Starting phenix.real_space_refine on Thu Jul 25 07:30:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xuq_38680/07_2024/8xuq_38680.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xuq_38680/07_2024/8xuq_38680.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xuq_38680/07_2024/8xuq_38680.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xuq_38680/07_2024/8xuq_38680.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xuq_38680/07_2024/8xuq_38680.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xuq_38680/07_2024/8xuq_38680.cif" } resolution = 3.17 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= 0.002 sd= 0.021 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 32 5.49 5 S 128 5.16 5 C 18240 2.51 5 N 4968 2.21 5 O 5368 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 22": "OE1" <-> "OE2" Residue "A GLU 74": "OE1" <-> "OE2" Residue "A GLU 120": "OE1" <-> "OE2" Residue "A ASP 125": "OD1" <-> "OD2" Residue "A GLU 151": "OE1" <-> "OE2" Residue "A PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 172": "OE1" <-> "OE2" Residue "A TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 245": "OD1" <-> "OD2" Residue "A GLU 249": "OE1" <-> "OE2" Residue "A GLU 322": "OE1" <-> "OE2" Residue "A GLU 334": "OE1" <-> "OE2" Residue "A ASP 404": "OD1" <-> "OD2" Residue "A GLU 433": "OE1" <-> "OE2" Residue "A TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 450": "OD1" <-> "OD2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "A GLU 483": "OE1" <-> "OE2" Residue "A GLU 493": "OE1" <-> "OE2" Residue "A PHE 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 536": "OE1" <-> "OE2" Residue "A GLU 572": "OE1" <-> "OE2" Residue "A ASP 597": "OD1" <-> "OD2" Residue "A GLU 634": "OE1" <-> "OE2" Residue "A GLU 674": "OE1" <-> "OE2" Residue "A ASP 701": "OD1" <-> "OD2" Residue "A TYR 716": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 770": "OE1" <-> "OE2" Residue "E GLU 11": "OE1" <-> "OE2" Residue "E ASP 19": "OD1" <-> "OD2" Residue "E GLU 22": "OE1" <-> "OE2" Residue "E GLU 32": "OE1" <-> "OE2" Residue "E ASP 37": "OD1" <-> "OD2" Residue "E GLU 120": "OE1" <-> "OE2" Residue "E ASP 159": "OD1" <-> "OD2" Residue "E GLU 160": "OE1" <-> "OE2" Residue "E GLU 172": "OE1" <-> "OE2" Residue "E GLU 177": "OE1" <-> "OE2" Residue "E TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 222": "OE1" <-> "OE2" Residue "E PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 314": "OE1" <-> "OE2" Residue "E GLU 322": "OE1" <-> "OE2" Residue "E GLU 334": "OE1" <-> "OE2" Residue "E TYR 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 465": "OE1" <-> "OE2" Residue "E GLU 488": "OE1" <-> "OE2" Residue "E GLU 493": "OE1" <-> "OE2" Residue "E TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 512": "OE1" <-> "OE2" Residue "E PHE 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 536": "OE1" <-> "OE2" Residue "E GLU 572": "OE1" <-> "OE2" Residue "E TYR 584": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 634": "OE1" <-> "OE2" Residue "E TYR 716": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 770": "OE1" <-> "OE2" Residue "E ASP 811": "OD1" <-> "OD2" Residue "E PHE 840": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 177": "OE1" <-> "OE2" Residue "F ASP 245": "OD1" <-> "OD2" Residue "F GLU 252": "OE1" <-> "OE2" Residue "F GLU 274": "OE1" <-> "OE2" Residue "F GLU 314": "OE1" <-> "OE2" Residue "F ASP 315": "OD1" <-> "OD2" Residue "F GLU 322": "OE1" <-> "OE2" Residue "F TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 449": "OE1" <-> "OE2" Residue "F ASP 469": "OD1" <-> "OD2" Residue "F ASP 527": "OD1" <-> "OD2" Residue "F ASP 555": "OD1" <-> "OD2" Residue "F ASP 570": "OD1" <-> "OD2" Residue "F GLU 678": "OE1" <-> "OE2" Residue "F PHE 681": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 725": "OD1" <-> "OD2" Residue "F ASP 864": "OD1" <-> "OD2" Residue "F PHE 876": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 19": "OD1" <-> "OD2" Residue "G PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 245": "OD1" <-> "OD2" Residue "G PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 322": "OE1" <-> "OE2" Residue "G GLU 388": "OE1" <-> "OE2" Residue "G TYR 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 449": "OE1" <-> "OE2" Residue "G ASP 454": "OD1" <-> "OD2" Residue "G GLU 465": "OE1" <-> "OE2" Residue "G PHE 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 715": "OE1" <-> "OE2" Residue "G ASP 825": "OD1" <-> "OD2" Residue "G ASP 864": "OD1" <-> "OD2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 28736 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 