 (m) cc_final: 0.7779 (m) REVERT: A 737 LEU cc_start: 0.9256 (mt) cc_final: 0.8956 (tp) REVERT: A 738 SER cc_start: 0.9313 (p) cc_final: 0.8883 (m) REVERT: A 743 LEU cc_start: 0.8974 (tp) cc_final: 0.7778 (tt) REVERT: A 751 ASN cc_start: 0.8725 (m-40) cc_final: 0.8248 (m110) REVERT: A 755 ASP cc_start: 0.8396 (m-30) cc_final: 0.7890 (t0) REVERT: A 762 CYS cc_start: 0.9104 (m) cc_final: 0.8551 (p) REVERT: A 790 ILE cc_start: 0.8845 (mt) cc_final: 0.8645 (tp) REVERT: A 802 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8349 (mt-10) REVERT: A 831 LYS cc_start: 0.8550 (mttt) cc_final: 0.8186 (mmtp) REVERT: A 989 PHE cc_start: 0.9211 (m-10) cc_final: 0.8461 (m-80) REVERT: A 1006 SER cc_start: 0.8466 (t) cc_final: 0.8108 (p) REVERT: A 1008 MET cc_start: 0.8258 (mmm) cc_final: 0.8013 (mmp) REVERT: B 220 HIS cc_start: 0.8278 (m90) cc_final: 0.7691 (p-80) REVERT: B 240 MET cc_start: 0.8143 (mtm) cc_final: 0.7699 (mmt) REVERT: B 288 HIS cc_start: 0.8941 (p-80) cc_final: 0.8721 (m90) REVERT: B 304 PHE cc_start: 0.8881 (t80) cc_final: 0.8536 (t80) REVERT: B 381 TYR cc_start: 0.8488 (t80) cc_final: 0.8048 (t80) REVERT: B 403 GLU cc_start: 0.8665 (tt0) cc_final: 0.7827 (tp30) REVERT: B 415 CYS cc_start: 0.8374 (p) cc_final: 0.8159 (p) REVERT: B 419 CYS cc_start: 0.7600 (m) cc_final: 0.7378 (p) REVERT: B 517 PHE cc_start: 0.7290 (p90) cc_final: 0.6683 (p90) REVERT: B 521 ILE cc_start: 0.8773 (tt) cc_final: 0.8299 (tt) REVERT: B 526 GLN cc_start: 0.9632 (tt0) cc_final: 0.9204 (tt0) REVERT: B 535 LEU cc_start: 0.9445 (mt) cc_final: 0.9212 (mm) REVERT: B 671 GLU cc_start: 0.8798 (tt0) cc_final: 0.8559 (tm-30) REVERT: B 743 LEU cc_start: 0.8976 (tp) cc_final: 0.7842 (tp) REVERT: B 751 ASN cc_start: 0.8823 (m-40) cc_final: 0.8161 (m110) REVERT: B 755 ASP cc_start: 0.8320 (m-30) cc_final: 0.7970 (t0) REVERT: B 761 LEU cc_start: 0.9553 (tp) cc_final: 0.9352 (tp) REVERT: B 790 ILE cc_start: 0.8923 (mt) cc_final: 0.8679 (tp) REVERT: B 802 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8202 (mt-10) REVERT: B 831 LYS cc_start: 0.8572 (mttt) cc_final: 0.8023 (mmtp) REVERT: B 953 LEU cc_start: 0.9123 (mt) cc_final: 0.8777 (mp) REVERT: B 989 PHE cc_start: 0.9154 (m-10) cc_final: 0.8370 (m-80) REVERT: B 1008 MET cc_start: 0.8331 (mmm) cc_final: 0.8041 (mmp) REVERT: C 220 HIS cc_start: 0.8537 (m-70) cc_final: 0.7439 (p-80) REVERT: C 240 MET cc_start: 0.8406 (mtm) cc_final: 0.7999 (mmt) REVERT: C 249 TYR cc_start: 0.8077 (m-80) cc_final: 0.7658 (m-80) REVERT: C 253 PHE cc_start: 0.7802 (m-80) cc_final: 0.5458 (m-80) REVERT: C 301 MET cc_start: 0.8641 (ttt) cc_final: 0.8399 (ptm) REVERT: C 403 GLU cc_start: 0.8759 (tt0) cc_final: 0.7872 (tp30) REVERT: C 419 CYS cc_start: 0.8256 (m) cc_final: 0.8015 (p) REVERT: C 517 PHE cc_start: 0.7460 (p90) cc_final: 0.7062 (p90) REVERT: C 526 GLN cc_start: 0.9537 (tt0) cc_final: 0.9001 (tt0) REVERT: C 535 LEU cc_start: 0.9479 (mt) cc_final: 0.9169 (mm) REVERT: C 669 CYS cc_start: 0.8627 (m) cc_final: 0.7394 (m) REVERT: C 737 LEU cc_start: 0.9313 (mt) cc_final: 0.8856 (tp) REVERT: C 738 SER cc_start: 0.9292 (p) cc_final: 0.8851 (m) REVERT: C 743 LEU cc_start: 0.8936 (tp) cc_final: 0.7536 (tp) REVERT: C 748 LEU cc_start: 0.8950 (mt) cc_final: 0.8054 (tp) REVERT: C 751 ASN cc_start: 0.8724 (m-40) cc_final: 0.7970 (m-40) REVERT: C 755 ASP cc_start: 0.8397 (m-30) cc_final: 0.7868 (t0) REVERT: C 802 GLU cc_start: 0.8559 (mt-10) cc_final: 0.7939 (mt-10) REVERT: C 831 LYS cc_start: 0.8541 (mttt) cc_final: 0.8195 (mmtp) REVERT: C 911 ASN cc_start: 0.8467 (t0) cc_final: 0.8243 (t0) REVERT: C 940 ASP cc_start: 0.8553 (m-30) cc_final: 0.7972 (t70) REVERT: C 953 LEU cc_start: 0.8970 (mt) cc_final: 0.8651 (mp) REVERT: C 989 PHE cc_start: 0.9144 (m-10) cc_final: 0.8834 (m-80) REVERT: C 1006 SER cc_start: 0.8607 (t) cc_final: 0.7493 (p) REVERT: C 1008 MET cc_start: 0.8184 (mmm) cc_final: 0.7607 (mmm) REVERT: D 220 HIS cc_start: 0.8380 (m90) cc_final: 0.7704 (p-80) REVERT: D 304 PHE cc_start: 0.8719 (t80) cc_final: 0.8362 (t80) REVERT: D 381 TYR cc_start: 0.8681 (t80) cc_final: 0.8126 (t80) REVERT: D 408 MET cc_start: 0.8402 (mtm) cc_final: 0.7881 (mtm) REVERT: D 415 CYS cc_start: 0.9181 (t) cc_final: 0.8688 (t) REVERT: D 492 HIS cc_start: 0.7837 (m90) cc_final: 0.7610 (m170) REVERT: D 517 PHE cc_start: 0.7390 (p90) cc_final: 0.6781 (p90) REVERT: D 526 GLN cc_start: 0.9477 (tt0) cc_final: 0.8939 (tt0) REVERT: D 535 LEU cc_start: 0.9440 (mt) cc_final: 0.9149 (mm) REVERT: D 669 CYS cc_start: 0.8646 (m) cc_final: 0.7513 (m) REVERT: D 671 GLU cc_start: 0.8785 (tt0) cc_final: 0.8567 (tm-30) REVERT: D 737 LEU cc_start: 0.9262 (mt) cc_final: 0.8901 (tp) REVERT: D 738 SER cc_start: 0.9371 (p) cc_final: 0.8906 (m) REVERT: D 743 LEU cc_start: 0.8978 (tp) cc_final: 0.7765 (tt) REVERT: D 751 ASN cc_start: 0.8781 (m-40) cc_final: 0.8364 (m110) REVERT: D 755 ASP cc_start: 0.8370 (m-30) cc_final: 0.7888 (t0) REVERT: D 802 GLU cc_start: 0.8549 (mt-10) cc_final: 0.7989 (mt-10) REVERT: D 831 LYS cc_start: 0.8543 (mttt) cc_final: 0.8199 (mmtp) REVERT: D 911 ASN cc_start: 0.8472 (t0) cc_final: 0.8246 (t0) REVERT: D 989 PHE cc_start: 0.9226 (m-10) cc_final: 0.8514 (m-80) REVERT: D 1006 SER cc_start: 0.8689 (t) cc_final: 0.7512 (p) REVERT: D 1008 MET cc_start: 0.8191 (mmm) cc_final: 0.7677 (mmm) REVERT: E 220 HIS cc_start: 0.8406 (m90) cc_final: 0.8191 (m-70) REVERT: E 235 LEU cc_start: 0.9394 (tp) cc_final: 0.9133 (tp) REVERT: E 240 MET cc_start: 0.8436 (mtm) cc_final: 0.7704 (mmt) REVERT: E 253 PHE cc_start: 0.6471 (m-80) cc_final: 0.6177 (m-80) REVERT: E 291 VAL cc_start: 0.8448 (t) cc_final: 0.8098 (t) REVERT: E 381 TYR cc_start: 0.8458 (t80) cc_final: 0.7957 (t80) REVERT: E 407 THR cc_start: 0.9162 (m) cc_final: 0.8748 (p) REVERT: E 408 MET cc_start: 0.8421 (mtm) cc_final: 0.7943 (mtm) REVERT: E 415 CYS cc_start: 0.9066 (t) cc_final: 0.8594 (t) REVERT: E 505 MET cc_start: 0.7829 (mtm) cc_final: 0.7303 (mtm) REVERT: E 526 GLN cc_start: 0.9599 (tt0) cc_final: 0.9080 (tt0) REVERT: E 527 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8625 (tt0) REVERT: E 535 LEU cc_start: 0.9463 (mt) cc_final: 0.9140 (mm) REVERT: E 669 CYS cc_start: 0.8762 (m) cc_final: 0.7733 (m) REVERT: E 730 CYS cc_start: 0.8808 (p) cc_final: 0.8579 (t) REVERT: E 737 LEU cc_start: 0.9236 (mt) cc_final: 0.8979 (tp) REVERT: E 738 SER cc_start: 0.9278 (p) cc_final: 0.8681 (m) REVERT: E 743 LEU cc_start: 0.8891 (tp) cc_final: 0.8082 (tp) REVERT: E 751 ASN cc_start: 0.8845 (m-40) cc_final: 0.8298 (m110) REVERT: E 755 ASP cc_start: 0.8438 (m-30) cc_final: 0.7951 (t0) REVERT: E 802 GLU cc_start: 0.8641 (mt-10) cc_final: 0.8317 (mt-10) REVERT: E 831 LYS cc_start: 0.8538 (mttt) cc_final: 0.8151 (mmtm) REVERT: E 940 ASP cc_start: 0.8610 (m-30) cc_final: 0.8029 (t70) REVERT: E 953 LEU cc_start: 0.9074 (mt) cc_final: 0.8853 (mt) REVERT: E 989 PHE cc_start: 0.9215 (m-10) cc_final: 0.8507 (m-80) REVERT: E 1008 MET cc_start: 0.8210 (mmm) cc_final: 0.7972 (mmp) REVERT: F 220 HIS cc_start: 0.8308 (m90) cc_final: 0.7823 (p-80) REVERT: F 235 LEU cc_start: 0.9428 (tp) cc_final: 0.9181 (tp) REVERT: F 240 MET cc_start: 0.8232 (mtm) cc_final: 0.7745 (mmt) REVERT: F 253 PHE cc_start: 0.7973 (m-80) cc_final: 0.5782 (m-80) REVERT: F 300 LEU cc_start: 0.7692 (tt) cc_final: 0.7125 (tt) REVERT: F 304 PHE cc_start: 0.8839 (t80) cc_final: 0.8610 (t80) REVERT: F 381 TYR cc_start: 0.8672 (t80) cc_final: 0.7982 (t80) REVERT: F 407 THR cc_start: 0.9082 (m) cc_final: 0.8839 (p) REVERT: F 415 CYS cc_start: 0.9196 (t) cc_final: 0.8587 (t) REVERT: F 517 PHE cc_start: 0.7247 (p90) cc_final: 0.6965 (p90) REVERT: F 535 LEU cc_start: 0.9440 (mt) cc_final: 0.9126 (mm) REVERT: F 671 GLU cc_start: 0.8821 (tt0) cc_final: 0.8538 (tm-30) REVERT: F 737 LEU cc_start: 0.9313 (mt) cc_final: 0.8947 (tp) REVERT: F 738 SER cc_start: 0.9257 (p) cc_final: 0.8860 (m) REVERT: F 743 LEU cc_start: 0.8909 (tp) cc_final: 0.7785 (tp) REVERT: F 751 ASN cc_start: 0.8786 (m-40) cc_final: 0.8174 (m110) REVERT: F 755 ASP cc_start: 0.8084 (m-30) cc_final: 0.7812 (t0) REVERT: F 802 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8266 (mt-10) REVERT: F 831 LYS cc_start: 0.8489 (mttt) cc_final: 0.8064 (mmtp) REVERT: F 940 ASP cc_start: 0.8632 (m-30) cc_final: 0.8048 (t70) REVERT: F 989 PHE cc_start: 0.9154 (m-10) cc_final: 0.8341 (m-80) REVERT: F 1006 SER cc_start: 0.8531 (t) cc_final: 0.8132 (m) outliers start: 0 outliers final: 0 residues processed: 1604 average time/residue: 0.5438 time to fit residues: 1398.5520 Evaluate side-chains 933 residues out of total 4452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 933 time to evaluate : 4.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 410 optimal weight: 10.0000 chunk 368 optimal weight: 0.1980 chunk 204 optimal weight: 5.9990 chunk 125 optimal weight: 4.9990 chunk 248 optimal weight: 20.0000 chunk 196 optimal weight: 0.9980 chunk 380 optimal weight: 0.6980 chunk 147 optimal weight: 0.8980 chunk 231 optimal weight: 3.9990 chunk 283 optimal weight: 5.9990 chunk 441 optimal weight: 3.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 HIS A 260 HIS A 400 GLN ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 434 GLN A 465 HIS ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1001 GLN B 215 HIS B 260 HIS B 400 GLN ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 434 GLN B 465 HIS B1001 GLN C 260 HIS C 465 HIS C 506 ASN C1001 GLN D 215 HIS ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 HIS D 522 HIS D1001 GLN E 364 HIS E 465 HIS ** E 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1001 GLN ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 465 HIS F1001 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 40266 Z= 0.215 Angle : 0.635 8.468 54372 Z= 0.324 Chirality : 0.039 0.273 6156 Planarity : 0.005 0.075 6810 Dihedral : 11.183 173.924 5544 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.15 % Favored : 95.65 % Rotamer: Outliers : 0.13 % Allowed : 2.47 % Favored : 97.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.12), residues: 4848 helix: 0.28 (0.10), residues: 2244 sheet: 0.30 (0.22), residues: 588 loop : -0.70 (0.14), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 467 HIS 0.007 0.001 HIS C 288 PHE 0.024 0.002 PHE B 396 TYR 0.022 0.002 TYR D 258 ARG 0.008 0.001 ARG B 292 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1098 residues out of total 4452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1092 time to evaluate : 5.100 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: 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 142 LYS cc_start: 0.9426 (mttt) cc_final: 0.9049 (pttm) REVERT: A 208 LEU cc_start: 0.9478 (mt) cc_final: 0.9183 (mt) REVERT: A 220 HIS cc_start: 0.8288 (m90) cc_final: 0.7705 (p-80) REVERT: A 240 MET cc_start: 0.8801 (mtm) cc_final: 0.8111 (mmt) REVERT: A 251 ASP cc_start: 0.8677 (p0) cc_final: 0.8393 (m-30) REVERT: A 253 PHE cc_start: 0.6878 (m-80) cc_final: 0.6015 (m-10) REVERT: A 291 VAL cc_start: 0.8366 (t) cc_final: 0.8150 (t) REVERT: A 326 GLU cc_start: 0.8000 (tp30) cc_final: 0.7772 (tt0) REVERT: A 336 ILE cc_start: 0.9615 (mt) cc_final: 0.9340 (tt) REVERT: A 403 GLU cc_start: 0.8875 (tt0) cc_final: 0.8099 (tp30) REVERT: A 527 GLU cc_start: 0.8956 (mt-10) cc_final: 0.8601 (tt0) REVERT: A 576 VAL cc_start: 0.9396 (t) cc_final: 0.9172 (t) REVERT: A 738 SER cc_start: 0.9426 (p) cc_final: 0.8931 (m) REVERT: A 743 LEU cc_start: 0.8995 (tp) cc_final: 0.8704 (tt) REVERT: A 751 ASN cc_start: 0.8832 (m-40) cc_final: 0.8443 (m110) REVERT: A 755 ASP cc_start: 0.8490 (m-30) cc_final: 0.7931 (t0) REVERT: A 761 LEU cc_start: 0.9651 (tp) cc_final: 0.9435 (tp) REVERT: A 802 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8374 (mt-10) REVERT: A 831 LYS cc_start: 0.8721 (mttt) cc_final: 0.8427 (mmtp) REVERT: A 860 LEU cc_start: 0.9534 (tp) cc_final: 0.9248 (tt) REVERT: A 953 LEU cc_start: 0.8971 (mt) cc_final: 0.8640 (mt) REVERT: A 1005 LEU cc_start: 0.8850 (mt) cc_final: 0.8611 (tt) REVERT: A 1006 SER cc_start: 0.8567 (t) cc_final: 0.8037 (p) REVERT: A 1008 MET cc_start: 0.8282 (mmm) cc_final: 0.7929 (mmp) REVERT: B 142 LYS cc_start: 0.9375 (mtmm) cc_final: 0.9128 (pttm) REVERT: B 220 HIS cc_start: 0.8215 (m90) cc_final: 0.7678 (p-80) REVERT: B 239 MET cc_start: 0.9185 (mtm) cc_final: 0.8976 (mtp) REVERT: B 240 MET cc_start: 0.8335 (mtm) cc_final: 0.7928 (mmt) REVERT: B 242 ASP cc_start: 0.9335 (m-30) cc_final: 0.9071 (m-30) REVERT: B 253 PHE cc_start: 0.7415 (m-10) cc_final: 0.7190 (m-10) REVERT: B 304 PHE cc_start: 0.8891 (t80) cc_final: 0.8654 (t80) REVERT: B 336 ILE cc_start: 0.9623 (mt) cc_final: 0.9367 (tt) REVERT: B 403 GLU cc_start: 0.8750 (tt0) cc_final: 0.8100 (tp30) REVERT: B 527 GLU cc_start: 0.9129 (tt0) cc_final: 0.8811 (tt0) REVERT: B 639 GLU cc_start: 0.8894 (tm-30) cc_final: 0.8600 (tm-30) REVERT: B 654 GLU cc_start: 0.9048 (tm-30) cc_final: 0.8723 (tm-30) REVERT: B 730 CYS cc_start: 0.9185 (m) cc_final: 0.8948 (m) REVERT: B 738 SER cc_start: 0.9381 (p) cc_final: 0.9019 (m) REVERT: B 751 ASN cc_start: 0.8770 (m-40) cc_final: 0.8437 (m-40) REVERT: B 790 ILE cc_start: 0.8852 (mt) cc_final: 0.8642 (tp) REVERT: B 831 LYS cc_start: 0.8826 (mttt) cc_final: 0.8284 (mmtp) REVERT: B 860 LEU cc_start: 0.9494 (tp) cc_final: 0.9272 (tt) REVERT: B 953 LEU cc_start: 0.9019 (mt) cc_final: 0.8794 (mt) REVERT: B 989 PHE cc_start: 0.8941 (m-10) cc_final: 0.8334 (m-80) REVERT: B 1008 MET cc_start: 0.8417 (mmm) cc_final: 0.8107 (mmp) REVERT: C 220 HIS cc_start: 0.8398 (m-70) cc_final: 0.7511 (p-80) REVERT: C 225 GLN cc_start: 0.8618 (pp30) cc_final: 0.8237 (pp30) REVERT: C 240 MET cc_start: 0.8681 (mtm) cc_final: 0.8049 (mmt) REVERT: C 242 ASP cc_start: 0.9301 (m-30) cc_final: 0.9085 (m-30) REVERT: C 253 PHE cc_start: 0.7406 (m-80) cc_final: 0.6537 (m-10) REVERT: C 291 VAL cc_start: 0.8257 (t) cc_final: 0.8054 (t) REVERT: C 298 LEU cc_start: 0.8504 (tp) cc_final: 0.8195 (tp) REVERT: C 379 LYS cc_start: 0.9177 (tttt) cc_final: 0.8902 (tptt) REVERT: C 403 GLU cc_start: 0.8844 (tt0) cc_final: 0.8135 (tp30) REVERT: C 526 GLN cc_start: 0.9509 (tt0) cc_final: 0.9150 (tt0) REVERT: C 639 GLU cc_start: 0.9070 (tm-30) cc_final: 0.8281 (tm-30) REVERT: C 730 CYS cc_start: 0.8602 (m) cc_final: 0.8277 (m) REVERT: C 738 SER cc_start: 0.9324 (p) cc_final: 0.8956 (m) REVERT: C 743 LEU cc_start: 0.8962 (tp) cc_final: 0.8643 (tt) REVERT: C 751 ASN cc_start: 0.8744 (m-40) cc_final: 0.8432 (m-40) REVERT: C 755 ASP cc_start: 0.8474 (m-30) cc_final: 0.7977 (t0) REVERT: C 761 LEU cc_start: 0.9566 (tp) cc_final: 0.9365 (tp) REVERT: C 802 GLU cc_start: 0.8629 (mt-10) cc_final: 0.7921 (mt-10) REVERT: C 831 LYS cc_start: 0.8773 (mttt) cc_final: 0.8293 (mmtp) REVERT: C 860 LEU cc_start: 0.9520 (tp) cc_final: 0.9279 (tt) REVERT: C 911 ASN cc_start: 0.8456 (t0) cc_final: 0.8249 (t0) REVERT: C 917 LEU cc_start: 0.7561 (mt) cc_final: 0.7252 (mp) REVERT: C 919 LEU cc_start: 0.8641 (mt) cc_final: 0.8376 (mp) REVERT: C 940 ASP cc_start: 0.8594 (m-30) cc_final: 0.7932 (t70) REVERT: C 1006 SER cc_start: 0.8754 (t) cc_final: 0.7787 (p) REVERT: C 1008 MET cc_start: 0.8154 (mmm) cc_final: 0.7523 (mmm) REVERT: C 1021 LEU cc_start: 0.9032 (mp) cc_final: 0.8623 (mt) REVERT: D 142 LYS cc_start: 0.9295 (mtmm) cc_final: 0.9052 (pttm) REVERT: D 220 HIS cc_start: 0.8102 (m90) cc_final: 0.7635 (p-80) REVERT: D 239 MET cc_start: 0.9179 (mtm) cc_final: 0.8920 (mtp) REVERT: D 242 ASP cc_start: 0.9318 (m-30) cc_final: 0.9022 (m-30) REVERT: D 304 PHE cc_start: 0.8927 (t80) cc_final: 0.8682 (t80) REVERT: D 381 TYR cc_start: 0.8803 (t80) cc_final: 0.8077 (t80) REVERT: D 403 GLU cc_start: 0.8919 (tt0) cc_final: 0.8461 (pm20) REVERT: D 415 CYS cc_start: 0.9123 (t) cc_final: 0.8450 (t) REVERT: D 419 CYS cc_start: 0.8200 (m) cc_final: 0.7521 (p) REVERT: D 477 ILE cc_start: 0.9135 (OUTLIER) cc_final: 0.8906 (mp) REVERT: D 492 HIS cc_start: 0.7714 (m90) cc_final: 0.7460 (m170) REVERT: D 521 ILE cc_start: 0.8772 (tt) cc_final: 0.8430 (pt) REVERT: D 526 GLN cc_start: 0.9289 (tt0) cc_final: 0.8203 (tm-30) REVERT: D 527 GLU cc_start: 0.9049 (tt0) cc_final: 0.8764 (tt0) REVERT: D 639 GLU cc_start: 0.9062 (tm-30) cc_final: 0.8501 (tm-30) REVERT: D 654 GLU cc_start: 0.9008 (tm-30) cc_final: 0.8778 (tm-30) REVERT: D 665 VAL cc_start: 0.9371 (m) cc_final: 0.8738 (p) REVERT: D 671 GLU cc_start: 0.8823 (tt0) cc_final: 0.8620 (tm-30) REVERT: D 737 LEU cc_start: 0.9518 (mt) cc_final: 0.9050 (tp) REVERT: D 738 SER cc_start: 0.9436 (p) cc_final: 0.8919 (m) REVERT: D 743 LEU cc_start: 0.9001 (tp) cc_final: 0.7723 (tt) REVERT: D 751 ASN cc_start: 0.8863 (m-40) cc_final: 0.8516 (m-40) REVERT: D 762 CYS cc_start: 0.9105 (m) cc_final: 0.8615 (p) REVERT: D 789 ASP cc_start: 0.8132 (m-30) cc_final: 0.7707 (m-30) REVERT: D 790 ILE cc_start: 0.8799 (mm) cc_final: 0.7942 (tp) REVERT: D 802 GLU cc_start: 0.8662 (mt-10) cc_final: 0.7990 (mt-10) REVERT: D 831 LYS cc_start: 0.8778 (mttt) cc_final: 0.8282 (mmtp) REVERT: D 917 LEU cc_start: 0.7844 (mt) cc_final: 0.7471 (mp) REVERT: D 1005 LEU cc_start: 0.8830 (mt) cc_final: 0.8598 (tt) REVERT: D 1006 SER cc_start: 0.8799 (t) cc_final: 0.7686 (p) REVERT: D 1008 MET cc_start: 0.8186 (mmm) cc_final: 0.7666 (mmm) REVERT: E 240 MET cc_start: 0.8650 (mtm) cc_final: 0.7964 (mmt) REVERT: E 242 ASP cc_start: 0.9320 (m-30) cc_final: 0.9054 (m-30) REVERT: E 253 PHE cc_start: 0.7190 (m-80) cc_final: 0.5558 (m-10) REVERT: E 304 PHE cc_start: 0.8836 (t80) cc_final: 0.8466 (t80) REVERT: E 381 TYR cc_start: 0.8657 (t80) cc_final: 0.8012 (t80) REVERT: E 407 THR cc_start: 0.8806 (m) cc_final: 0.8485 (p) REVERT: E 415 CYS cc_start: 0.9299 (t) cc_final: 0.8559 (t) REVERT: E 417 ILE cc_start: 0.9490 (mt) cc_final: 0.9245 (tp) REVERT: E 527 GLU cc_start: 0.8954 (mt-10) cc_final: 0.8583 (tt0) REVERT: E 669 CYS cc_start: 0.8439 (m) cc_final: 0.7511 (m) REVERT: E 738 SER cc_start: 0.9312 (p) cc_final: 0.8807 (m) REVERT: E 743 LEU cc_start: 0.8933 (tp) cc_final: 0.8585 (tt) REVERT: E 761 LEU cc_start: 0.9619 (tp) cc_final: 0.9418 (tp) REVERT: E 802 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8395 (mt-10) REVERT: E 831 LYS cc_start: 0.8729 (mttt) cc_final: 0.8289 (mmtp) REVERT: E 911 ASN cc_start: 0.8241 (t0) cc_final: 0.8025 (t0) REVERT: E 917 LEU cc_start: 0.7566 (mt) cc_final: 0.7256 (mp) REVERT: E 919 LEU cc_start: 0.8596 (mt) cc_final: 0.8290 (mp) REVERT: E 940 ASP cc_start: 0.8632 (m-30) cc_final: 0.8031 (t70) REVERT: E 989 PHE cc_start: 0.9056 (m-10) cc_final: 0.8519 (m-80) REVERT: E 1005 LEU cc_start: 0.8874 (mt) cc_final: 0.8628 (tt) REVERT: F 142 LYS cc_start: 0.9409 (mtmm) cc_final: 0.9160 (pttm) REVERT: F 208 LEU cc_start: 0.9183 (mp) cc_final: 0.7824 (tp) REVERT: F 220 HIS cc_start: 0.8012 (m90) cc_final: 0.7725 (p-80) REVERT: F 238 LYS cc_start: 0.8675 (tttt) cc_final: 0.8376 (tttt) REVERT: F 240 MET cc_start: 0.8396 (mtm) cc_final: 0.7910 (mmt) REVERT: F 242 ASP cc_start: 0.9279 (m-30) cc_final: 0.9070 (m-30) REVERT: F 253 PHE cc_start: 0.7179 (m-80) cc_final: 0.6806 (m-10) REVERT: F 255 TYR cc_start: 0.7842 (m-80) cc_final: 0.7327 (m-80) REVERT: F 304 PHE cc_start: 0.8855 (t80) cc_final: 0.8451 (t80) REVERT: F 326 GLU cc_start: 0.8063 (tp30) cc_final: 0.7827 (tt0) REVERT: F 336 ILE cc_start: 0.9674 (mt) cc_final: 0.9401 (tt) REVERT: F 381 TYR cc_start: 0.8821 (t80) cc_final: 0.7923 (t80) REVERT: F 407 THR cc_start: 0.8834 (m) cc_final: 0.8595 (p) REVERT: F 415 CYS cc_start: 0.9092 (t) cc_final: 0.8802 (t) REVERT: F 527 GLU cc_start: 0.9175 (tt0) cc_final: 0.8925 (tt0) REVERT: F 639 GLU cc_start: 0.8854 (tm-30) cc_final: 0.8091 (tm-30) REVERT: F 654 GLU cc_start: 0.9017 (tm-30) cc_final: 0.8678 (tm-30) REVERT: F 671 GLU cc_start: 0.8870 (tt0) cc_final: 0.8604 (tm-30) REVERT: F 738 SER cc_start: 0.9371 (p) cc_final: 0.9044 (m) REVERT: F 743 LEU cc_start: 0.8966 (tp) cc_final: 0.8678 (tt) REVERT: F 751 ASN cc_start: 0.8749 (m-40) cc_final: 0.8414 (m-40) REVERT: F 755 ASP cc_start: 0.8194 (m-30) cc_final: 0.7852 (t0) REVERT: F 802 GLU cc_start: 0.8779 (mt-10) cc_final: 0.8383 (mt-10) REVERT: F 831 LYS cc_start: 0.8727 (mttt) cc_final: 0.8362 (mmtp) REVERT: F 860 LEU cc_start: 0.9494 (tp) cc_final: 0.9262 (tt) REVERT: F 917 LEU cc_start: 0.7386 (mt) cc_final: 0.7032 (mp) REVERT: F 919 LEU cc_start: 0.8625 (mt) cc_final: 0.8318 (mp) REVERT: F 940 ASP cc_start: 0.8653 (m-30) cc_final: 0.8021 (t70) REVERT: F 953 LEU cc_start: 0.8992 (mt) cc_final: 0.8779 (mt) REVERT: F 989 PHE cc_start: 0.8951 (m-10) cc_final: 0.8459 (m-80) REVERT: F 1005 LEU cc_start: 0.8917 (mt) cc_final: 0.8649 (tt) REVERT: F 1006 SER cc_start: 0.8820 (t) cc_final: 0.7778 (p) REVERT: F 1021 LEU cc_start: 0.9094 (mp) cc_final: 0.8771 (mt) REVERT: F 1024 GLU cc_start: 0.9125 (tt0) cc_final: 0.8924 (tm-30) outliers start: 6 outliers final: 0 residues processed: 1094 average time/residue: 0.4842 time to fit residues: 889.9572 Evaluate side-chains 788 residues out of total 4452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 787 time to evaluate : 4.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 245 optimal weight: 10.0000 chunk 136 optimal weight: 5.9990 chunk 367 optimal weight: 0.9980 chunk 300 optimal weight: 4.9990 chunk 121 optimal weight: 0.6980 chunk 442 optimal weight: 8.9990 chunk 477 optimal weight: 10.0000 chunk 393 optimal weight: 5.9990 chunk 438 optimal weight: 3.9990 chunk 150 optimal weight: 9.9990 chunk 354 optimal weight: 6.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 HIS ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 HIS B 288 HIS ** B 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 522 HIS C 260 HIS C 391 GLN C 506 ASN C 522 HIS D 391 GLN ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 260 HIS ** E 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 663 HIS F 260 HIS F 288 HIS ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 522 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.4735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 40266 Z= 0.302 Angle : 0.653 13.240 54372 Z= 0.328 Chirality : 0.040 0.184 6156 Planarity : 0.004 0.054 6810 Dihedral : 11.021 174.865 5544 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.04 % Allowed : 2.67 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.12), residues: 4848 helix: 0.18 (0.11), residues: 2256 sheet: -0.06 (0.22), residues: 588 loop : -0.73 (0.14), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 833 HIS 0.009 0.001 HIS B 522 PHE 0.072 0.002 PHE A 383 TYR 0.021 0.002 TYR E 861 ARG 0.018 0.001 ARG A 292 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 916 residues out of total 4452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 914 time to evaluate : 4.396 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: 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 142 LYS cc_start: 0.9398 (mttt) cc_final: 0.9081 (pttm) REVERT: A 144 VAL cc_start: 0.9515 (t) cc_final: 0.9309 (m) REVERT: A 220 HIS cc_start: 0.8146 (m90) cc_final: 0.7741 (p-80) REVERT: A 239 MET cc_start: 0.9310 (mtp) cc_final: 0.9049 (mtp) REVERT: A 240 MET cc_start: 0.8917 (mtm) cc_final: 0.8254 (mmt) REVERT: A 242 ASP cc_start: 0.9249 (m-30) cc_final: 0.8986 (m-30) REVERT: A 253 PHE cc_start: 0.7404 (m-80) cc_final: 0.6989 (m-10) REVERT: A 263 GLU cc_start: 0.9253 (mp0) cc_final: 0.8921 (pm20) REVERT: A 336 ILE cc_start: 0.9618 (mt) cc_final: 0.9389 (tt) REVERT: A 358 LEU cc_start: 0.8736 (tp) cc_final: 0.8409 (tp) REVERT: A 403 GLU cc_start: 0.8873 (tt0) cc_final: 0.8084 (tp30) REVERT: A 521 ILE cc_start: 0.8187 (tt) cc_final: 0.7894 (pt) REVERT: A 527 GLU cc_start: 0.9132 (mt-10) cc_final: 0.8682 (tt0) REVERT: A 639 GLU cc_start: 0.9003 (tm-30) cc_final: 0.8491 (tm-30) REVERT: A 664 MET cc_start: 0.8869 (tpp) cc_final: 0.8608 (tpp) REVERT: A 738 SER cc_start: 0.9466 (p) cc_final: 0.9012 (m) REVERT: A 751 ASN cc_start: 0.8731 (m-40) cc_final: 0.8392 (m110) REVERT: A 802 GLU cc_start: 0.8720 (mt-10) cc_final: 0.7999 (mt-10) REVERT: A 831 LYS cc_start: 0.8904 (mttt) cc_final: 0.8376 (mttt) REVERT: A 953 LEU cc_start: 0.8930 (mt) cc_final: 0.8609 (mt) REVERT: A 1005 LEU cc_start: 0.9006 (mt) cc_final: 0.8516 (tt) REVERT: B 142 LYS cc_start: 0.9417 (mtmm) cc_final: 0.9154 (pttm) REVERT: B 220 HIS cc_start: 0.8595 (m90) cc_final: 0.7744 (p-80) REVERT: B 235 LEU cc_start: 0.9433 (tp) cc_final: 0.9200 (tt) REVERT: B 239 MET cc_start: 0.9277 (mtm) cc_final: 0.8931 (mtp) REVERT: B 242 ASP cc_start: 0.9392 (m-30) cc_final: 0.9116 (m-30) REVERT: B 253 PHE cc_start: 0.7753 (m-10) cc_final: 0.7214 (m-10) REVERT: B 358 LEU cc_start: 0.8736 (tp) cc_final: 0.8481 (tp) REVERT: B 403 GLU cc_start: 0.8880 (tt0) cc_final: 0.8052 (tp30) REVERT: B 523 MET cc_start: 0.8992 (pmm) cc_final: 0.8790 (pmm) REVERT: B 524 THR cc_start: 0.9095 (p) cc_final: 0.8762 (p) REVERT: B 527 GLU cc_start: 0.8932 (mt-10) cc_final: 0.8464 (tt0) REVERT: B 631 PHE cc_start: 0.8520 (m-80) cc_final: 0.8185 (m-80) REVERT: B 639 GLU cc_start: 0.8699 (tm-30) cc_final: 0.8493 (tm-30) REVERT: B 654 GLU cc_start: 0.9182 (tm-30) cc_final: 0.8920 (tm-30) REVERT: B 664 MET cc_start: 0.8928 (mmt) cc_final: 0.8593 (mmm) REVERT: B 669 CYS cc_start: 0.8729 (m) cc_final: 0.8161 (m) REVERT: B 730 CYS cc_start: 0.9269 (m) cc_final: 0.8978 (m) REVERT: B 738 SER cc_start: 0.9460 (p) cc_final: 0.9121 (m) REVERT: B 751 ASN cc_start: 0.8726 (m-40) cc_final: 0.8358 (m-40) REVERT: B 940 ASP cc_start: 0.8663 (m-30) cc_final: 0.7847 (t0) REVERT: B 989 PHE cc_start: 0.8993 (m-10) cc_final: 0.8463 (m-80) REVERT: B 1005 LEU cc_start: 0.9069 (mt) cc_final: 0.8699 (tt) REVERT: B 1008 MET cc_start: 0.8472 (mmm) cc_final: 0.7991 (mmp) REVERT: C 239 MET cc_start: 0.9328 (mtp) cc_final: 0.9057 (mtp) REVERT: C 240 MET cc_start: 0.8794 (mtm) cc_final: 0.8230 (mmt) REVERT: C 242 ASP cc_start: 0.9334 (m-30) cc_final: 0.9093 (m-30) REVERT: C 249 TYR cc_start: 0.8405 (m-80) cc_final: 0.7092 (m-80) REVERT: C 253 PHE cc_start: 0.8065 (m-80) cc_final: 0.4552 (m-10) REVERT: C 263 GLU cc_start: 0.9206 (mp0) cc_final: 0.8947 (pm20) REVERT: C 298 LEU cc_start: 0.8430 (tp) cc_final: 0.8196 (tp) REVERT: C 403 GLU cc_start: 0.8981 (tt0) cc_final: 0.8136 (tp30) REVERT: C 408 MET cc_start: 0.8874 (mtm) cc_final: 0.8492 (mtm) REVERT: C 575 PHE cc_start: 0.8398 (m-80) cc_final: 0.8172 (m-80) REVERT: C 664 MET cc_start: 0.8860 (mmt) cc_final: 0.8562 (tpp) REVERT: C 730 CYS cc_start: 0.8897 (m) cc_final: 0.8559 (m) REVERT: C 738 SER cc_start: 0.9364 (p) cc_final: 0.8990 (m) REVERT: C 802 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8174 (mt-10) REVERT: C 831 LYS cc_start: 0.8942 (mttt) cc_final: 0.8409 (mmtp) REVERT: C 940 ASP cc_start: 0.8700 (m-30) cc_final: 0.8095 (t70) REVERT: C 1001 GLN cc_start: 0.7721 (mm110) cc_final: 0.7378 (mm110) REVERT: C 1006 SER cc_start: 0.8860 (t) cc_final: 0.7902 (p) REVERT: C 1008 MET cc_start: 0.8181 (mmm) cc_final: 0.7807 (mmm) REVERT: D 142 LYS cc_start: 0.9326 (mtmm) cc_final: 0.9036 (pttm) REVERT: D 220 HIS cc_start: 0.8463 (m90) cc_final: 0.7717 (p-80) REVERT: D 239 MET cc_start: 0.9259 (mtm) cc_final: 0.8190 (mmp) REVERT: D 242 ASP cc_start: 0.9342 (m-30) cc_final: 0.8940 (m-30) REVERT: D 253 PHE cc_start: 0.7778 (m-10) cc_final: 0.7136 (m-10) REVERT: D 381 TYR cc_start: 0.8842 (t80) cc_final: 0.8388 (t80) REVERT: D 403 GLU cc_start: 0.8968 (tt0) cc_final: 0.8157 (tp30) REVERT: D 408 MET cc_start: 0.8652 (mtp) cc_final: 0.7785 (mmm) REVERT: D 415 CYS cc_start: 0.9286 (t) cc_final: 0.8777 (t) REVERT: D 526 GLN cc_start: 0.9289 (tt0) cc_final: 0.8922 (tt0) REVERT: D 527 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8421 (tt0) REVERT: D 654 GLU cc_start: 0.9103 (tm-30) cc_final: 0.8891 (tm-30) REVERT: D 665 VAL cc_start: 0.9384 (m) cc_final: 0.9179 (p) REVERT: D 671 GLU cc_start: 0.8877 (tt0) cc_final: 0.8676 (tm-30) REVERT: D 738 SER cc_start: 0.9453 (p) cc_final: 0.9046 (m) REVERT: D 751 ASN cc_start: 0.8764 (m-40) cc_final: 0.8457 (m-40) REVERT: D 802 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8268 (mt-10) REVERT: D 831 LYS cc_start: 0.8961 (mttt) cc_final: 0.8462 (mmtp) REVERT: D 989 PHE cc_start: 0.9132 (m-80) cc_final: 0.8698 (m-80) REVERT: D 1005 LEU cc_start: 0.9051 (mt) cc_final: 0.8766 (tt) REVERT: D 1006 SER cc_start: 0.9008 (t) cc_final: 0.8280 (m) REVERT: D 1008 MET cc_start: 0.8272 (mmm) cc_final: 0.7711 (mmm) REVERT: E 140 TYR cc_start: 0.7718 (t80) cc_final: 0.6887 (t80) REVERT: E 220 HIS cc_start: 0.8413 (m90) cc_final: 0.8050 (m90) REVERT: E 235 LEU cc_start: 0.9530 (tt) cc_final: 0.9329 (tt) REVERT: E 240 MET cc_start: 0.8805 (mtm) cc_final: 0.8199 (mmt) REVERT: E 242 ASP cc_start: 0.9356 (m-30) cc_final: 0.9097 (m-30) REVERT: E 253 PHE cc_start: 0.7439 (m-80) cc_final: 0.5494 (m-10) REVERT: E 403 GLU cc_start: 0.8779 (tt0) cc_final: 0.8089 (tp30) REVERT: E 407 THR cc_start: 0.8835 (m) cc_final: 0.8557 (p) REVERT: E 415 CYS cc_start: 0.9395 (t) cc_final: 0.9124 (t) REVERT: E 527 GLU cc_start: 0.9041 (mt-10) cc_final: 0.8632 (tt0) REVERT: E 637 MET cc_start: 0.9142 (tmm) cc_final: 0.8878 (tmm) REVERT: E 730 CYS cc_start: 0.9093 (p) cc_final: 0.8750 (p) REVERT: E 738 SER cc_start: 0.9368 (p) cc_final: 0.8927 (m) REVERT: E 802 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8472 (mt-10) REVERT: E 922 ASN cc_start: 0.8127 (m-40) cc_final: 0.7593 (m-40) REVERT: E 940 ASP cc_start: 0.8703 (m-30) cc_final: 0.8100 (t70) REVERT: E 987 MET cc_start: 0.9208 (mmm) cc_final: 0.8948 (mmm) REVERT: E 989 PHE cc_start: 0.9102 (m-10) cc_final: 0.8566 (m-80) REVERT: F 142 LYS cc_start: 0.9425 (mtmm) cc_final: 0.9165 (pttm) REVERT: F 205 MET cc_start: 0.7843 (pmm) cc_final: 0.7365 (pmm) REVERT: F 220 HIS cc_start: 0.8180 (m90) cc_final: 0.7867 (p-80) REVERT: F 238 LYS cc_start: 0.8644 (tttt) cc_final: 0.8099 (tttt) REVERT: F 239 MET cc_start: 0.9167 (mtm) cc_final: 0.7964 (mmp) REVERT: F 240 MET cc_start: 0.8524 (mtm) cc_final: 0.8053 (mmt) REVERT: F 242 ASP cc_start: 0.9321 (m-30) cc_final: 0.9038 (m-30) REVERT: F 253 PHE cc_start: 0.7482 (m-80) cc_final: 0.7132 (m-10) REVERT: F 255 TYR cc_start: 0.8022 (m-80) cc_final: 0.7491 (m-80) REVERT: F 326 GLU cc_start: 0.8201 (tp30) cc_final: 0.7961 (tt0) REVERT: F 358 LEU cc_start: 0.8752 (tp) cc_final: 0.8491 (tp) REVERT: F 381 TYR cc_start: 0.8483 (t80) cc_final: 0.8142 (t80) REVERT: F 403 GLU cc_start: 0.8818 (tt0) cc_final: 0.8078 (tp30) REVERT: F 407 THR cc_start: 0.8833 (m) cc_final: 0.8517 (p) REVERT: F 415 CYS cc_start: 0.9316 (t) cc_final: 0.8901 (t) REVERT: F 505 MET cc_start: 0.7925 (ptp) cc_final: 0.7465 (ptp) REVERT: F 527 GLU cc_start: 0.8961 (mt-10) cc_final: 0.8536 (tt0) REVERT: F 654 GLU cc_start: 0.9172 (tm-30) cc_final: 0.8893 (tm-30) REVERT: F 664 MET cc_start: 0.8908 (mmt) cc_final: 0.8578 (tpp) REVERT: F 738 SER cc_start: 0.9382 (p) cc_final: 0.9080 (m) REVERT: F 762 CYS cc_start: 0.9010 (m) cc_final: 0.8718 (m) REVERT: F 802 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8373 (mt-10) REVERT: F 831 LYS cc_start: 0.9011 (mttt) cc_final: 0.8474 (mmtp) REVERT: F 940 ASP cc_start: 0.8747 (m-30) cc_final: 0.8125 (t70) REVERT: F 987 MET cc_start: 0.9471 (mmm) cc_final: 0.9261 (mmm) REVERT: F 989 PHE cc_start: 0.9122 (m-10) cc_final: 0.8561 (m-80) REVERT: F 1024 GLU cc_start: 0.9229 (tt0) cc_final: 0.8968 (tm-30) outliers start: 2 outliers final: 0 residues processed: 914 average time/residue: 0.4925 time to fit residues: 754.7540 Evaluate side-chains 659 residues out of total 4452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 659 time to evaluate : 4.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 436 optimal weight: 6.9990 chunk 332 optimal weight: 5.9990 chunk 229 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 211 optimal weight: 9.9990 chunk 296 optimal weight: 0.0970 chunk 443 optimal weight: 9.9990 chunk 469 optimal weight: 0.9990 chunk 231 optimal weight: 10.0000 chunk 420 optimal weight: 0.0470 chunk 126 optimal weight: 0.6980 overall best weight: 0.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 GLN ** B 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 495 GLN C 495 GLN ** C 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 495 GLN E 260 HIS ** E 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 480 GLN E 495 GLN ** E 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 260 HIS ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 495 GLN F 522 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.5183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 40266 Z= 0.166 Angle : 0.575 10.247 54372 Z= 0.286 Chirality : 0.038 0.150 6156 Planarity : 0.004 0.058 6810 Dihedral : 10.901 176.456 5544 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.28 % Favored : 94.70 % Rotamer: Outliers : 0.02 % Allowed : 1.93 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.12), residues: 4848 helix: 0.11 (0.11), residues: 2256 sheet: -0.26 (0.22), residues: 594 loop : -0.63 (0.14), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 959 HIS 0.010 0.001 HIS A 916 PHE 0.025 0.002 PHE A 383 TYR 0.016 0.001 TYR A 533 ARG 0.007 0.000 ARG C 675 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 874 residues out of total 4452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 873 time to evaluate : 4.763 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 142 LYS cc_start: 0.9382 (mttt) cc_final: 0.9076 (pttm) REVERT: A 220 HIS cc_start: 0.8014 (m90) cc_final: 0.7723 (p-80) REVERT: A 239 MET cc_start: 0.9294 (mtp) cc_final: 0.9071 (mtp) REVERT: A 240 MET cc_start: 0.8793 (mtm) cc_final: 0.8309 (mmt) REVERT: A 242 ASP cc_start: 0.9261 (m-30) cc_final: 0.9002 (m-30) REVERT: A 253 PHE cc_start: 0.7428 (m-80) cc_final: 0.6962 (m-10) REVERT: A 263 GLU cc_start: 0.9242 (mp0) cc_final: 0.8999 (mp0) REVERT: A 336 ILE cc_start: 0.9624 (mt) cc_final: 0.9415 (tt) REVERT: A 403 GLU cc_start: 0.8801 (tt0) cc_final: 0.8069 (tp30) REVERT: A 527 GLU cc_start: 0.8955 (mt-10) cc_final: 0.8535 (tt0) REVERT: A 576 VAL cc_start: 0.9454 (t) cc_final: 0.9242 (t) REVERT: A 664 MET cc_start: 0.8781 (tpp) cc_final: 0.8375 (tpp) REVERT: A 738 SER cc_start: 0.9480 (p) cc_final: 0.9008 (m) REVERT: A 758 MET cc_start: 0.8989 (tpp) cc_final: 0.8663 (tpp) REVERT: A 802 GLU cc_start: 0.8844 (mt-10) cc_final: 0.8593 (mt-10) REVERT: A 981 LEU cc_start: 0.8849 (mt) cc_final: 0.8512 (tt) REVERT: A 987 MET cc_start: 0.9370 (mmp) cc_final: 0.9076 (mmp) REVERT: A 1008 MET cc_start: 0.8370 (mmm) cc_final: 0.7977 (mmp) REVERT: B 142 LYS cc_start: 0.9415 (mtmm) cc_final: 0.9139 (pttm) REVERT: B 220 HIS cc_start: 0.8602 (m90) cc_final: 0.7717 (p-80) REVERT: B 235 LEU cc_start: 0.9434 (tp) cc_final: 0.9216 (tt) REVERT: B 239 MET cc_start: 0.9121 (mtm) cc_final: 0.8888 (mtp) REVERT: B 240 MET cc_start: 0.8865 (tpp) cc_final: 0.8250 (mmt) REVERT: B 242 ASP cc_start: 0.9344 (m-30) cc_final: 0.9086 (m-30) REVERT: B 253 PHE cc_start: 0.7667 (m-10) cc_final: 0.7057 (m-10) REVERT: B 403 GLU cc_start: 0.8828 (tt0) cc_final: 0.8148 (tp30) REVERT: B 517 PHE cc_start: 0.7447 (p90) cc_final: 0.7017 (p90) REVERT: B 524 THR cc_start: 0.8932 (p) cc_final: 0.8681 (p) REVERT: B 527 GLU cc_start: 0.8908 (mt-10) cc_final: 0.8432 (tt0) REVERT: B 631 PHE cc_start: 0.8409 (m-80) cc_final: 0.8202 (m-80) REVERT: B 654 GLU cc_start: 0.9176 (tm-30) cc_final: 0.8912 (tm-30) REVERT: B 669 CYS cc_start: 0.8628 (m) cc_final: 0.8256 (m) REVERT: B 730 CYS cc_start: 0.9207 (m) cc_final: 0.8932 (m) REVERT: B 738 SER cc_start: 0.9437 (p) cc_final: 0.9092 (m) REVERT: B 751 ASN cc_start: 0.8740 (m-40) cc_final: 0.8435 (m110) REVERT: B 802 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8331 (mt-10) REVERT: B 831 LYS cc_start: 0.8962 (mttt) cc_final: 0.8422 (mttt) REVERT: B 989 PHE cc_start: 0.8973 (m-10) cc_final: 0.8456 (m-80) REVERT: B 1005 LEU cc_start: 0.9075 (mt) cc_final: 0.8733 (tt) REVERT: B 1008 MET cc_start: 0.8351 (mmm) cc_final: 0.7918 (mmp) REVERT: C 220 HIS cc_start: 0.8568 (m90) cc_final: 0.7717 (p-80) REVERT: C 239 MET cc_start: 0.9292 (mtp) cc_final: 0.9076 (mtp) REVERT: C 240 MET cc_start: 0.8723 (mtm) cc_final: 0.8422 (mmt) REVERT: C 242 ASP cc_start: 0.9304 (m-30) cc_final: 0.9093 (m-30) REVERT: C 249 TYR cc_start: 0.8342 (m-80) cc_final: 0.7507 (m-80) REVERT: C 263 GLU cc_start: 0.9245 (mp0) cc_final: 0.8975 (pm20) REVERT: C 298 LEU cc_start: 0.8410 (tp) cc_final: 0.8080 (tp) REVERT: C 379 LYS cc_start: 0.9153 (tttt) cc_final: 0.8840 (tptm) REVERT: C 403 GLU cc_start: 0.8926 (tt0) cc_final: 0.8229 (tp30) REVERT: C 405 LEU cc_start: 0.9496 (tt) cc_final: 0.9261 (tt) REVERT: C 517 PHE cc_start: 0.7518 (p90) cc_final: 0.6887 (p90) REVERT: C 526 GLN cc_start: 0.9501 (tt0) cc_final: 0.9091 (tt0) REVERT: C 527 GLU cc_start: 0.9081 (tt0) cc_final: 0.8750 (tt0) REVERT: C 575 PHE cc_start: 0.8284 (m-80) cc_final: 0.7906 (m-80) REVERT: C 730 CYS cc_start: 0.8879 (m) cc_final: 0.8527 (m) REVERT: C 738 SER cc_start: 0.9376 (p) cc_final: 0.8995 (m) REVERT: C 802 GLU cc_start: 0.8785 (mt-10) cc_final: 0.8289 (mt-10) REVERT: C 940 ASP cc_start: 0.8670 (m-30) cc_final: 0.8094 (t70) REVERT: C 1006 SER cc_start: 0.8760 (t) cc_final: 0.7875 (p) REVERT: C 1008 MET cc_start: 0.8040 (mmm) cc_final: 