885, 7121 Classifications: {'peptide': 885} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 37, 'TRANS': 847} Chain: "E" Number of atoms: 7121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 885, 7121 Classifications: {'peptide': 885} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 37, 'TRANS': 847} Chain: "F" Number of atoms: 7121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 885, 7121 Classifications: {'peptide': 885} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 37, 'TRANS': 847} Chain: "G" Number of atoms: 7121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 885, 7121 Classifications: {'peptide': 885} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 37, 'TRANS': 847} Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'ADP': 1, 'IHP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'ADP': 1, 'IHP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'ADP': 1, 'IHP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'ADP': 1, 'IHP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 15.61, per 1000 atoms: 0.54 Number of scatterers: 28736 At special positions: 0 Unit cell: (195.5, 198.9, 124.1, 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 128 16.00 P 32 15.00 O 5368 8.00 N 4968 7.00 C 18240 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.03 Conformation dependent library (CDL) restraints added in 4.8 seconds 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6776 Finding SS restraints... Secondary structure from input PDB file: 158 helices and 29 sheets defined 49.2% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.64 Creating SS restraints... Processing helix chain 'A' and resid 1 through 20 removed outlier: 4.364A pdb=" N ALA A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 51 Processing helix chain 'A' and resid 56 through 63 removed outlier: 3.530A pdb=" N ARG A 60 " --> pdb=" O ASN A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 91 Processing helix chain 'A' and resid 101 through 127 removed outlier: 3.818A pdb=" N ILE A 127 " --> pdb=" O GLN A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 135 removed outlier: 4.227A pdb=" N LEU A 132 " --> pdb=" O GLY A 128 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASP A 134 " --> pdb=" O GLN A 130 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP A 135 " --> pdb=" O ALA A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 169 Processing helix chain 'A' and resid 188 through 198 Processing helix chain 'A' and resid 199 through 206 removed outlier: 3.546A pdb=" N GLY A 203 " --> pdb=" O HIS A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 232 removed outlier: 4.002A pdb=" N PHE A 231 " --> pdb=" O ILE A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 240 removed outlier: 4.139A pdb=" N GLY A 240 " --> pdb=" O LYS A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 257 Processing helix chain 'A' and resid 269 through 277 removed outlier: 3.543A pdb=" N TRP A 273 " --> pdb=" O SER A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 280 No H-bonds generated for 'chain 'A' and resid 278 through 280' Processing helix chain 'A' and resid 295 through 303 removed outlier: 3.888A pdb=" N ALA A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 327 Processing helix chain 'A' and resid 332 through 334 No H-bonds generated for 'chain 'A' and resid 332 through 334' Processing helix chain 'A' and resid 335 through 346 Processing helix chain 'A' and resid 349 through 364 Processing helix chain 'A' and resid 366 through 380 removed outlier: 3.705A pdb=" N GLU A 379 " --> pdb=" O ASP A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 400 removed outlier: 3.571A pdb=" N LEU A 393 " --> pdb=" O ASN A 389 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ARG A 400 " --> pdb=" O MET A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 412 removed outlier: 3.676A pdb=" N ALA A 407 " --> pdb=" O TYR A 403 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N CYS A 408 " --> pdb=" O ASP A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 433 Processing helix chain 'A' and resid 443 through 458 Processing helix chain 'A' and resid 478 through 492 Processing helix chain 'A' and resid 509 through 514 Processing helix chain 'A' and resid 525 through 530 Processing helix chain 'A' and resid 557 through 563 Processing helix chain 'A' and resid 582 through 586 Processing helix chain 'A' and resid 603 through 609 Processing helix chain 'A' and resid 672 through 676 Processing helix chain 'A' and resid 677 through 682 Processing helix chain 