0.7709 (mmm) REVERT: D 142 LYS cc_start: 0.9296 (mtmm) cc_final: 0.8995 (pttm) REVERT: D 220 HIS cc_start: 0.8414 (m90) cc_final: 0.7651 (p-80) REVERT: D 238 LYS cc_start: 0.8709 (tttt) cc_final: 0.8140 (mmmt) REVERT: D 239 MET cc_start: 0.9225 (mtm) cc_final: 0.8178 (mmp) REVERT: D 242 ASP cc_start: 0.9347 (m-30) cc_final: 0.9064 (m-30) REVERT: D 253 PHE cc_start: 0.7787 (m-10) cc_final: 0.7172 (m-10) REVERT: D 381 TYR cc_start: 0.8758 (t80) cc_final: 0.8074 (t80) REVERT: D 403 GLU cc_start: 0.8962 (tt0) cc_final: 0.8178 (tp30) REVERT: D 415 CYS cc_start: 0.9260 (t) cc_final: 0.8252 (t) REVERT: D 419 CYS cc_start: 0.8172 (m) cc_final: 0.7693 (m) REVERT: D 527 GLU cc_start: 0.8888 (mt-10) cc_final: 0.8425 (tt0) REVERT: D 654 GLU cc_start: 0.9044 (tm-30) cc_final: 0.8835 (tm-30) REVERT: D 671 GLU cc_start: 0.8821 (tt0) cc_final: 0.8588 (tm-30) REVERT: D 738 SER cc_start: 0.9463 (p) cc_final: 0.9019 (m) REVERT: D 802 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8448 (mt-10) REVERT: D 864 GLU cc_start: 0.8815 (tp30) cc_final: 0.8608 (tp30) REVERT: D 922 ASN cc_start: 0.8034 (m-40) cc_final: 0.7701 (m-40) REVERT: D 989 PHE cc_start: 0.9111 (m-80) cc_final: 0.8774 (m-80) REVERT: D 1005 LEU cc_start: 0.9049 (mt) cc_final: 0.8754 (tt) REVERT: D 1006 SER cc_start: 0.8895 (t) cc_final: 0.8234 (m) REVERT: D 1008 MET cc_start: 0.8176 (mmm) cc_final: 0.7552 (mmp) REVERT: E 140 TYR cc_start: 0.7651 (t80) cc_final: 0.7134 (t80) REVERT: E 220 HIS cc_start: 0.8414 (m90) cc_final: 0.7971 (m90) REVERT: E 238 LYS cc_start: 0.8729 (ttpt) cc_final: 0.8526 (tttt) REVERT: E 240 MET cc_start: 0.8622 (mtm) cc_final: 0.8150 (mmt) REVERT: E 242 ASP cc_start: 0.9340 (m-30) cc_final: 0.9099 (m-30) REVERT: E 253 PHE cc_start: 0.7538 (m-80) cc_final: 0.5553 (m-10) REVERT: E 263 GLU cc_start: 0.9246 (mp0) cc_final: 0.8915 (pm20) REVERT: E 381 TYR cc_start: 0.8608 (t80) cc_final: 0.8248 (t80) REVERT: E 403 GLU cc_start: 0.8726 (tt0) cc_final: 0.7980 (tp30) REVERT: E 407 THR cc_start: 0.8822 (m) cc_final: 0.8484 (p) REVERT: E 408 MET cc_start: 0.8684 (mtp) cc_final: 0.8273 (mmm) REVERT: E 415 CYS cc_start: 0.9350 (t) cc_final: 0.8820 (t) REVERT: E 417 ILE cc_start: 0.9475 (mt) cc_final: 0.9244 (tp) REVERT: E 517 PHE cc_start: 0.7808 (p90) cc_final: 0.7495 (p90) REVERT: E 527 GLU cc_start: 0.8986 (mt-10) cc_final: 0.8553 (tt0) REVERT: E 637 MET cc_start: 0.9194 (tmm) cc_final: 0.8884 (tmm) REVERT: E 654 GLU cc_start: 0.9122 (tm-30) cc_final: 0.8893 (tm-30) REVERT: E 730 CYS cc_start: 0.9045 (p) cc_final: 0.8683 (p) REVERT: E 738 SER cc_start: 0.9373 (p) cc_final: 0.8925 (m) REVERT: E 751 ASN cc_start: 0.8769 (m-40) cc_final: 0.8487 (m110) REVERT: E 758 MET cc_start: 0.9013 (tpp) cc_final: 0.8716 (tpp) REVERT: E 790 ILE cc_start: 0.8906 (mm) cc_final: 0.7851 (tp) REVERT: E 802 GLU cc_start: 0.8920 (mt-10) cc_final: 0.8560 (mt-10) REVERT: E 831 LYS cc_start: 0.8971 (mttt) cc_final: 0.8373 (mmtp) REVERT: E 940 ASP cc_start: 0.8685 (m-30) cc_final: 0.8133 (t70) REVERT: E 989 PHE cc_start: 0.9076 (m-10) cc_final: 0.8509 (m-80) REVERT: E 1008 MET cc_start: 0.8421 (mmm) cc_final: 0.8150 (mmp) REVERT: F 142 LYS cc_start: 0.9422 (mtmm) cc_final: 0.9172 (pttm) REVERT: F 220 HIS cc_start: 0.8165 (m90) cc_final: 0.7841 (p-80) REVERT: F 238 LYS cc_start: 0.8587 (tttt) cc_final: 0.8221 (tttt) REVERT: F 239 MET cc_start: 0.9106 (mtm) cc_final: 0.8893 (mtp) REVERT: F 240 MET cc_start: 0.8451 (mtm) cc_final: 0.8019 (mmt) REVERT: F 242 ASP cc_start: 0.9314 (m-30) cc_final: 0.9108 (m-30) REVERT: F 253 PHE cc_start: 0.7598 (m-80) cc_final: 0.7226 (m-10) REVERT: F 255 TYR cc_start: 0.8039 (m-80) cc_final: 0.7779 (m-80) REVERT: F 263 GLU cc_start: 0.9284 (mp0) cc_final: 0.8877 (pm20) REVERT: F 381 TYR cc_start: 0.8362 (t80) cc_final: 0.8053 (t80) REVERT: F 403 GLU cc_start: 0.8800 (tt0) cc_final: 0.8580 (pm20) REVERT: F 407 THR cc_start: 0.8810 (m) cc_final: 0.8407 (p) REVERT: F 415 CYS cc_start: 0.9344 (t) cc_final: 0.8672 (t) REVERT: F 419 CYS cc_start: 0.7982 (m) cc_final: 0.7695 (p) REVERT: F 508 PHE cc_start: 0.8228 (m-80) cc_final: 0.7982 (m-10) REVERT: F 517 PHE cc_start: 0.7441 (p90) cc_final: 0.7032 (p90) REVERT: F 524 THR cc_start: 0.8879 (p) cc_final: 0.8644 (p) REVERT: F 527 GLU cc_start: 0.8961 (mt-10) cc_final: 0.8576 (tt0) REVERT: F 654 GLU cc_start: 0.9082 (tm-30) cc_final: 0.8770 (tm-30) REVERT: F 738 SER cc_start: 0.9430 (p) cc_final: 0.9076 (m) REVERT: F 751 ASN cc_start: 0.8774 (m-40) cc_final: 0.8549 (m-40) REVERT: F 762 CYS cc_start: 0.8901 (m) cc_final: 0.8700 (m) REVERT: F 802 GLU cc_start: 0.8910 (mt-10) cc_final: 0.8498 (mt-10) REVERT: F 940 ASP cc_start: 0.8735 (m-30) cc_final: 0.8161 (t70) REVERT: F 987 MET cc_start: 0.9463 (mmm) cc_final: 0.9247 (mmm) REVERT: F 989 PHE cc_start: 0.9117 (m-10) cc_final: 0.8509 (m-80) REVERT: F 1008 MET cc_start: 0.7057 (mmp) cc_final: 0.6847 (mmm) REVERT: F 1024 GLU cc_start: 0.9200 (tt0) cc_final: 0.8992 (tm-30) outliers start: 1 outliers final: 0 residues processed: 873 average time/residue: 0.4823 time to fit residues: 713.1570 Evaluate side-chains 685 residues out of total 4452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 685 time to evaluate : 4.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 391 optimal weight: 6.9990 chunk 266 optimal weight: 8.9990 chunk 6 optimal weight: 5.9990 chunk 349 optimal weight: 4.9990 chunk 193 optimal weight: 0.8980 chunk 400 optimal weight: 9.9990 chunk 324 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 239 optimal weight: 0.9990 chunk 421 optimal weight: 5.9990 chunk 118 optimal weight: 10.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 HIS ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 GLN ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 495 GLN ** B 663 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 480 GLN C 495 GLN C 506 ASN ** C 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 495 GLN ** D 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 495 GLN E 922 ASN ** F 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 495 GLN F 506 ASN F 922 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.6121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 40266 Z= 0.332 Angle : 0.699 13.534 54372 Z= 0.351 Chirality : 0.042 0.182 6156 Planarity : 0.005 0.062 6810 Dihedral : 10.889 178.926 5544 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.95 % Favored : 93.03 % Rotamer: Outliers : 0.04 % Allowed : 2.88 % Favored : 97.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.12), residues: 4848 helix: 0.10 (0.11), residues: 2214 sheet: -1.20 (0.21), residues: 594 loop : -0.79 (0.14), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 833 HIS 0.010 0.001 HIS C 916 PHE 0.041 0.002 PHE C 382 TYR 0.036 0.002 TYR C 861 ARG 0.022 0.001 ARG F 327 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 813 residues out of total 4452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 811 time to evaluate : 4.268 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 LYS cc_start: 0.9397 (mttt) cc_final: 0.9004 (pttm) REVERT: A 220 HIS cc_start: 0.8228 (m90) cc_final: 0.7974 (p-80) REVERT: A 240 MET cc_start: 0.8949 (mtm) cc_final: 0.8545 (mmt) REVERT: A 242 ASP cc_start: 0.9292 (m-30) cc_final: 0.9052 (m-30) REVERT: A 253 PHE cc_start: 0.7408 (m-80) cc_final: 0.6330 (m-10) REVERT: A 291 VAL cc_start: 0.8685 (t) cc_final: 0.8309 (t) REVERT: A 403 GLU cc_start: 0.8819 (tt0) cc_final: 0.8194 (tp30) REVERT: A 527 GLU cc_start: 0.9129 (mt-10) cc_final: 0.8739 (tt0) REVERT: A 758 MET cc_start: 0.9094 (tpp) cc_final: 0.8726 (tpp) REVERT: A 802 GLU cc_start: 0.8748 (mt-10) cc_final: 0.8051 (mt-10) REVERT: A 831 LYS cc_start: 0.9124 (mttt) cc_final: 0.8422 (mttt) REVERT: A 987 MET cc_start: 0.9457 (mmp) cc_final: 0.9245 (mmm) REVERT: B 142 LYS cc_start: 0.9415 (mtmm) cc_final: 0.9160 (pttm) REVERT: B 220 HIS cc_start: 0.8850 (m90) cc_final: 0.7901 (p-80) REVERT: B 239 MET cc_start: 0.9246 (mtm) cc_final: 0.8215 (mmp) REVERT: B 242 ASP cc_start: 0.9357 (m-30) cc_final: 0.8985 (m-30) REVERT: B 253 PHE cc_start: 0.7667 (m-10) cc_final: 0.7216 (m-10) REVERT: B 403 GLU cc_start: 0.8884 (tt0) cc_final: 0.8200 (tp30) REVERT: B 408 MET cc_start: 0.8953 (mtm) cc_final: 0.8494 (mtm) REVERT: B 411 ILE cc_start: 0.8805 (mt) cc_final: 0.8509 (mt) REVERT: B 465 HIS cc_start: 0.7526 (m90) cc_final: 0.7293 (m90) REVERT: B 517 PHE cc_start: 0.7632 (p90) cc_final: 0.7060 (p90) REVERT: B 527 GLU cc_start: 0.9080 (mt-10) cc_final: 0.8620 (tt0) REVERT: B 654 GLU cc_start: 0.9309 (tm-30) cc_final: 0.9066 (tm-30) REVERT: B 730 CYS cc_start: 0.9244 (m) cc_final: 0.8992 (m) REVERT: B 751 ASN cc_start: 0.8644 (m-40) cc_final: 0.8386 (m-40) REVERT: B 831 LYS cc_start: 0.9186 (mttt) cc_final: 0.8801 (mttt) REVERT: B 922 ASN cc_start: 0.7959 (m110) cc_final: 0.7071 (m-40) REVERT: B 989 PHE cc_start: 0.8998 (m-10) cc_final: 0.8476 (m-80) REVERT: C 220 HIS cc_start: 0.8849 (m90) cc_final: 0.8549 (m90) REVERT: C 240 MET cc_start: 0.8827 (mtm) cc_final: 0.8535 (mmt) REVERT: C 242 ASP cc_start: 0.9290 (m-30) cc_final: 0.9049 (m-30) REVERT: C 253 PHE cc_start: 0.8006 (m-80) cc_final: 0.7121 (m-80) REVERT: C 379 LYS cc_start: 0.9166 (tttt) cc_final: 0.8834 (tptm) REVERT: C 403 GLU cc_start: 0.9019 (tt0) cc_final: 0.8324 (tp30) REVERT: C 405 LEU cc_start: 0.9510 (tt) cc_final: 0.9309 (tt) REVERT: C 408 MET cc_start: 0.8993 (mtm) cc_final: 0.8458 (mmt) REVERT: C 517 PHE cc_start: 0.7682 (p90) cc_final: 0.6925 (p90) REVERT: C 575 PHE cc_start: 0.8581 (m-80) cc_final: 0.8326 (m-80) REVERT: C 662 ASP cc_start: 0.8689 (m-30) cc_final: 0.8262 (m-30) REVERT: C 730 CYS cc_start: 0.9052 (m) cc_final: 0.8722 (m) REVERT: C 802 GLU cc_start: 0.8727 (mt-10) cc_final: 0.7759 (mt-10) REVERT: C 831 LYS cc_start: 0.9118 (mttt) cc_final: 0.8395 (mttt) REVERT: C 922 ASN cc_start: 0.7977 (m110) cc_final: 0.7187 (m110) REVERT: C 940 ASP cc_start: 0.8767 (m-30) cc_final: 0.8275 (t70) REVERT: C 1006 SER cc_start: 0.9089 (t) cc_final: 0.8736 (m) REVERT: C 1008 MET cc_start: 0.8162 (mmm) cc_final: 0.7821 (mmm) REVERT: D 220 HIS cc_start: 0.8556 (m90) cc_final: 0.7856 (p-80) REVERT: D 238 LYS cc_start: 0.8658 (tttt) cc_final: 0.8151 (mmmt) REVERT: D 239 MET cc_start: 0.9353 (mtm) cc_final: 0.8348 (mmp) REVERT: D 242 ASP cc_start: 0.9373 (m-30) cc_final: 0.9109 (m-30) REVERT: D 253 PHE cc_start: 0.7826 (m-10) cc_final: 0.7358 (m-10) REVERT: D 327 ARG cc_start: 0.8509 (mmp80) cc_final: 0.8299 (mmp-170) REVERT: D 403 GLU cc_start: 0.9045 (tt0) cc_final: 0.8098 (tp30) REVERT: D 408 MET cc_start: 0.8862 (mtm) cc_final: 0.8536 (mtm) REVERT: D 527 GLU cc_start: 0.9112 (mt-10) cc_final: 0.8681 (tt0) REVERT: D 576 VAL cc_start: 0.9651 (t) cc_final: 0.9264 (t) REVERT: D 664 MET cc_start: 0.8966 (mmt) cc_final: 0.8575 (tpp) REVERT: D 802 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8373 (mt-10) REVERT: D 1001 GLN cc_start: 0.7825 (mm110) cc_final: 0.7303 (mm110) REVERT: D 1006 SER cc_start: 0.9210 (t) cc_final: 0.8590 (m) REVERT: D 1008 MET cc_start: 0.8404 (mmm) cc_final: 0.7835 (mmp) REVERT: E 220 HIS cc_start: 0.8502 (m90) cc_final: 0.8101 (m-70) REVERT: E 239 MET cc_start: 0.9306 (mtp) cc_final: 0.9085 (mtp) REVERT: E 242 ASP cc_start: 0.9358 (m-30) cc_final: 0.9092 (m-30) REVERT: E 253 PHE cc_start: 0.7760 (m-80) cc_final: 0.6590 (m-10) REVERT: E 403 GLU cc_start: 0.8829 (tt0) cc_final: 0.8079 (tp30) REVERT: E 407 THR cc_start: 0.8905 (m) cc_final: 0.8479 (p) REVERT: E 527 GLU cc_start: 0.9135 (mt-10) cc_final: 0.8653 (tt0) REVERT: E 557 ASP cc_start: 0.8190 (t0) cc_final: 0.7570 (t0) REVERT: E 630 LEU cc_start: 0.9193 (mp) cc_final: 0.8900 (mp) REVERT: E 730 CYS cc_start: 0.9050 (p) cc_final: 0.8637 (p) REVERT: E 738 SER cc_start: 0.9361 (p) cc_final: 0.8930 (m) REVERT: E 758 MET cc_start: 0.9074 (tpp) cc_final: 0.8696 (tpp) REVERT: E 802 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8080 (mt-10) REVERT: E 831 LYS cc_start: 0.9131 (mttt) cc_final: 0.8419 (mttt) REVERT: E 922 ASN cc_start: 0.8094 (OUTLIER) cc_final: 0.7237 (m-40) REVERT: E 940 ASP cc_start: 0.8763 (m-30) cc_final: 0.8229 (t0) REVERT: E 987 MET cc_start: 0.9204 (mmm) cc_final: 0.8999 (mmm) REVERT: E 989 PHE cc_start: 0.9060 (m-10) cc_final: 0.8571 (m-80) REVERT: E 1008 MET cc_start: 0.8443 (mmm) cc_final: 0.8235 (mmp) REVERT: F 142 LYS cc_start: 0.9457 (mtmm) cc_final: 0.9217 (pttm) REVERT: F 239 MET cc_start: 0.9244 (mtm) cc_final: 0.8970 (mtp) REVERT: F 240 MET cc_start: 0.8684 (mtm) cc_final: 0.8386 (mmt) REVERT: F 242 ASP cc_start: 0.9356 (m-30) cc_final: 0.9087 (m-30) REVERT: F 253 PHE cc_start: 0.8032 (m-80) cc_final: 0.7437 (m-10) REVERT: F 407 THR cc_start: 0.8873 (m) cc_final: 0.8454 (p) REVERT: F 415 CYS cc_start: 0.9426 (t) cc_final: 0.9161 (p) REVERT: F 465 HIS cc_start: 0.7558 (m90) cc_final: 0.7290 (m90) REVERT: F 517 PHE cc_start: 0.7656 (p90) cc_final: 0.6954 (p90) REVERT: F 523 MET cc_start: 0.8920 (pmm) cc_final: 0.8668 (pmm) REVERT: F 527 GLU cc_start: 0.9069 (mt-10) cc_final: 0.8616 (tt0) REVERT: F 576 VAL cc_start: 0.9587 (t) cc_final: 0.9342 (t) REVERT: F 654 GLU cc_start: 0.9241 (tm-30) cc_final: 0.8959 (tm-30) REVERT: F 751 ASN cc_start: 0.8682 (m-40) cc_final: 0.8450 (m-40) REVERT: F 762 CYS cc_start: 0.9052 (m) cc_final: 0.8728 (m) REVERT: F 802 GLU cc_start: 0.8751 (mt-10) cc_final: 0.7909 (mt-10) REVERT: F 831 LYS cc_start: 0.9168 (mttt) cc_final: 0.8372 (mttt) REVERT: F 922 ASN cc_start: 0.7829 (OUTLIER) cc_final: 0.6981 (m-40) REVERT: F 940 ASP cc_start: 0.8829 (m-30) cc_final: 0.8294 (t70) REVERT: F 989 PHE cc_start: 0.9145 (m-10) cc_final: 0.8655 (m-80) REVERT: F 1021 LEU cc_start: 0.8809 (mt) cc_final: 0.8580 (mt) REVERT: F 1024 GLU cc_start: 0.9306 (tt0) cc_final: 0.9008 (tm-30) outliers start: 2 outliers final: 0 residues processed: 811 average time/residue: 0.4798 time to fit residues: 659.0924 Evaluate side-chains 600 residues out of total 4452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 598 time to evaluate : 4.