'A' and resid 695 through 701 removed outlier: 4.513A pdb=" N LEU A 699 " --> pdb=" O LYS A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 712 Processing helix chain 'A' and resid 759 through 766 removed outlier: 3.725A pdb=" N LEU A 763 " --> pdb=" O ASP A 759 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU A 766 " --> pdb=" O ILE A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 837 removed outlier: 3.683A pdb=" N ILE A 837 " --> pdb=" O LEU A 834 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 869 Processing helix chain 'E' and resid 2 through 20 Processing helix chain 'E' and resid 22 through 26 removed outlier: 4.524A pdb=" N GLY E 26 " --> pdb=" O LEU E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 51 removed outlier: 3.734A pdb=" N CYS E 51 " --> pdb=" O GLN E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 55 Processing helix chain 'E' and resid 56 through 64 removed outlier: 3.596A pdb=" N ARG E 60 " --> pdb=" O ASN E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 91 Processing helix chain 'E' and resid 97 through 127 removed outlier: 3.538A pdb=" N LYS E 102 " --> pdb=" O LEU E 98 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ARG E 103 " --> pdb=" O PRO E 99 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE E 121 " --> pdb=" O LYS E 117 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG E 122 " --> pdb=" O VAL E 118 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN E 123 " --> pdb=" O ARG E 119 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N THR E 124 " --> pdb=" O GLU E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 133 Processing helix chain 'E' and resid 158 through 169 Processing helix chain 'E' and resid 188 through 198 Processing helix chain 'E' and resid 199 through 206 Processing helix chain 'E' and resid 219 through 232 removed outlier: 3.539A pdb=" N LEU E 223 " --> pdb=" O ARG E 219 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE E 231 " --> pdb=" O ILE E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 241 removed outlier: 3.548A pdb=" N MET E 241 " --> pdb=" O TYR E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 242 through 257 Processing helix chain 'E' and resid 269 through 277 removed outlier: 3.556A pdb=" N TRP E 273 " --> pdb=" O SER E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 280 No H-bonds generated for 'chain 'E' and resid 278 through 280' Processing helix chain 'E' and resid 295 through 303 removed outlier: 3.991A pdb=" N ALA E 299 " --> pdb=" O ASP E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 327 Processing helix chain 'E' and resid 332 through 334 No H-bonds generated for 'chain 'E' and resid 332 through 334' Processing helix chain 'E' and resid 335 through 347 removed outlier: 3.511A pdb=" N LYS E 347 " --> pdb=" O ALA E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 364 Processing helix chain 'E' and resid 366 through 381 Processing helix chain 'E' and resid 387 through 400 removed outlier: 4.235A pdb=" N ARG E 400 " --> pdb=" O MET E 396 " (cutoff:3.500A) Processing helix chain 'E' and resid 402 through 413 Processing helix chain 'E' and resid 423 through 434 Processing helix chain 'E' and resid 443 through 458 Processing helix chain 'E' and resid 478 through 492 Processing helix chain 'E' and resid 509 through 514 Processing helix chain 'E' and resid 525 through 530 Processing helix chain 'E' and resid 557 through 563 Processing helix chain 'E' and resid 580 through 585 removed outlier: 3.682A pdb=" N TYR E 584 " --> pdb=" O SER E 580 " (cutoff:3.500A) Processing helix chain 'E' and resid 603 through 609 Processing helix chain 'E' and resid 672 through 676 Processing helix chain 'E' and resid 677 through 683 Processing helix chain 'E' and resid 695 through 701 removed outlier: 4.254A pdb=" N LEU E 699 " --> pdb=" O LYS E 695 " (cutoff:3.500A) Processing helix chain 'E' and resid 706 through 711 Processing helix chain 'E' and resid 712 through 714 No H-bonds generated for 'chain 'E' and resid 712 through 714' Processing helix chain 'E' and resid 759 through 766 removed outlier: 3.743A pdb=" N LEU E 763 " --> pdb=" O ASP E 759 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU E 766 " --> pdb=" O ILE E 762 " (cutoff:3.500A) Processing helix chain 'E' and resid 831 through 836 Processing helix chain 'E' and resid 849 through 869 Processing helix chain 'F' and resid 2 through 20 Processing helix chain 'F' and resid 27 through 51 removed outlier: 3.595A pdb=" N CYS F 51 " --> pdb=" O GLN F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 64 removed outlier: 3.809A pdb=" N ARG F 60 " --> pdb=" O ASN F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 91 removed outlier: 3.524A pdb=" N VAL F 69 " --> pdb=" O LYS F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 125 Processing helix chain 'F' and resid 129 through 135 Processing helix chain 'F' and resid 158 through 169 Processing helix chain 'F' and resid 188 through 198 removed outlier: 3.655A pdb=" N LYS F 198 " --> pdb=" O ASN F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 206 Processing helix chain 'F' and resid 219 through 232 removed outlier: 3.843A pdb=" N PHE F 231 " --> pdb=" O ILE F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 257 removed outlier: 3.619A pdb=" N GLY F 257 " --> pdb=" O PHE F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 277 removed outlier: 3.983A pdb=" N TRP F 273 " --> pdb=" O SER F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 280 No H-bonds generated for 'chain 'F' and resid 278 through 280' Processing helix chain 'F' and resid 296 through 303 Processing helix chain 'F' and resid 313 through 327 Processing helix chain 'F' and resid 332 through 334 No H-bonds generated for 'chain 'F' and resid 332 through 334' Processing helix chain 'F' and resid 335 through 346 Processing helix chain 'F' and resid 349 through 364 Processing helix chain 'F' and resid 366 through 381 Processing helix chain 'F' and resid 387 through 400 removed outlier: 3.792A pdb=" N ASN F 391 " --> pdb=" O PRO F 387 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG F 400 " --> pdb=" O MET F 396 " (cutoff:3.500A) Processing helix chain 'F' and resid 402 through 410 Processing helix chain 'F' and resid 423 through 433 Processing helix chain 'F' and resid 443 through 459 Processing helix chain 'F' and resid 478 through 492 Processing helix chain 'F' and resid 509 through 515 removed outlier: 3.962A pdb=" N THR F 515 " --> pdb=" O ARG F 511 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 531 Processing helix chain 'F' and resid 552 through 556 removed outlier: 3.666A pdb=" N ILE F 556 " --> pdb=" O SER F 553 " (cutoff:3.500A) Processing helix chain 'F' and resid 557 through 563 Processing helix chain 'F' and resid 580 through 586 Processing helix chain 'F' and resid 603 through 609 Processing helix chain 'F' and resid 629 through 633 Processing helix chain 'F' and resid 672 through 676 Processing helix chain 'F' and resid 677 through 683 removed outlier: 3.593A pdb=" N PHE F 681 " --> pdb=" O THR F 677 " (cutoff:3.500A) Processing helix chain 'F' and resid 696 through 701 Processing helix chain 'F' and resid 706 through 711 Processing helix chain 'F' and resid 712 through 714 No H-bonds generated for 'chain 'F' and resid 712 through 714' Processing helix chain 'F' and resid 737 through 741 Processing helix chain 'F' and resid 756 through 758 No H-bonds generated for 'chain 'F' and resid 756 through 758' Processing helix chain 'F' and resid 759 through 766 removed outlier: 3.539A pdb=" N LEU F 763 " --> pdb=" O ASP F 759 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU F 766 " --> pdb=" O ILE F 762 " (cutoff:3.500A) Processing helix chain 'F' and resid 831 through 837 Processing helix chain 'F' and resid 849 through 869 Processing helix chain 'G' and resid 2 through 20 Processing helix chain 'G' and resid 27 through 51 removed outlier: 3.766A pdb=" N CYS G 51 " --> pdb=" O GLN G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 64 removed outlier: 3.684A pdb=" N ARG G 60 " --> pdb=" O ASN G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 91 removed outlier: 3.709A pdb=" N VAL G 69 " --> pdb=" O LYS G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 126 removed outlier: 3.661A pdb=" N LYS G 102 " --> pdb=" O LEU G 98 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ARG G 103 " --> pdb=" O PRO G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 135 removed outlier: 3.716A pdb=" N ASP G 135 " --> pdb=" O ALA G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 158 through 169 Processing helix chain 'G' and resid 188 through 197 Processing helix chain 'G' and resid 199 through 206 Processing helix chain 'G' and resid 219 through 232 removed outlier: 4.021A pdb=" N LYS G 230 " --> pdb=" O ASN G 226 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N PHE G 231 " --> pdb=" O ILE G 227 " (cutoff:3.500A) Processing helix chain 'G' and resid 242 through 257 removed outlier: 3.742A pdb=" N GLY G 257 " --> pdb=" O PHE G 253 " (cutoff:3.500A) Processing helix chain 'G' and resid 269 through 278 removed outlier: 3.985A pdb=" N TRP G 273 " --> pdb=" O SER G 269 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE G 278 " --> pdb=" O GLU G 274 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 303 Processing helix chain 'G' and resid 313 through 327 Processing helix chain 'G' and resid 332 through 334 No H-bonds generated for 'chain 'G' and resid 332 through 334' Processing helix chain 'G' and resid 335 through 346 Processing helix chain 'G' and resid 349 through 364 Processing helix chain 'G' and resid 366 through 381 Processing helix chain 'G' and resid 387 through 400 removed outlier: 3.834A pdb=" N ASN G 391 " --> pdb=" O PRO G 387 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG G 400 " --> pdb=" O MET G 396 " (cutoff:3.500A) Processing helix chain 'G' and resid 402 through 410 removed outlier: 4.534A pdb=" N CYS G 408 " --> pdb=" O ASP G 404 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU G 410 " --> pdb=" O LYS G 406 " (cutoff:3.500A) Processing helix chain 'G' and resid 411 through 415 Processing helix chain 'G' and resid 423 through 433 Processing helix chain 'G' and resid 443 through 458 removed outlier: 3.613A pdb=" N ARG G 458 " --> pdb=" O ASP G 454 " (cutoff:3.500A) Processing helix chain 'G' and resid 478 through 492 Processing helix chain 'G' and resid 509 through 515 removed outlier: 3.798A pdb=" N THR G 515 " --> pdb=" O ARG G 511 " (cutoff:3.500A) Processing helix chain 'G' and resid 524 through 531 Processing helix chain 'G' and resid 552 through 556 removed outlier: 3.860A pdb=" N ILE G 556 " --> pdb=" O SER G 553 " (cutoff:3.500A) Processing helix chain 'G' and resid 557 through 563 Processing helix chain 'G' and resid 580 through 586 Processing helix chain 'G' and resid 603 through 609 removed outlier: 3.525A pdb=" N LEU G 609 " --> pdb=" O MET G 606 " (cutoff:3.500A) Processing helix chain 'G' and resid 629 through 633 Processing helix chain 'G' and resid 672 through 676 Processing helix chain 'G' and resid 677 through 683 Processing helix chain 'G' and resid 696 through 701 Processing helix chain 'G' and resid 706 through 713 removed outlier: 3.905A pdb=" N ARG G 713 " --> pdb=" O LYS G 709 " (cutoff:3.500A) Processing helix chain 'G' and resid 737 through 741 Processing helix chain 'G' and resid 756 through 758 No H-bonds generated for 'chain 'G' and resid 756 through 758' Processing helix chain 'G' and resid 759 through 766 removed outlier: 3.729A pdb=" N LEU G 763 " --> pdb=" O ASP G 759 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU G 766 " --> pdb=" O ILE G 762 " (cutoff:3.500A) Processing helix chain 'G' and resid 833 through 837 Processing helix chain 'G' and resid 849 through 870 Processing sheet with id=AA1, first strand: chain 'A' and resid 177 through 179 removed outlier: 6.416A pdb=" N GLU A 177 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N LEU A 291 " --> pdb=" O GLU A 177 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N VAL A 179 " --> pdb=" O LEU A 291 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N TYR A 260 " --> pdb=" O ARG A 288 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N LEU A 290 " --> pdb=" O TYR A 260 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL A 262 " --> pdb=" O LEU A 290 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 181 through 182 removed outlier: 3.713A pdb=" N VAL A 182 " --> pdb=" O HIS A 307 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 421 through 422 removed outlier: 6.566A pdb=" N GLU A 465 " --> pdb=" O LYS A 473 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N CYS A 475 " --> pdb=" O VAL A 463 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL A 463 " --> pdb=" O CYS A 475 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 497 through 498 removed outlier: 7.002A pdb=" N GLN A 497 " --> pdb=" O CYS A 520 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 549 through 550 removed outlier: 6.566A pdb=" N ILE A 549 " --> pdb=" O ASN A 575 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU A 569 " --> pdb=" O ALA A 593 " (cutoff:3.500A) removed outlier: 8.636A pdb=" N SER A 595 " --> pdb=" O LEU A 569 " (cutoff:3.500A) removed outlier: 8.926A pdb=" N VAL A 571 " --> pdb=" O SER A 595 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 601 through 602 removed outlier: 7.413A pdb=" N LEU A 624 " --> pdb=" O LYS A 646 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 668 through 671 removed outlier: 5.741A pdb=" N SER A 669 " --> pdb=" O LYS A 689 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY A 691 " --> pdb=" O SER A 669 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LEU