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 158 optimal weight: 2.9990 chunk 423 optimal weight: 2.9990 chunk 92 optimal weight: 20.0000 chunk 275 optimal weight: 20.0000 chunk 115 optimal weight: 0.0870 chunk 470 optimal weight: 0.9990 chunk 390 optimal weight: 1.9990 chunk 217 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 155 optimal weight: 4.9990 chunk 246 optimal weight: 9.9990 overall best weight: 1.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 HIS ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 HIS A 808 ASN A 922 ASN ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 808 ASN B 922 ASN C 922 ASN ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 522 HIS E 808 ASN ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 522 HIS F 893 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.6352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 40266 Z= 0.188 Angle : 0.613 13.275 54372 Z= 0.298 Chirality : 0.039 0.177 6156 Planarity : 0.004 0.067 6810 Dihedral : 10.779 175.272 5544 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.13 % Favored : 93.85 % Rotamer: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.12), residues: 4848 helix: 0.10 (0.11), residues: 2244 sheet: -1.18 (0.22), residues: 582 loop : -0.70 (0.14), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 959 HIS 0.009 0.001 HIS A 916 PHE 0.047 0.002 PHE D 989 TYR 0.016 0.001 TYR D 861 ARG 0.011 0.001 ARG B 351 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 819 residues out of total 4452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 819 time to evaluate : 4.602 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 232 LYS cc_start: 0.8291 (pttt) cc_final: 0.7708 (ptpp) REVERT: A 239 MET cc_start: 0.9208 (mtm) cc_final: 0.9007 (mtp) REVERT: A 240 MET cc_start: 0.8816 (mtm) cc_final: 0.8431 (mmt) REVERT: A 242 ASP cc_start: 0.9247 (m-30) cc_final: 0.9018 (m-30) REVERT: A 253 PHE cc_start: 0.7450 (m-80) cc_final: 0.7062 (m-10) REVERT: A 291 VAL cc_start: 0.8627 (t) cc_final: 0.8253 (t) REVERT: A 403 GLU cc_start: 0.8807 (tt0) cc_final: 0.8143 (tp30) REVERT: A 517 PHE cc_start: 0.7847 (p90) cc_final: 0.7411 (p90) REVERT: A 527 GLU cc_start: 0.9067 (mt-10) cc_final: 0.8733 (tt0) REVERT: A 532 MET cc_start: 0.8850 (tpp) cc_final: 0.8443 (tpt) REVERT: A 576 VAL cc_start: 0.9656 (t) cc_final: 0.9438 (t) REVERT: A 738 SER cc_start: 0.9446 (p) cc_final: 0.9001 (m) REVERT: A 758 MET cc_start: 0.8907 (tpp) cc_final: 0.8639 (tpp) REVERT: A 802 GLU cc_start: 0.8733 (mt-10) cc_final: 0.8043 (mt-10) REVERT: A 831 LYS cc_start: 0.9144 (mttt) cc_final: 0.8355 (mttt) REVERT: A 940 ASP cc_start: 0.8643 (m-30) cc_final: 0.8309 (m-30) REVERT: A 987 MET cc_start: 0.9442 (mmp) cc_final: 0.9218 (mmm) REVERT: B 142 LYS cc_start: 0.9417 (mtmm) cc_final: 0.9125 (pttm) REVERT: B 220 HIS cc_start: 0.8827 (m90) cc_final: 0.7824 (p-80) REVERT: B 239 MET cc_start: 0.9307 (mtm) cc_final: 0.8196 (mmp) REVERT: B 242 ASP cc_start: 0.9305 (m-30) cc_final: 0.8878 (m-30) REVERT: B 253 PHE cc_start: 0.7688 (m-10) cc_final: 0.7034 (m-10) REVERT: B 255 TYR cc_start: 0.7995 (m-80) cc_final: 0.7496 (m-80) REVERT: B 403 GLU cc_start: 0.8860 (tt0) cc_final: 0.8201 (tp30) REVERT: B 517 PHE cc_start: 0.7656 (p90) cc_final: 0.7095 (p90) REVERT: B 527 GLU cc_start: 0.8900 (mt-10) cc_final: 0.8577 (tt0) REVERT: B 576 VAL cc_start: 0.9666 (t) cc_final: 0.9382 (t) REVERT: B 631 PHE cc_start: 0.8418 (m-10) cc_final: 0.8218 (m-80) REVERT: B 654 GLU cc_start: 0.9267 (tm-30) cc_final: 0.9030 (tm-30) REVERT: B 669 CYS cc_start: 0.8629 (m) cc_final: 0.8209 (m) REVERT: B 751 ASN cc_start: 0.8784 (m-40) cc_final: 0.8583 (m-40) REVERT: B 802 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8291 (mt-10) REVERT: B 831 LYS cc_start: 0.9263 (mttt) cc_final: 0.8768 (mttt) REVERT: B 940 ASP cc_start: 0.8703 (m-30) cc_final: 0.8338 (m-30) REVERT: C 220 HIS cc_start: 0.8767 (m90) cc_final: 0.7726 (p-80) REVERT: C 232 LYS cc_start: 0.8279 (pttt) cc_final: 0.7759 (ptpp) REVERT: C 242 ASP cc_start: 0.9286 (m-30) cc_final: 0.9047 (m-30) REVERT: C 253 PHE cc_start: 0.8018 (m-80) cc_final: 0.6811 (m-80) REVERT: C 350 THR cc_start: 0.8601 (t) cc_final: 0.8252 (t) REVERT: C 379 LYS cc_start: 0.9146 (tttt) cc_final: 0.8847 (tptp) REVERT: C 403 GLU cc_start: 0.9012 (tt0) cc_final: 0.8324 (tp30) REVERT: C 408 MET cc_start: 0.8983 (mtm) cc_final: 0.8438 (mmt) REVERT: C 517 PHE cc_start: 0.7605 (p90) cc_final: 0.7025 (p90) REVERT: C 527 GLU cc_start: 0.9245 (tt0) cc_final: 0.8984 (tt0) REVERT: C 575 PHE cc_start: 0.8508 (m-80) cc_final: 0.8237 (m-80) REVERT: C 730 CYS cc_start: 0.8964 (m) cc_final: 0.8644 (m) REVERT: C 802 GLU cc_start: 0.8688 (mt-10) cc_final: 0.7813 (mt-10) REVERT: C 831 LYS cc_start: 0.9179 (mttt) cc_final: 0.8481 (mttt) REVERT: C 940 ASP cc_start: 0.8732 (m-30) cc_final: 0.8175 (t0) REVERT: C 1006 SER cc_start: 0.9010 (t) cc_final: 0.8679 (m) REVERT: C 1008 MET cc_start: 0.8130 (mmm) cc_final: 0.7761 (mmm) REVERT: D 239 MET cc_start: 0.9368 (mtm) cc_final: 0.9082 (mtp) REVERT: D 242 ASP cc_start: 0.9352 (m-30) cc_final: 0.9020 (m-30) REVERT: D 253 PHE cc_start: 0.7799 (m-10) cc_final: 0.7277 (m-10) REVERT: D 358 LEU cc_start: 0.9150 (tp) cc_final: 0.8940 (tt) REVERT: D 381 TYR cc_start: 0.8736 (t80) cc_final: 0.8510 (t80) REVERT: D 403 GLU cc_start: 0.8958 (tt0) cc_final: 0.8045 (tp30) REVERT: D 405 LEU cc_start: 0.9575 (tt) cc_final: 0.9349 (mt) REVERT: D 415 CYS cc_start: 0.9071 (t) cc_final: 0.8858 (p) REVERT: D 417 ILE cc_start: 0.9563 (mt) cc_final: 0.9301 (tp) REVERT: D 527 GLU cc_start: 0.9035 (mt-10) cc_final: 0.8716 (tt0) REVERT: D 532 MET cc_start: 0.8578 (tpp) cc_final: 0.8351 (tpp) REVERT: D 630 LEU cc_start: 0.9124 (mp) cc_final: 0.8902 (mp) REVERT: D 738 SER cc_start: 0.9435 (p) cc_final: 0.8932 (m) REVERT: D 802 GLU cc_start: 0.8730 (mt-10) cc_final: 0.7992 (mt-10) REVERT: D 831 LYS cc_start: 0.9237 (mttt) cc_final: 0.8491 (mttt) REVERT: D 1006 SER cc_start: 0.9040 (t) cc_final: 0.8393 (m) REVERT: D 1008 MET cc_start: 0.8344 (mmm) cc_final: 0.7847 (mmp) REVERT: E 240 MET cc_start: 0.8798 (mmt) cc_final: 0.8357 (mmt) REVERT: E 242 ASP cc_start: 0.9337 (m-30) cc_final: 0.9063 (m-30) REVERT: E 253 PHE cc_start: 0.7679 (m-80) cc_final: 0.6560 (m-10) REVERT: E 263 GLU cc_start: 0.9190 (mp0) cc_final: 0.8933 (pm20) REVERT: E 403 GLU cc_start: 0.8862 (tt0) cc_final: 0.8137 (tp30) REVERT: E 409 CYS cc_start: 0.8886 (m) cc_final: 0.8675 (m) REVERT: E 415 CYS cc_start: 0.9328 (t) cc_final: 0.9097 (t) REVERT: E 517 PHE cc_start: 0.7841 (p90) cc_final: 0.7357 (p90) REVERT: E 527 GLU cc_start: 0.9061 (mt-10) cc_final: 0.8646 (tt0) REVERT: E 532 MET cc_start: 0.8599 (tpt) cc_final: 0.8377 (tpt) REVERT: E 557 ASP cc_start: 0.8238 (t0) cc_final: 0.7547 (t0) REVERT: E 738 SER cc_start: 0.9400 (p) cc_final: 0.8945 (m) REVERT: E 758 MET cc_start: 0.8957 (tpp) cc_final: 0.8656 (ttt) REVERT: E 802 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8154 (mt-10) REVERT: E 807 ASP cc_start: 0.8980 (m-30) cc_final: 0.8645 (t0) REVERT: E 831 LYS cc_start: 0.9166 (mttt) cc_final: 0.8519 (mttt) REVERT: E 940 ASP cc_start: 0.8711 (m-30) cc_final: 0.8176 (t70) REVERT: E 989 PHE cc_start: 0.8999 (m-10) cc_final: 0.8421 (m-80) REVERT: E 1008 MET cc_start: 0.8400 (mmm) cc_final: 0.8154 (mmp) REVERT: F 142 LYS cc_start: 0.9457 (mtmm) cc_final: 0.9188 (pttm) REVERT: F 220 HIS cc_start: 0.8750 (m90) cc_final: 0.7914 (p-80) REVERT: F 239 MET cc_start: 0.9191 (mtm) cc_final: 0.8898 (mtp) REVERT: F 240 MET cc_start: 0.8545 (mtm) cc_final: 0.8215 (mmt) REVERT: F 242 ASP cc_start: 0.9317 (m-30) cc_final: 0.9034 (m-30) REVERT: F 253 PHE cc_start: 0.8192 (m-80) cc_final: 0.7015 (m-80) REVERT: F 415 CYS cc_start: 0.9495 (t) cc_final: 0.9249 (p) REVERT: F 417 ILE cc_start: 0.9562 (mt) cc_final: 0.9287 (tp) REVERT: F 517 PHE cc_start: 0.7729 (p90) cc_final: 0.7151 (p90) REVERT: F 527 GLU cc_start: 0.8936 (mt-10) cc_final: 0.8606 (tt0) REVERT: F 630 LEU cc_start: 0.9174 (mp) cc_final: 0.8973 (mp) REVERT: F 636 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8083 (mm-30) REVERT: F 654 GLU cc_start: 0.9183 (tm-30) cc_final: 0.8894 (tm-30) REVERT: F 738 SER cc_start: 0.9343 (p) cc_final: 0.8957 (m) REVERT: F 762 CYS cc_start: 0.8971 (m) cc_final: 0.8615 (m) REVERT: F 802 GLU cc_start: 0.8725 (mt-10) cc_final: 0.7839 (mt-10) REVERT: F 807 ASP cc_start: 0.8916 (m-30) cc_final: 0.8611 (t0) REVERT: F 831 LYS cc_start: 0.9207 (mttt) cc_final: 0.8491 (mttt) REVERT: F 940 ASP cc_start: 0.8791 (m-30) cc_final: 0.8270 (t70) REVERT: F 989 PHE cc_start: 0.9056 (m-10) cc_final: 0.8479 (m-80) REVERT: F 1021 LEU cc_start: 0.8746 (mt) cc_final: 0.8503 (mt) REVERT: F 1024 GLU cc_start: 0.9326 (tt0) cc_final: 0.9019 (tm-30) outliers start: 0 outliers final: 0 residues processed: 819 average time/residue: 0.4797 time to fit residues: 664.4095 Evaluate side-chains 623 residues out of total 4452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 623 time to evaluate : 4.