A 690 " --> pdb=" O LYS A 721 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N ILE A 723 " --> pdb=" O LEU A 690 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ILE A 692 " --> pdb=" O ILE A 723 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU A 748 " --> pdb=" O LYS A 773 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N LYS A 775 " --> pdb=" O LEU A 748 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU A 750 " --> pdb=" O LYS A 775 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N LEU A 796 " --> pdb=" O VAL A 820 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ILE A 822 " --> pdb=" O LEU A 796 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ILE A 798 " --> pdb=" O ILE A 822 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N LEU A 819 " --> pdb=" O MET A 844 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 755 through 756 removed outlier: 5.324A pdb=" N LEU A 755 " --> pdb=" O SER A 780 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 783 through 785 Processing sheet with id=AB1, first strand: chain 'E' and resid 177 through 179 removed outlier: 6.432A pdb=" N GLU E 177 " --> pdb=" O VAL E 289 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N LEU E 291 " --> pdb=" O GLU E 177 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N VAL E 179 " --> pdb=" O LEU E 291 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N THR E 293 " --> pdb=" O VAL E 179 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N TYR E 260 " --> pdb=" O ARG E 288 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N LEU E 290 " --> pdb=" O TYR E 260 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL E 262 " --> pdb=" O LEU E 290 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N THR E 292 " --> pdb=" O VAL E 262 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N LEU E 264 " --> pdb=" O THR E 292 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 181 through 182 removed outlier: 3.501A pdb=" N VAL E 182 " --> pdb=" O HIS E 307 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'E' and resid 421 through 422 removed outlier: 6.653A pdb=" N ILE E 472 " --> pdb=" O ARG E 466 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ARG E 466 " --> pdb=" O ILE E 472 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N THR E 474 " --> pdb=" O MET E 464 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 497 through 498 removed outlier: 6.439A pdb=" N LEU E 519 " --> pdb=" O LEU E 542 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 549 through 550 removed outlier: 6.637A pdb=" N ILE E 549 " --> pdb=" O ASN E 575 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU E 569 " --> pdb=" O ALA E 593 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N SER E 595 " --> pdb=" O LEU E 569 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N VAL E 571 " --> pdb=" O SER E 595 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 601 through 602 removed outlier: 7.235A pdb=" N LEU E 624 " --> pdb=" O LYS E 646 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 667 through 671 removed outlier: 6.899A pdb=" N LYS E 689 " --> pdb=" O THR E 667 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N SER E 669 " --> pdb=" O LYS E 689 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY E 691 " --> pdb=" O SER E 669 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N LEU E 690 " --> pdb=" O LYS E 721 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N ILE E 723 " --> pdb=" O LEU E 690 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ILE E 692 " --> pdb=" O ILE E 723 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU E 748 " --> pdb=" O LYS E 773 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N LYS E 775 " --> pdb=" O LEU E 748 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LEU E 750 " --> pdb=" O LYS E 775 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LEU E 796 " --> pdb=" O VAL E 820 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ILE E 822 " --> pdb=" O LEU E 796 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ILE E 798 " --> pdb=" O ILE E 822 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N LEU E 819 " --> pdb=" O MET E 844 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N GLN E 846 " --> pdb=" O LEU E 819 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU E 821 " --> pdb=" O GLN E 846 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 755 through 756 removed outlier: 5.521A pdb=" N LEU E 755 " --> pdb=" O SER E 780 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'E' and resid 783 through 785 Processing sheet with id=AC1, first strand: chain 'F' and resid 208 through 213 removed outlier: 4.929A pdb=" N TYR F 260 " --> pdb=" O PRO F 286 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG F 288 " --> pdb=" O TYR F 260 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N HIS F 175 " --> pdb=" O ASN F 287 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N VAL F 289 " --> pdb=" O HIS F 175 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLU F 177 " --> pdb=" O VAL F 289 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N LEU F 291 " --> pdb=" O GLU F 177 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N VAL F 179 " --> pdb=" O LEU F 291 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N THR F 293 " --> pdb=" O VAL F 179 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N VAL F 181 " --> pdb=" O THR F 293 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N HIS F 307 " --> pdb=" O VAL F 178 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 421 through 422 removed outlier: 6.689A pdb=" N THR F 474 " --> pdb=" O MET F 464 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 497 through 498 removed outlier: 5.951A pdb=" N GLN F 497 " --> pdb=" O CYS F 520 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N PHE F 541 " --> pdb=" O ASP F 570 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N GLU F 572 " --> pdb=" O PHE F 541 " (cutoff:3.500A) removed outlier: 9.196A pdb=" N SER F 543 " --> pdb=" O GLU F 572 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ILE F 574 " --> pdb=" O SER F 543 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N SER F 595 " --> pdb=" O VAL F 571 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N SER F 573 " --> pdb=" O SER F 595 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN F 618 " --> pdb=" O PHE F 594 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N ILE F 615 " --> pdb=" O HIS F 640 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU F 639 " --> pdb=" O THR F 667 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER F 669 " --> pdb=" O LEU F 639 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY F 691 " --> pdb=" O LEU F 668 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ARG F 693 " --> pdb=" O THR F 670 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU F 796 " --> pdb=" O VAL F 820 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ILE F 822 " --> pdb=" O LEU F 796 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE F 798 " --> pdb=" O ILE F 822 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU F 819 " --> pdb=" O MET F 844 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N GLN F 846 " --> pdb=" O LEU F 819 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LEU F 821 " --> pdb=" O GLN F 846 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 601 through 602 removed outlier: 4.175A pdb=" N LEU F 624 " --> pdb=" O SER F 644 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 783 through 785 Processing sheet with id=AC6, first strand: chain 'G' and resid 210 through 213 removed outlier: 5.890A pdb=" N HIS G 175 " --> pdb=" O ASN G 287 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N VAL G 289 " --> pdb=" O HIS G 175 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N GLU G 177 " --> pdb=" O VAL G 289 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N LEU G 291 " --> pdb=" O GLU G 177 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N VAL G 179 " --> pdb=" O LEU G 291 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N THR G 293 " --> pdb=" O VAL G 179 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N VAL G 181 " --> pdb=" O THR G 293 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 421 through 422 removed outlier: 7.044A pdb=" N ILE G 472 " --> pdb=" O ARG G 466 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ARG G 466 " --> pdb=" O ILE G 472 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N THR G 474 " --> pdb=" O MET G 464 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 497 through 498 removed outlier: 6.140A pdb=" N GLN G 497 " --> pdb=" O CYS G 520 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N GLU G 572 " --> pdb=" O SER G 543 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE G 549 " --> pdb=" O ASN G 575 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 497 through 498 removed outlier: 6.140A pdb=" N GLN G 497 " --> pdb=" O CYS G 520 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N GLU G 572 " --> pdb=" O SER G 543 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER G 595 " --> pdb=" O