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 453 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 267 optimal weight: 9.9990 chunk 343 optimal weight: 0.9990 chunk 266 optimal weight: 6.9990 chunk 395 optimal weight: 0.9990 chunk 262 optimal weight: 3.9990 chunk 468 optimal weight: 0.8980 chunk 293 optimal weight: 4.9990 chunk 285 optimal weight: 4.9990 chunk 216 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 HIS ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 922 ASN ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 922 ASN C 922 ASN ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 808 ASN ** E 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 522 HIS E 922 ASN ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 751 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.6606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 40266 Z= 0.203 Angle : 0.604 12.947 54372 Z= 0.295 Chirality : 0.039 0.181 6156 Planarity : 0.004 0.063 6810 Dihedral : 10.702 179.565 5544 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.77 % Favored : 93.21 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.12), residues: 4848 helix: 0.13 (0.11), residues: 2268 sheet: -1.34 (0.22), residues: 582 loop : -0.80 (0.15), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 959 HIS 0.007 0.001 HIS A 916 PHE 0.045 0.002 PHE B 989 TYR 0.017 0.001 TYR E 861 ARG 0.014 0.000 ARG B 327 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 808 residues out of total 4452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 808 time to evaluate : 4.829 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 151 ILE cc_start: 0.8707 (mm) cc_final: 0.8136 (mt) REVERT: A 232 LYS cc_start: 0.8305 (pttt) cc_final: 0.8072 (ptpp) REVERT: A 239 MET cc_start: 0.9218 (mtm) cc_final: 0.8964 (mtp) REVERT: A 240 MET cc_start: 0.8833 (mtm) cc_final: 0.8539 (mmt) REVERT: A 242 ASP cc_start: 0.9251 (m-30) cc_final: 0.9020 (m-30) REVERT: A 253 PHE cc_start: 0.7455 (m-80) cc_final: 0.6837 (m-10) REVERT: A 291 VAL cc_start: 0.8622 (t) cc_final: 0.8249 (t) REVERT: A 343 GLU cc_start: 0.7513 (tp30) cc_final: 0.7171 (pt0) REVERT: A 403 GLU cc_start: 0.8816 (tt0) cc_final: 0.8188 (tp30) REVERT: A 517 PHE cc_start: 0.7882 (p90) cc_final: 0.7400 (p90) REVERT: A 527 GLU cc_start: 0.9101 (mt-10) cc_final: 0.8762 (tt0) REVERT: A 630 LEU cc_start: 0.9042 (mp) cc_final: 0.8698 (mp) REVERT: A 738 SER cc_start: 0.9449 (p) cc_final: 0.9022 (m) REVERT: A 758 MET cc_start: 0.8888 (tpp) cc_final: 0.8643 (tpp) REVERT: A 802 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8072 (mt-10) REVERT: A 831 LYS cc_start: 0.9116 (mttt) cc_final: 0.8457 (mttt) REVERT: A 940 ASP cc_start: 0.8641 (m-30) cc_final: 0.8327 (m-30) REVERT: A 959 TRP cc_start: 0.8280 (t60) cc_final: 0.8011 (t60) REVERT: A 987 MET cc_start: 0.9469 (mmp) cc_final: 0.9248 (mmm) REVERT: B 142 LYS cc_start: 0.9421 (mtmm) cc_final: 0.9113 (pttm) REVERT: B 220 HIS cc_start: 0.8818 (m90) cc_final: 0.7814 (p-80) REVERT: B 239 MET cc_start: 0.9318 (mtm) cc_final: 0.8212 (mmp) REVERT: B 242 ASP cc_start: 0.9307 (m-30) cc_final: 0.8893 (m-30) REVERT: B 253 PHE cc_start: 0.7715 (m-80) cc_final: 0.6943 (m-10) REVERT: B 403 GLU cc_start: 0.8888 (tt0) cc_final: 0.8235 (tp30) REVERT: B 411 ILE cc_start: 0.8664 (mt) cc_final: 0.8370 (mt) REVERT: B 517 PHE cc_start: 0.7656 (p90) cc_final: 0.7114 (p90) REVERT: B 527 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8602 (tt0) REVERT: B 631 PHE cc_start: 0.8439 (m-10) cc_final: 0.8220 (m-80) REVERT: B 654 GLU cc_start: 0.9279 (tm-30) cc_final: 0.9040 (tm-30) REVERT: B 669 CYS cc_start: 0.8586 (m) cc_final: 0.8178 (m) REVERT: B 802 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8314 (mt-10) REVERT: B 831 LYS cc_start: 0.9305 (mttt) cc_final: 0.8766 (mttt) REVERT: B 940 ASP cc_start: 0.8712 (m-30) cc_final: 0.8363 (m-30) REVERT: B 1008 MET cc_start: 0.8383 (mmm) cc_final: 0.7827 (mmp) REVERT: C 220 HIS cc_start: 0.8825 (m90) cc_final: 0.7799 (p-80) REVERT: C 232 LYS cc_start: 0.8355 (pttt) cc_final: 0.7751 (ptpp) REVERT: C 242 ASP cc_start: 0.9267 (m-30) cc_final: 0.9014 (m-30) REVERT: C 253 PHE cc_start: 0.8029 (m-80) cc_final: 0.6795 (m-80) REVERT: C 350 THR cc_start: 0.8615 (t) cc_final: 0.8246 (t) REVERT: C 379 LYS cc_start: 0.9153 (tttt) cc_final: 0.8652 (tptp) REVERT: C 403 GLU cc_start: 0.9032 (tt0) cc_final: 0.8331 (tp30) REVERT: C 517 PHE cc_start: 0.7628 (p90) cc_final: 0.7064 (p90) REVERT: C 575 PHE cc_start: 0.8497 (m-80) cc_final: 0.8175 (m-80) REVERT: C 730 CYS cc_start: 0.8974 (m) cc_final: 0.8654 (m) REVERT: C 738 SER cc_start: 0.9343 (p) cc_final: 0.9127 (p) REVERT: C 762 CYS cc_start: 0.9122 (m) cc_final: 0.8851 (p) REVERT: C 785 GLU cc_start: 0.8513 (tt0) cc_final: 0.8095 (tm-30) REVERT: C 789 ASP cc_start: 0.8321 (m-30) cc_final: 0.7893 (m-30) REVERT: C 802 GLU cc_start: 0.8686 (mt-10) cc_final: 0.7757 (mt-10) REVERT: C 831 LYS cc_start: 0.9162 (mttt) cc_final: 0.8531 (mttt) REVERT: C 940 ASP cc_start: 0.8748 (m-30) cc_final: 0.8175 (t70) REVERT: C 1006 SER cc_start: 0.9037 (t) cc_final: 0.8731 (m) REVERT: C 1008 MET cc_start: 0.8213 (mmm) cc_final: 0.7821 (mmm) REVERT: D 239 MET cc_start: 0.9385 (mtm) cc_final: 0.8295 (mmp) REVERT: D 242 ASP cc_start: 0.9324 (m-30) cc_final: 0.8840 (m-30) REVERT: D 253 PHE cc_start: 0.7875 (m-10) cc_final: 0.7316 (m-10) REVERT: D 358 LEU cc_start: 0.9191 (tp) cc_final: 0.8975 (tt) REVERT: D 403 GLU cc_start: 0.8907 (tt0) cc_final: 0.8223 (tp30) REVERT: D 409 CYS cc_start: 0.9115 (m) cc_final: 0.8669 (t) REVERT: D 417 ILE cc_start: 0.9576 (mt) cc_final: 0.9327 (tp) REVERT: D 527 GLU cc_start: 0.9106 (mt-10) cc_final: 0.8787 (tt0) REVERT: D 532 MET cc_start: 0.8586 (tpp) cc_final: 0.8384 (tpp) REVERT: D 576 VAL cc_start: 0.9584 (t) cc_final: 0.9313 (t) REVERT: D 762 CYS cc_start: 0.9148 (m) cc_final: 0.8602 (p) REVERT: D 789 ASP cc_start: 0.8086 (m-30) cc_final: 0.7622 (m-30) REVERT: D 802 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8013 (mt-10) REVERT: D 831 LYS cc_start: 0.9226 (mttt) cc_final: 0.8612 (mttt) REVERT: D 940 ASP cc_start: 0.8749 (m-30) cc_final: 0.8384 (m-30) REVERT: D 989 PHE cc_start: 0.9028 (m-80) cc_final: 0.8726 (m-80) REVERT: D 1006 SER cc_start: 0.9037 (t) cc_final: 0.8334 (m) REVERT: D 1008 MET cc_start: 0.8357 (mmm) cc_final: 0.7820 (mmp) REVERT: E 232 LYS cc_start: 0.8217 (pttt) cc_final: 0.7645 (ptpp) REVERT: E 238 LYS cc_start: 0.8659 (ttpt) cc_final: 0.8067 (mmmt) REVERT: E 239 MET cc_start: 0.9269 (mtm) cc_final: 0.8177 (mmp) REVERT: E 242 ASP cc_start: 0.9327 (m-30) cc_final: 0.9063 (m-30) REVERT: E 253 PHE cc_start: 0.7732 (m-80) cc_final: 0.6110 (m-10) REVERT: E 298 LEU cc_start: 0.8645 (tp) cc_final: 0.8435 (tp) REVERT: E 350 THR cc_start: 0.8722 (t) cc_final: 0.8419 (t) REVERT: E 403 GLU cc_start: 0.8865 (tt0) cc_final: 0.8121 (tp30) REVERT: E 408 MET cc_start: 0.8920 (mmm) cc_final: 0.7463 (mmm) REVERT: E 415 CYS cc_start: 0.9386 (t) cc_final: 0.9180 (t) REVERT: E 517 PHE cc_start: 0.7891 (p90) cc_final: 0.7329 (p90) REVERT: E 527 GLU cc_start: 0.9081 (mt-10) cc_final: 0.8667 (tt0) REVERT: E 532 MET cc_start: 0.8617 (tpt) cc_final: 0.8395 (tpt) REVERT: E 557 ASP cc_start: 0.8212 (t0) cc_final: 0.7513 (t0) REVERT: E 576 VAL cc_start: 0.9638 (t) cc_final: 0.9412 (t) REVERT: E 661 MET cc_start: 0.9271 (tpt) cc_final: 0.8844 (tpt) REVERT: E 738 SER cc_start: 0.9358 (p) cc_final: 0.8941 (m) REVERT: E 802 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8154 (mt-10) REVERT: E 807 ASP cc_start: 0.8930 (m-30) cc_final: 0.8674 (t70) REVERT: E 831 LYS cc_start: 0.9160 (mttt) cc_final: 0.8392 (mttt) REVERT: E 940 ASP cc_start: 0.8722 (m-30) cc_final: 0.8161 (t70) REVERT: E 989 PHE cc_start: 0.9018 (m-10) cc_final: 0.8364 (m-80) REVERT: E 1008 MET cc_start: 0.8418 (mmm) cc_final: 0.7864 (mmp) REVERT: F 142 LYS cc_start: 0.9452 (mtmm) cc_final: 0.9166 (pttm) REVERT: F 220 HIS cc_start: 0.8779 (m90) cc_final: 0.7914 (p-80) REVERT: F 239 MET cc_start: 0.9188 (mtm) cc_final: 0.8055 (mmp) REVERT: F 240 MET cc_start: 0.8576 (mtm) cc_final: 0.8245 (mmt) REVERT: F 242 ASP cc_start: 0.9310 (m-30) cc_final: 0.8924 (m-30) REVERT: F 253 PHE cc_start: 0.8217 (m-80) cc_final: 0.7455 (m-10) REVERT: F 415 CYS cc_start: 0.9538 (t) cc_final: 0.9201 (p) REVERT: F 417 ILE cc_start: 0.9580 (mt) cc_final: 0.9300 (tp) REVERT: F 517 PHE cc_start: 0.7746 (p90) cc_final: 0.7135 (p90) REVERT: F 527 GLU cc_start: 0.8957 (mt-10) cc_final: 0.8625 (mp0) REVERT: F 636 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8055 (mm-30) REVERT: F 654 GLU cc_start: 0.9199 (tm-30) cc_final: 0.8901 (tm-30) REVERT: F 751 ASN cc_start: 0.8922 (m-40) cc_final: 0.8719 (m110) REVERT: F 762 CYS cc_start: 0.9019 (m) cc_final: 0.8632 (m) REVERT: F 802 GLU cc_start: 0.8723 (mt-10) cc_final: 0.7905 (mt-10) REVERT: F 807 ASP cc_start: 0.8942 (m-30) cc_final: 0.8626 (t0) REVERT: F 831 LYS cc_start: 0.9178 (mttt) cc_final: 0.8361 (mttt) REVERT: F 940 ASP cc_start: 0.8800 (m-30) cc_final: 0.8284 (t70) REVERT: F 989 PHE cc_start: 0.9079 (m-10) cc_final: 0.8484 (m-80) REVERT: F 1021 LEU cc_start: 0.8759 (mt) cc_final: 0.8521 (mt) REVERT: F 1024 GLU cc_start: 0.9325 (tt0) cc_final: 0.8997 (tm-30) outliers start: 0 outliers final: 0 residues processed: 808 average time/residue: 0.4809 time to fit residues: 658.3540 Evaluate side-chains 603 residues out of total 4452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 603 time to evaluate : 4.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 289 optimal weight: 4.9990 chunk 187 optimal weight: 3.9990 chunk 279 optimal weight: 0.8980 chunk 141 optimal weight: 6.9990 chunk 92 optimal weight: 0.8980 chunk 90 optimal weight: 20.0000 chunk 297 optimal weight: 0.6980 chunk 319 optimal weight: 2.9990 chunk 231 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 368 optimal weight: 0.7980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 HIS ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 808 ASN A 922 ASN ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 865 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 922 ASN C 766 GLN ** C 865 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 808 ASN ** D 865 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 808 ASN E 922 ASN ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 522 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.6799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 40266 Z= 0.179 Angle : 0.608 14.711 54372 Z= 0.293 Chirality : 0.039 0.185 6156 Planarity : 0.003 0.032 6810 Dihedral : 10.662 179.707 5544 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.27 % Favored : 93.69 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.12), residues: 4848 helix: 0.30 (0.11), residues: 2208 sheet: -1.36 (0.22), residues: 588 loop : -0.80 (0.14), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 959 HIS 0.006 0.001 HIS A 916 PHE 0.020 0.002 PHE F 813 TYR 0.013 0.001 TYR F 565 ARG 0.006 0.000 ARG E 378 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 786 residues out of total 4452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 786 time to evaluate : 4.841 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: A 151 ILE cc_start: 0.8666 (mm) cc_final: 0.8189 (mt) REVERT: A 232 LYS cc_start: 0.8219 (pttt) cc_final: 0.7969 (ptpp) REVERT: A 239 MET cc_start: 0.9204 (mtm) cc_final: 0.8964 (mtp) REVERT: A 240 MET cc_start: 0.8807 (mtm) cc_final: 0.8517 (mmt) REVERT: A 242 ASP cc_start: 0.9245 (m-30) cc_final: 0.9022 (m-30) REVERT: A 253 PHE cc_start: 0.7466 (m-80) cc_final: 0.6856 (m-10) REVERT: A 291 VAL cc_start: 0.8658 (t) cc_final: 0.8220 (t) REVERT: A 343 GLU cc_start: 0.7567 (tp30) cc_final: 0.7227 (pt0) REVERT: A 403 GLU cc_start: 0.8817 (tt0) cc_final: 0.8162 (tp30) REVERT: A 517 PHE cc_start: 0.7864 (p90) cc_final: 0.7379 (p90) REVERT: A 527 GLU cc_start: 0.9044 (mt-10) cc_final: 0.8664 (mp0) REVERT: A 630 LEU cc_start: 0.9011 (mp) cc_final: 0.8648 (mp) REVERT: A 738 SER cc_start: 0.9430 (p) cc_final: 0.9042 (m) REVERT: A 802 GLU cc_start: 0.8800 (mt-10) cc_final: 0.8303 (mt-10) REVERT: A 831 LYS cc_start: 0.9110 (mttt) cc_final: 0.8539 (mttm) REVERT: A 922 ASN cc_start: 0.7888 (m-40) cc_final: 0.6595 (m-40) REVERT: A 959 TRP cc_start: 0.8300 (t60) cc_final: 0.8064 (t60) REVERT: B 151 ILE cc_start: 0.8795 (mm) cc_final: 0.8216 (mt) REVERT: B 220 HIS cc_start: 0.8867 (m90) cc_final: 0.7833 (p-80) REVERT: B 239 MET cc_start: 0.9317 (mtm) cc_final: 0.9086 (mtp) REVERT: B 242 ASP cc_start: 0.9306 (m-30) cc_final: 0.9014 (m-30) REVERT: B 253 PHE cc_start: 0.7643 (m-80) cc_final: 0.7140 (m-10) REVERT: B 255 TYR cc_start: 0.7930 (m-80) cc_final: 0.7430 (m-80) REVERT: B 327 ARG cc_start: 0.7714 (mmp80) cc_final: 0.7253 (mmm160) REVERT: B 403 GLU cc_start: 0.8882 (tt0) cc_final: 0.8247 (tp30) REVERT: B 411 ILE cc_start: 0.8657 (mt) cc_final: 0.8367 (mt) REVERT: B 517 PHE cc_start: 0.7639 (p90) cc_final: 0.7042 (p90) REVERT: B 527 GLU cc_start: 0.8961 (mt-10) cc_final: 0.8603 (tt0) REVERT: B 576 VAL cc_start: 0.9671 (t) cc_final: 0.9463 (t) REVERT: B 654 GLU cc_start: 0.9267 (tm-30) cc_final: 0.9027 (tm-30) REVERT: B 669 CYS cc_start: 0.8567 (m) cc_final: 0.8143 (m) REVERT: B 802 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8359 (mt-10) REVERT: B 831 LYS cc_start: 0.9294 (mttt) cc_final: 0.8887 (mttt) REVERT: B 922 ASN cc_start: 0.7891 (m-40) cc_final: 0.6856 (m-40) REVERT: B 940 ASP cc_start: 0.8704 (m-30) cc_final: 0.8379 (m-30) REVERT: B 989 PHE cc_start: 0.9154 (m-10) cc_final: 0.8788 (m-80) REVERT: B 1008 MET cc_start: 0.8460 (mmm) cc_final: 0.7919 (mmp) REVERT: C 220 HIS cc_start: 0.8834 (m90) cc_final: 0.8547 (m90) REVERT: C 232 LYS cc_start: 0.8334 (pttt) cc_final: 0.7742 (ptpp) REVERT: C 239 MET cc_start: 0.9232 (mtp) cc_final: 0.8237 (mmp) REVERT: C 242 ASP cc_start: 0.9278 (m-30) cc_final: 0.8912 (m-30) REVERT: C 253 PHE cc_start: 0.7955 (m-80) cc_final: 0.6731 (m-80) REVERT: C 403 GLU cc_start: 0.9030 (tt0) cc_final: 0.8260 (tp30) REVERT: C 409 CYS cc_start: 0.9180 (m) cc_final: 0.8198 (t) REVERT: C 415 CYS cc_start: 0.9317 (m) cc_final: 0.8745 (m) REVERT: C 517 PHE cc_start: 0.7631 (p90) cc_final: 0.7055 (p90) REVERT: C 575 PHE cc_start: 0.8408 (m-80) cc_final: 0.8104 (m-80) REVERT: C 730 CYS cc_start: 0.8963 (m) cc_final: 0.8629 (m) REVERT: C 738 SER cc_start: 0.9324 (p) cc_final: 0.9118 (p) REVERT: C 802 GLU cc_start: 0.8695 (mt-10) cc_final: 0.7745 (mt-10) REVERT: C 831 LYS cc_start: 0.9163 (mttt) cc_final: 0.8605 (mttt) REVERT: C 940 ASP cc_start: 0.8736 (m-30) cc_final: 0.8182 (t70) REVERT: C 964 LEU cc_start: 0.9407 (tp) cc_final: 0.9180 (tp) REVERT: C 1006 SER cc_start: 0.9015 (t) cc_final: 0.8622 (m) REVERT: C 1008 MET cc_start: 0.8224 (mmm) cc_final: 0.7843 (mmm) REVERT: D 151 ILE cc_start: 0.8699 (mm) cc_final: 0.8238 (mt) REVERT: D 239 MET cc_start: 0.9372 (mtm) cc_final: 0.9081 (mtp) REVERT: D 242 ASP cc_start: 0.9332 (m-30) cc_final: 0.9014 (m-30) REVERT: D 253 PHE cc_start: 0.7876 (m-10) cc_final: 0.7271 (m-10) REVERT: D 358 LEU cc_start: 0.9181 (tp) cc_final: 0.8932 (tt) REVERT: D 403 GLU cc_start: 0.8924 (tt0) cc_final: 0.8049 (tp30) REVERT: D 417 ILE cc_start: 0.9552 (mt) cc_final: 0.9311 (tp) REVERT: D 507 LEU cc_start: 0.8589 (tt) cc_final: 0.7826 (tt) REVERT: D 508 PHE cc_start: 0.7780 (m-10) cc_final: 0.7242 (m-80) REVERT: D 526 GLN cc_start: 0.9359 (tt0) cc_final: 0.8918 (tt0) REVERT: D 527 GLU cc_start: 0.9087 (mt-10) cc_final: 0.8694 (tt0) REVERT: D 664 MET cc_start: 0.8741 (mmt) cc_final: 0.8399 (tpp) REVERT: D 738 SER cc_start: 0.9434 (p) cc_final: 0.9001 (m) REVERT: D 762 CYS cc_start: 0.9131 (m) cc_final: 0.8635 (p) REVERT: D 789 ASP cc_start: 0.8087 (m-30) cc_final: 0.7652 (m-30) REVERT: D 802 GLU cc_start: 0.8781 (mt-10) cc_final: 0.7983 (mt-10) REVERT: D 831 LYS cc_start: 0.9208 (mttt) cc_final: 0.8516 (mttt) REVERT: D 940 ASP cc_start: 0.8714 (m-30) cc_final: 0.8356 (m-30) REVERT: D 989 PHE cc_start: 0.8986 (m-80) cc_final: 0.8758 (m-80) REVERT: D 1006 SER cc_start: 0.8946 (t) cc_final: 0.8316 (m) REVERT: D 1008 MET cc_start: 0.8371 (mmm) cc_final: 0.7850 (mmp) REVERT: E 232 LYS cc_start: 0.8307 (pttt) cc_final: 0.7603 (ptpp) REVERT: E 238 LYS cc_start: 0.8641 (ttpt) cc_final: 0.8249 (mmmt) REVERT: E 239 MET cc_start: 0.9238 (mtm) cc_final: 0.8125 (mmp) REVERT: E 242 ASP cc_start: 0.9325 (m-30) cc_final: 0.9114 (m-30) REVERT: E 253 PHE cc_start: 0.7780 (m-80) cc_final: 0.6131 (m-10) REVERT: E 350 THR cc_start: 0.8690 (t) cc_final: 0.8400 (t) REVERT: E 403 GLU cc_start: 0.8823 (tt0) cc_final: 0.8031 (tp30) REVERT: E 409 CYS cc_start: 0.9120 (m) cc_final: 0.8847 (m) REVERT: E 517 PHE cc_start: 0.7907 (p90) cc_final: 0.7332 (p90) REVERT: E 527 GLU cc_start: 0.9056 (mt-10) cc_final: 0.8635 (tt0) REVERT: E 532 MET cc_start: 0.8608 (tpt) cc_final: 0.8388 (tpt) REVERT: E 557 ASP cc_start: 0.8141 (t0) cc_final: 0.7447 (t0) REVERT: E 630 LEU cc_start: 0.9116 (mp) cc_final: 0.8738 (mp) REVERT: E 645 ARG cc_start: 0.8891 (mtt-85) cc_final: 0.8452 (ttm110) REVERT: E 661 MET cc_start: 0.9269 (tpt) cc_final: 0.8978 (tpt) REVERT: E 664 MET cc_start: 0.8888 (tpp) cc_final: 0.8471 (tpp) REVERT: E 738 SER cc_start: 0.9348 (p) cc_final: 0.8954 (m) REVERT: E 758 MET cc_start: 0.8414 (ttm) cc_final: 0.8204 (ttt) REVERT: E 802 GLU cc_start: 0.8865 (mt-10) cc_final: 0.8380 (mt-10) REVERT: E 807 ASP cc_start: 0.8903 (m-30) cc_final: 0.8498 (t70) REVERT: E 831 LYS cc_start: 0.9155 (mttt) cc_final: 0.8542 (mttm) REVERT: E 940 ASP cc_start: 0.8733 (m-30) cc_final: 0.8078 (t70) REVERT: E 989 PHE cc_start: 0.8991 (m-10) cc_final: 0.8381 (m-80) REVERT: E 1008 MET cc_start: 0.8439 (mmm) cc_final: 0.7921 (mmp) REVERT: F 142 LYS cc_start: 0.9437 (mtmm) cc_final: 0.9171 (pttm) REVERT: F 151 ILE cc_start: 0.8689 (mm) cc_final: 0.8349 (mt) REVERT: F 220 HIS cc_start: 0.8731 (m90) cc_final: 0.7854 (p-80) REVERT: F 239 MET cc_start: 0.9180 (mtm) cc_final: 0.8048 (mmp) REVERT: F 240 MET cc_start: 0.8563 (mtm) cc_final: 0.8233 (mmt) REVERT: F 242 ASP cc_start: 0.9309 (m-30) cc_final: 0.8911 (m-30) REVERT: F 253 PHE cc_start: 0.8162 (m-80) cc_final: 0.7073 (m-80) REVERT: F 255 TYR cc_start: 0.7854 (m-80) cc_final: 0.7511 (m-80) REVERT: F 403 GLU cc_start: 0.8922 (tt0) cc_final: 0.8525 (pm20) REVERT: F 415 CYS cc_start: 0.9467 (t) cc_final: 0.9232 (p) REVERT: F 417 ILE cc_start: 0.9579 (mt) cc_final: 0.9296 (tp) REVERT: F 517 PHE cc_start: 0.7750 (p90) cc_final: 0.7116 (p90) REVERT: F 527 GLU cc_start: 0.8975 (mt-10) cc_final: 0.8629 (mp0) REVERT: F 636 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8009 (mm-30) REVERT: F 654 GLU cc_start: 0.9180 (tm-30) cc_final: 0.8876 (tm-30) REVERT: F 738 SER cc_start: 0.9380 (p) cc_final: 0.9068 (m) REVERT: F 762 CYS cc_start: 0.8977 (m) cc_final: 0.8707 (m) REVERT: F 802 GLU cc_start: 0.8778 (mt-10) cc_final: 0.7970 (mt-10) REVERT: F 807 ASP cc_start: 0.8922 (m-30) cc_final: 0.8552 (t0) REVERT: F 831 LYS cc_start: 0.9163 (mttt) cc_final: 0.8355 (mttt) REVERT: F 940 ASP cc_start: 0.8791 (m-30) cc_final: 0.8232 (t70) REVERT: F 989 PHE cc_start: 0.9050 (m-10) cc_final: 0.8510 (m-80) REVERT: F 1021 LEU cc_start: 0.8754 (mt) cc_final: 0.8541 (mt) REVERT: F 1024 GLU cc_start: 0.9333 (tt0) cc_final: 0.8991 (tm-30) outliers start: 0 outliers final: 0 residues processed: 786 average time/residue: 0.4730 time to fit residues: 633.4204 Evaluate side-chains 610 residues out of total 4452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 610 time to evaluate : 4.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 426 optimal weight: 10.0000 chunk 448 optimal weight: 1.9990 chunk 409 optimal weight: 9.9990 chunk 436 optimal weight: 10.0000 chunk 262 optimal weight: 2.9990 chunk 190 optimal weight: 10.0000 chunk 342 optimal weight: 0.0010 chunk 133 optimal weight: 8.9990 chunk 394 optimal weight: 0.8980 chunk 412 optimal weight: 0.5980 chunk 434 optimal weight: 1.9990 overall best weight: 1.0990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 HIS ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 391 GLN C 922 ASN D 391 GLN ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 922 ASN E 367 HIS ** E 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 922 ASN ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.6972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 40266 Z= 0.169 Angle : 0.617 14.740 54372 Z= 0.294 Chirality : 0.039 0.152 6156 Planarity : 0.003 0.038 6810 Dihedral : 10.591 177.973 5544 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.58 % Favored : 93.38 % Rotamer: Outliers : 0.04 % Allowed : 0.31 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.12), residues: 4848 helix: 0.38 (0.11), residues: 2166 sheet: -1.31 (0.22), residues: 582 loop : -0.83 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 959 HIS 0.006 0.001 HIS A 314 PHE 0.018 0.002 PHE E 813 TYR 0.012 0.001 TYR A 443 ARG 0.007 0.000 ARG E 675 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 789 residues out of total 4452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 787 time to evaluate : 4.865 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ILE cc_start: 0.8639 (mm) cc_final: 0.8171 (mt) REVERT: A 232 LYS cc_start: 0.8199 (pttt) cc_final: 0.7907 (ptpp) REVERT: A 239 MET cc_start: 0.9211 (mtm) cc_final: 0.8967 (mtp) REVERT: A 240 MET cc_start: 0.8792 (mtm) cc_final: 0.8517 (mmt) REVERT: A 242 ASP cc_start: 0.9239 (m-30) cc_final: 0.9011 (m-30) REVERT: A 253 PHE cc_start: 0.7435 (m-80) cc_final: 0.6805 (m-10) REVERT: A 291 VAL cc_start: 0.8647 (t) cc_final: 0.8217 (t) REVERT: A 403 GLU cc_start: 0.8805 (tt0) cc_final: 0.8203 (tp30) REVERT: A 517 PHE cc_start: 0.7902 (p90) cc_final: 0.7414 (p90) REVERT: A 527 GLU cc_start: 0.9028 (mt-10) cc_final: 0.8659 (mp0) REVERT: A 630 LEU cc_start: 0.8981 (mp) cc_final: 0.8626 (mp) REVERT: A 738 SER cc_start: 0.9430 (p) cc_final: 0.9048 (m) REVERT: A 758 MET cc_start: 0.8850 (tpp) cc_final: 0.8564 (ttm) REVERT: A 802 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8079 (mt-10) REVERT: A 831 LYS cc_start: 0.9151 (mttt) cc_final: 0.8389 (mttt) REVERT: A 922 ASN cc_start: 0.7693 (m-40) cc_final: 0.6564 (m-40) REVERT: A 959 TRP cc_start: 0.8310 (t60) cc_final: 0.8082 (t60) REVERT: A 989 PHE cc_start: 0.9095 (m-80) cc_final: 0.8478 (m-80) REVERT: A 1008 MET cc_start: 0.8310 (mmm) cc_final: 0.7846 (mmm) REVERT: B 151 ILE cc_start: 0.8762 (mm) cc_final: 0.8192 (mt) REVERT: B 239 MET cc_start: 0.9312 (mtm) cc_final: 0.9068 (mtp) REVERT: B 242 ASP cc_start: 0.9296 (m-30) cc_final: 0.8989 (m-30) REVERT: B 253 PHE cc_start: 0.7518 (m-80) cc_final: 0.7175 (m-10) REVERT: B 255 TYR cc_start: 0.7992 (m-80) cc_final: 0.7504 (m-80) REVERT: B 327 ARG cc_start: 0.7625 (mmp80) cc_final: 0.7173 (mmm160) REVERT: B 403 GLU cc_start: 0.8888 (tt0) cc_final: 0.8263 (tp30) REVERT: B 411 ILE cc_start: 0.8641 (mt) cc_final: 0.8370 (mt) REVERT: B 494 LEU cc_start: 0.8495 (mt) cc_final: 0.8260 (mp) REVERT: B 517 PHE cc_start: 0.7691 (p90) cc_final: 0.7052 (p90) REVERT: B 654 GLU cc_start: 0.9251 (tm-30) cc_final: 0.9006 (tm-30) REVERT: B 738 SER cc_start: 0.9523 (p) cc_final: 0.9111 (m) REVERT: B 802 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8232 (mt-10) REVERT: B 831 LYS cc_start: 0.9310 (mttt) cc_final: 0.8694 (mttt) REVERT: B 922 ASN cc_start: 0.7825 (m-40) cc_final: 0.6936 (m-40) REVERT: B 940 ASP cc_start: 0.8720 (m-30) cc_final: 0.8400 (m-30) REVERT: B 989 PHE cc_start: 0.9114 (m-10) cc_final: 0.8830 (m-80) REVERT: B 1008 MET cc_start: 0.8457 (mmm) cc_final: 0.8234 (mmp) REVERT: C 151 ILE cc_start: 0.8821 (mm) cc_final: 0.8398 (mt) REVERT: C 220 HIS cc_start: 0.8846 (m90) cc_final: 0.8568 (m90) REVERT: C 239 MET cc_start: 0.9276 (mtp) cc_final: 0.8278 (mmp) REVERT: C 240 MET cc_start: 0.8729 (mmt) cc_final: 0.8133 (mmt) REVERT: C 242 ASP cc_start: 0.9277 (m-30) cc_final: 0.8904 (m-30) REVERT: C 253 PHE cc_start: 0.7811 (m-80) cc_final: 0.6495 (m-80) REVERT: C 403 GLU cc_start: 0.9042 (tt0) cc_final: 0.8304 (tp30) REVERT: C 409 CYS cc_start: 0.9187 (m) cc_final: 0.8258 (t) REVERT: C 415 CYS cc_start: 0.9310 (m) cc_final: 0.8700 (m) REVERT: C 517 PHE cc_start: 0.7608 (p90) cc_final: 0.6682 (p90) REVERT: C 575 PHE cc_start: 0.8362 (m-80) cc_final: 0.8075 (m-80) REVERT: C 730 CYS cc_start: 0.8937 (m) cc_final: 0.8606 (m) REVERT: C 738 SER cc_start: 0.9332 (p) cc_final: 0.9126 (p) REVERT: C 802 GLU cc_start: 0.8688 (mt-10) cc_final: 0.7660 (mt-10) REVERT: C 831 LYS cc_start: 0.9193 (mttt) cc_final: 0.8537 (mttt) REVERT: C 922 ASN cc_start: 0.7938 (OUTLIER) cc_final: 0.7194 (m-40) REVERT: C 940 ASP cc_start: 0.8702 (m-30) cc_final: 0.8103 (t0) REVERT: C 1006 SER cc_start: 0.8957 (t) cc_final: 0.8516 (m) REVERT: C 1008 MET cc_start: 0.8213 (mmm) cc_final: 0.7827 (mmm) REVERT: D 151 ILE cc_start: 0.8658 (mm) cc_final: 0.8202 (mt) REVERT: D 239 MET cc_start: 0.9374 (mtm) cc_final: 0.9084 (mtp) REVERT: D 242 ASP cc_start: 0.9340 (m-30) cc_final: 0.9025 (m-30) REVERT: D 253 PHE cc_start: 0.7846 (m-10) cc_final: 0.7198 (m-10) REVERT: D 358 LEU cc_start: 0.9162 (tp) cc_final: 0.8846 (tt) REVERT: D 403 GLU cc_start: 0.8940 (tt0) cc_final: 0.8086 (tp30) REVERT: D 417 ILE cc_start: 0.9545 (mt) cc_final: 0.9327 (tp) REVERT: D 507 LEU cc_start: 0.8605 (tt) cc_final: 0.7573 (tt) REVERT: D 508 PHE cc_start: 0.7758 (m-10) cc_final: 0.7259 (m-80) REVERT: D 527 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8688 (mp0) REVERT: D 576 VAL cc_start: 0.9565 (t) cc_final: 0.9347 (t) REVERT: D 664 MET cc_start: 0.8752 (mmt) cc_final: 0.8449 (tpp) REVERT: D 738 SER cc_start: 0.9449 (p) cc_final: 0.9002 (m) REVERT: D 762 CYS cc_start: 0.9133 (m) cc_final: 0.8622 (p) REVERT: D 789 ASP cc_start: 0.8095 (m-30) cc_final: 0.7583 (m-30) REVERT: D 802 GLU cc_start: 0.8816 (mt-10) cc_final: 0.7979 (mt-10) REVERT: D 831 LYS cc_start: 0.9224 (mttt) cc_final: 0.8510 (mttt) REVERT: D 922 ASN cc_start: 0.7963 (OUTLIER) cc_final: 0.7000 (m-40) REVERT: D 989 PHE cc_start: 0.9027 (m-80) cc_final: 0.8801 (m-80) REVERT: E 232 LYS cc_start: 0.8328 (pttt) cc_final: 0.7661 (ptpp) REVERT: E 238 LYS cc_start: 0.8665 (ttpt) cc_final: 0.8265 (mmmt) REVERT: E 239 MET cc_start: 0.9256 (mtm) cc_final: 0.8166 (mmp) REVERT: E 242 ASP cc_start: 0.9340 (m-30) cc_final: 0.9125 (m-30) REVERT: E 253 PHE cc_start: 0.7831 (m-80) cc_final: 0.6906 (m-10) REVERT: E 350 THR cc_start: 0.8615 (t) cc_final: 0.8314 (t) REVERT: E 403 GLU cc_start: 0.8772 (tt0) cc_final: 0.7959 (tp30) REVERT: E 409 