VAL G 571 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N SER G 573 " --> pdb=" O SER G 595 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL G 592 " --> pdb=" O ILE G 616 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N ASN G 618 " --> pdb=" O VAL G 592 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N PHE G 594 " --> pdb=" O ASN G 618 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ILE G 615 " --> pdb=" O HIS G 640 " (cutoff:3.500A) removed outlier: 9.636A pdb=" N LEU G 639 " --> pdb=" O SER G 669 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE G 671 " --> pdb=" O LEU G 639 " (cutoff:3.500A) removed outlier: 9.391A pdb=" N THR G 641 " --> pdb=" O ILE G 671 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY G 691 " --> pdb=" O LEU G 668 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR G 670 " --> pdb=" O GLY G 691 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ARG G 693 " --> pdb=" O THR G 670 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU G 796 " --> pdb=" O VAL G 820 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ILE G 822 " --> pdb=" O LEU G 796 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE G 798 " --> pdb=" O ILE G 822 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU G 819 " --> pdb=" O MET G 844 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N GLN G 846 " --> pdb=" O LEU G 819 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N LEU G 821 " --> pdb=" O GLN G 846 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER G 879 " --> pdb=" O MET G 843 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 601 through 602 Processing sheet with id=AD2, first strand: chain 'G' and resid 783 through 785 removed outlier: 6.626A pdb=" N TRP G 784 " --> pdb=" O LYS G 807 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 1235 hydrogen bonds defined for protein. 3492 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: 10.93 Time building geometry restraints manager: 11.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4971 1.32 - 1.44: 7051 1.44 - 1.57: 17049 1.57 - 1.69: 37 1.69 - 1.81: 192 Bond restraints: 29300 Sorted by residual: bond pdb=" N LYS F 259 " pdb=" CA LYS F 259 " ideal model delta sigma weight residual 1.455 1.501 -0.046 1.27e-02 6.20e+03 1.32e+01 bond pdb=" N ARG A 384 " pdb=" CA ARG A 384 " ideal model delta sigma weight residual 1.461 1.496 -0.035 9.70e-03 1.06e+04 1.30e+01 bond pdb=" N VAL G 179 " pdb=" CA VAL G 179 " ideal model delta sigma weight residual 1.457 1.490 -0.032 9.00e-03 1.23e+04 1.30e+01 bond pdb=" N VAL F 182 " pdb=" CA VAL F 182 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.17e-02 7.31e+03 1.12e+01 bond pdb=" N VAL A 150 " pdb=" CA VAL A 150 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.19e-02 7.06e+03 1.07e+01 ... (remaining 29295 not shown) Histogram of bond angle deviations from ideal: 96.34 - 104.27: 399 104.27 - 112.20: 14965 112.20 - 120.13: 12080 120.13 - 128.07: 11927 128.07 - 136.00: 269 Bond angle restraints: 39640 Sorted by residual: angle pdb=" N SER F 468 " pdb=" CA SER F 468 " pdb=" C SER F 468 " ideal model delta sigma weight residual 111.28 102.36 8.92 1.09e+00 8.42e-01 6.70e+01 angle pdb=" N ILE E 66 " pdb=" CA ILE E 66 " pdb=" C ILE E 66 " ideal model delta sigma weight residual 110.72 103.16 7.56 1.01e+00 9.80e-01 5.60e+01 angle pdb=" N PRO G 147 " pdb=" CA PRO G 147 " pdb=" C PRO G 147 " ideal model delta sigma weight residual 110.70 101.83 8.87 1.22e+00 6.72e-01 5.28e+01 angle pdb=" N SER G 468 " pdb=" CA SER G 468 " pdb=" C SER G 468 " ideal model delta sigma weight residual 111.28 104.67 6.61 1.09e+00 8.42e-01 3.67e+01 angle pdb=" CA LYS F 64 " pdb=" C LYS F 64 " pdb=" O LYS F 64 " ideal model delta sigma weight residual 121.55 115.49 6.06 1.06e+00 8.90e-01 3.26e+01 ... (remaining 39635 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.79: 17122 31.79 - 63.59: 848 63.59 - 95.38: 70 95.38 - 127.17: 32 127.17 - 158.97: 16 Dihedral angle restraints: 18088 sinusoidal: 7704 harmonic: 10384 Sorted by residual: dihedral pdb=" O1B ADP G 902 " pdb=" O3A ADP G 902 " pdb=" PB ADP G 902 " pdb=" PA ADP G 902 " ideal model delta sinusoidal sigma weight residual -60.00 98.96 -158.97 1 2.00e+01 2.50e-03 4.64e+01 dihedral pdb=" C2' ADP A 902 " pdb=" C1' ADP A 902 " pdb=" N9 ADP A 902 " pdb=" C4 ADP A 902 " ideal model delta sinusoidal sigma weight residual 91.55 -66.44 157.99 1 2.00e+01 2.50e-03 4.63e+01 dihedral pdb=" C2' ADP G 902 " pdb=" C1' ADP G 902 " pdb=" N9 ADP G 902 " pdb=" C4 ADP G 902 " ideal model delta sinusoidal sigma weight residual 91