CYS cc_start: 0.9062 (m) cc_final: 0.8792 (m) REVERT: E 517 PHE cc_start: 0.7879 (p90) cc_final: 0.7126 (p90) REVERT: E 527 GLU cc_start: 0.9037 (mt-10) cc_final: 0.8645 (tt0) REVERT: E 557 ASP cc_start: 0.8127 (t0) cc_final: 0.7431 (t0) REVERT: E 630 LEU cc_start: 0.9093 (mp) cc_final: 0.8732 (mp) REVERT: E 645 ARG cc_start: 0.8878 (mtt-85) cc_final: 0.8421 (ttm110) REVERT: E 661 MET cc_start: 0.9253 (tpt) cc_final: 0.8952 (tpt) REVERT: E 738 SER cc_start: 0.9353 (p) cc_final: 0.8971 (m) REVERT: E 802 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8339 (mt-10) REVERT: E 807 ASP cc_start: 0.8905 (m-30) cc_final: 0.8661 (t0) REVERT: E 831 LYS cc_start: 0.9178 (mttt) cc_final: 0.8549 (mttm) REVERT: E 940 ASP cc_start: 0.8739 (m-30) cc_final: 0.8117 (t70) REVERT: E 989 PHE cc_start: 0.8950 (m-10) cc_final: 0.8524 (m-80) REVERT: E 1008 MET cc_start: 0.8423 (mmm) cc_final: 0.7983 (mmm) REVERT: F 151 ILE cc_start: 0.8673 (mm) cc_final: 0.8356 (mt) REVERT: F 239 MET cc_start: 0.9176 (mtm) cc_final: 0.8916 (mtp) REVERT: F 240 MET cc_start: 0.8557 (mtm) cc_final: 0.8293 (mmt) REVERT: F 242 ASP cc_start: 0.9279 (m-30) cc_final: 0.9002 (m-30) REVERT: F 253 PHE cc_start: 0.8162 (m-80) cc_final: 0.7354 (m-10) REVERT: F 358 LEU cc_start: 0.9270 (tp) cc_final: 0.8896 (tt) REVERT: F 403 GLU cc_start: 0.8904 (tt0) cc_final: 0.8134 (tp30) REVERT: F 415 CYS cc_start: 0.9459 (t) cc_final: 0.9228 (p) REVERT: F 417 ILE cc_start: 0.9579 (mt) cc_final: 0.9295 (tp) REVERT: F 517 PHE cc_start: 0.7762 (p90) cc_final: 0.7143 (p90) REVERT: F 527 GLU cc_start: 0.8983 (mt-10) cc_final: 0.8662 (mp0) REVERT: F 636 GLU cc_start: 0.8637 (mm-30) cc_final: 0.7992 (mm-30) REVERT: F 654 GLU cc_start: 0.9159 (tm-30) cc_final: 0.8836 (tm-30) REVERT: F 738 SER cc_start: 0.9367 (p) cc_final: 0.9069 (m) REVERT: F 762 CYS cc_start: 0.9077 (m) cc_final: 0.8715 (m) REVERT: F 802 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8016 (mt-10) REVERT: F 807 ASP cc_start: 0.8961 (m-30) cc_final: 0.8575 (t0) REVERT: F 831 LYS cc_start: 0.9177 (mttt) cc_final: 0.8372 (mttt) REVERT: F 940 ASP cc_start: 0.8828 (m-30) cc_final: 0.8260 (t70) REVERT: F 989 PHE cc_start: 0.9041 (m-10) cc_final: 0.8676 (m-80) REVERT: F 1021 LEU cc_start: 0.8752 (mt) cc_final: 0.8517 (mt) outliers start: 2 outliers final: 0 residues processed: 787 average time/residue: 0.5201 time to fit residues: 700.4223 Evaluate side-chains 613 residues out of total 4452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 611 time to evaluate : 4.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 286 optimal weight: 0.0670 chunk 461 optimal weight: 0.4980 chunk 281 optimal weight: 6.9990 chunk 218 optimal weight: 0.0770 chunk 320 optimal weight: 9.9990 chunk 484 optimal weight: 9.9990 chunk 445 optimal weight: 0.9980 chunk 385 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 297 optimal weight: 0.3980 chunk 236 optimal weight: 0.7980 overall best weight: 0.3676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 808 ASN ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 808 ASN C 522 HIS D 367 HIS ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 522 HIS ** E 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 922 ASN ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 522 HIS F 808 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.7084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 40266 Z= 0.151 Angle : 0.616 14.093 54372 Z= 0.291 Chirality : 0.039 0.226 6156 Planarity : 0.003 0.031 6810 Dihedral : 10.544 177.100 5544 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.42 % Favored : 93.52 % Rotamer: Outliers : 0.02 % Allowed : 0.20 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.12), residues: 4848 helix: 0.29 (0.11), residues: 2172 sheet: -1.20 (0.22), residues: 582 loop : -0.82 (0.14), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP E 959 HIS 0.009 0.001 HIS D 522 PHE 0.022 0.001 PHE D 406 TYR 0.010 0.001 TYR F 565 ARG 0.008 0.000 ARG C 605 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 782 residues out of total 4452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 781 time to evaluate : 4.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 151 ILE cc_start: 0.8633 (mm) cc_final: 0.8205 (mt) REVERT: A 232 LYS cc_start: 0.8075 (pttt) cc_final: 0.7460 (ptpp) REVERT: A 239 MET cc_start: 0.9198 (mtm) cc_final: 0.8978 (mtp) REVERT: A 240 MET cc_start: 0.8783 (mtm) cc_final: 0.8481 (mmt) REVERT: A 242 ASP cc_start: 0.9244 (m-30) cc_final: 0.9015 (m-30) REVERT: A 253 PHE cc_start: 0.7269 (m-80) cc_final: 0.6667 (m-10) REVERT: A 291 VAL cc_start: 0.8607 (t) cc_final: 0.8145 (t) REVERT: A 343 GLU cc_start: 0.7545 (tp30) cc_final: 0.7292 (tp30) REVERT: A 403 GLU cc_start: 0.8816 (tt0) cc_final: 0.8291 (tp30) REVERT: A 517 PHE cc_start: 0.7869 (p90) cc_final: 0.7405 (p90) REVERT: A 526 GLN cc_start: 0.9455 (tt0) cc_final: 0.9045 (tt0) REVERT: A 527 GLU cc_start: 0.8983 (mt-10) cc_final: 0.8643 (mp0) REVERT: A 630 LEU cc_start: 0.8949 (mp) cc_final: 0.8588 (mp) REVERT: A 654 GLU cc_start: 0.9114 (tm-30) cc_final: 0.8872 (tt0) REVERT: A 738 SER cc_start: 0.9425 (p) cc_final: 0.9064 (m) REVERT: A 802 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8336 (mt-10) REVERT: A 831 LYS cc_start: 0.9121 (mttt) cc_final: 0.8507 (mttm) REVERT: A 922 ASN cc_start: 0.7610 (m-40) cc_final: 0.6528 (m-40) REVERT: A 959 TRP cc_start: 0.8295 (t60) cc_final: 0.8092 (t60) REVERT: A 989 PHE cc_start: 0.9070 (m-80) cc_final: 0.8573 (m-80) REVERT: A 1008 MET cc_start: 0.8298 (mmm) cc_final: 0.7869 (mmm) REVERT: B 151 ILE cc_start: 0.8736 (mm) cc_final: 0.8213 (mt) REVERT: B 220 HIS cc_start: 0.8817 (m90) cc_final: 0.8570 (m90) REVERT: B 232 LYS cc_start: 0.8199 (pttt) cc_final: 0.7501 (ptpp) REVERT: B 239 MET cc_start: 0.9324 (mtm) cc_final: 0.9109 (mtp) REVERT: B 242 ASP cc_start: 0.9299 (m-30) cc_final: 0.8990 (m-30) REVERT: B 253 PHE cc_start: 0.7612 (m-80) cc_final: 0.7115 (m-10) REVERT: B 255 TYR cc_start: 0.7963 (m-80) cc_final: 0.7486 (m-80) REVERT: B 403 GLU cc_start: 0.8906 (tt0) cc_final: 0.8691 (pm20) REVERT: B 411 ILE cc_start: 0.8590 (mt) cc_final: 0.8275 (mt) REVERT: B 517 PHE cc_start: 0.7747 (p90) cc_final: 0.7153 (p90) REVERT: B 527 GLU cc_start: 0.8992 (mt-10) cc_final: 0.8746 (mp0) REVERT: B 654 GLU cc_start: 0.9206 (tm-30) cc_final: 0.8965 (tm-30) REVERT: B 738 SER cc_start: 0.9497 (p) cc_final: 0.9104 (m) REVERT: B 802 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8215 (mt-10) REVERT: B 831 LYS cc_start: 0.9285 (mttt) cc_final: 0.8667 (mttt) REVERT: B 922 ASN cc_start: 0.7756 (m-40) cc_final: 0.6909 (m-40) REVERT: B 940 ASP cc_start: 0.8716 (m-30) cc_final: 0.8382 (m-30) REVERT: B 989 PHE cc_start: 0.9086 (m-10) cc_final: 0.8741 (m-80) REVERT: B 1008 MET cc_start: 0.8421 (mmm) cc_final: 0.7742 (mmp) REVERT: C 220 HIS cc_start: 0.8845 (m90) cc_final: 0.8558 (m90) REVERT: C 232 LYS cc_start: 0.8280 (pttt) cc_final: 0.7754 (ptpp) REVERT: C 238 LYS cc_start: 0.8634 (ttpt) cc_final: 0.8326 (tttt) REVERT: C 239 MET cc_start: 0.9250 (mtp) cc_final: 0.8266 (mmp) REVERT: C 242 ASP cc_start: 0.9294 (m-30) cc_final: 0.8925 (m-30) REVERT: C 253 PHE cc_start: 0.7795 (m-80) cc_final: 0.6562 (m-80) REVERT: C 403 GLU cc_start: 0.9012 (tt0) cc_final: 0.8253 (tp30) REVERT: C 436 SER cc_start: 0.8735 (m) cc_final: 0.8094 (t) REVERT: C 517 PHE cc_start: 0.7465 (p90) cc_final: 0.6709 (p90) REVERT: C 575 PHE cc_start: 0.8351 (m-80) cc_final: 0.7956 (m-80) REVERT: C 730 CYS cc_start: 0.8903 (m) cc_final: 0.8580 (m) REVERT: C 738 SER cc_start: 0.9306 (p) cc_final: 0.8983 (m) REVERT: C 802 GLU cc_start: 0.8690 (mt-10) cc_final: 0.7749 (mt-10) REVERT: C 831 LYS cc_start: 0.9169 (mttt) cc_final: 0.8414 (mttt) REVERT: C 940 ASP cc_start: 0.8669 (m-30) cc_final: 0.8411 (m-30) REVERT: C 1006 SER cc_start: 0.8897 (t) cc_final: 0.8433 (m) REVERT: C 1008 MET cc_start: 0.8206 (mmm) cc_final: 0.7815 (mmm) REVERT: D 151 ILE cc_start: 0.8637 (mm) cc_final: 0.8206 (mt) REVERT: D 238 LYS cc_start: 0.8177 (tttt) cc_final: 0.7969 (mmmt) REVERT: D 239 MET cc_start: 0.9366 (mtm) cc_final: 0.8393 (mmp) REVERT: D 242 ASP cc_start: 0.9352 (m-30) cc_final: 0.9053 (m-30) REVERT: D 253 PHE cc_start: 0.7822 (m-10) cc_final: 0.7244 (m-10) REVERT: D 358 LEU cc_start: 0.9142 (tp) cc_final: 0.8852 (tt) REVERT: D 403 GLU cc_start: 0.8914 (tt0) cc_final: 0.8097 (tp30) REVERT: D 417 ILE cc_start: 0.9544 (mt) cc_final: 0.9309 (tp) REVERT: D 492 HIS cc_start: 0.7884 (m90) cc_final: 0.7633 (m-70) REVERT: D 507 LEU cc_start: 0.8367 (tt) cc_final: 0.7490 (tt) REVERT: D 508 PHE cc_start: 0.7848 (m-10) cc_final: 0.7490 (m-80) REVERT: D 524 THR cc_start: 0.9097 (p) cc_final: 0.8820 (p) REVERT: D 526 GLN cc_start: 0.9366 (tt0) cc_final: 0.8930 (tt0) REVERT: D 527 GLU cc_start: 0.8988 (mt-10) cc_final: 0.8705 (mp0) REVERT: D 576 VAL cc_start: 0.9558 (t) cc_final: 0.9347 (t) REVERT: D 664 MET cc_start: 0.8719 (mmt) cc_final: 0.8429 (tpp) REVERT: D 738 SER cc_start: 0.9439 (p) cc_final: 0.9003 (m) REVERT: D 802 GLU cc_start: 0.8801 (mt-10) cc_final: 0.7994 (mt-10) REVERT: D 831 LYS cc_start: 0.9214 (mttt) cc_final: 0.8441 (mttt) REVERT: E 232 LYS cc_start: 0.8180 (pttt) cc_final: 0.7571 (ptpp) REVERT: E 238 LYS cc_start: 0.8665 (ttpt) cc_final: 0.8287 (mmmt) REVERT: E 239 MET cc_start: 0.9281 (mtm) cc_final: 0.8214 (mmp) REVERT: E 242 ASP cc_start: 0.9336 (m-30) cc_final: 0.9116 (m-30) REVERT: E 253 PHE cc_start: 0.7807 (m-80) cc_final: 0.6956 (m-10) REVERT: E 403 GLU cc_start: 0.8761 (tt0) cc_final: 0.7926 (tp30) REVERT: E 415 CYS cc_start: 0.9352 (t) cc_final: 0.9006 (t) REVERT: E 527 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8636 (tt0) REVERT: E 557 ASP cc_start: 0.8089 (t0) cc_final: 0.7438 (t0) REVERT: E 630 LEU cc_start: 0.9053 (mp) cc_final: 0.8675 (mp) REVERT: E 645 ARG cc_start: 0.8898 (mtt-85) cc_final: 0.8448 (ttm110) REVERT: E 661 MET cc_start: 0.9237 (tpt) cc_final: 0.8927 (tpt) REVERT: E 664 MET cc_start: 0.8889 (tpp) cc_final: 0.8485 (tpp) REVERT: E 738 SER cc_start: 0.9347 (p) cc_final: 0.8952 (m) REVERT: E 790 ILE cc_start: 0.8749 (mm) cc_final: 0.8371 (mm) REVERT: E 940 ASP cc_start: 0.8727 (m-30) cc_final: 0.8109 (t0) REVERT: E 1008 MET cc_start: 0.8375 (mmm) cc_final: 0.7984 (mmm) REVERT: F 151 ILE cc_start: 0.8638 (mm) cc_final: 0.8316 (mt) REVERT: F 220 HIS cc_start: 0.8777 (m90) cc_final: 0.7862 (p-80) REVERT: F 239 MET cc_start: 0.9129 (mtm) cc_final: 0.8877 (mtp) REVERT: F 240 MET cc_start: 0.8637 (mtm) cc_final: 0.8396 (mmt) REVERT: F 242 ASP cc_start: 0.9275 (m-30) cc_final: 0.8992 (m-30) REVERT: F 253 PHE cc_start: 0.8013 (m-80) cc_final: 0.7123 (m-80) REVERT: F 255 TYR cc_start: 0.7665 (m-80) cc_final: 0.7364 (m-80) REVERT: F 358 LEU cc_start: 0.9217 (tp) cc_final: 0.8879 (tt) REVERT: F 403 GLU cc_start: 0.8876 (tt0) cc_final: 0.8068 (tp30) REVERT: F 417 ILE cc_start: 0.9556 (mt) cc_final: 0.9277 (tp) REVERT: F 517 PHE cc_start: 0.7824 (p90) cc_final: 0.6986 (p90) REVERT: F 527 GLU cc_start: 0.8935 (mt-10) cc_final: 0.8639 (mp0) REVERT: F 636 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8258 (mm-30) REVERT: F 654 GLU cc_start: 0.9121 (tm-30) cc_final: 0.8804 (tm-30) REVERT: F 738 SER cc_start: 0.9360 (p) cc_final: 0.9077 (m) REVERT: F 762 CYS cc_start: 0.8991 (m) cc_final: 0.8665 (m) REVERT: F 802 GLU cc_start: 0.8798 (mt-10) cc_final: 0.8012 (mt-10) REVERT: F 807 ASP cc_start: 0.8949 (m-30) cc_final: 0.8704 (t0) REVERT: F 831 LYS cc_start: 0.9171 (mttt) cc_final: 0.8400 (mttt) REVERT: F 877 GLU cc_start: 0.8151 (pp20) cc_final: 0.7771 (tm-30) REVERT: F 940 ASP cc_start: 0.8805 (m-30) cc_final: 0.8237 (t70) REVERT: F 989 PHE cc_start: 0.8998 (m-10) cc_final: 0.8703 (m-80) outliers start: 1 outliers final: 0 residues processed: 781 average time/residue: 0.4372 time to fit residues: 581.3988 Evaluate side-chains 620 residues out of total 4452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 620 time to evaluate : 3.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 306 optimal weight: 0.1980 chunk 410 optimal weight: 20.0000 chunk 118 optimal weight: 1.9990 chunk 355 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 386 optimal weight: 0.0970 chunk 161 optimal weight: 6.9990 chunk 396 optimal weight: 6.9990 chunk 48 optimal weight: 0.8980 chunk 71 optimal weight: 9.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: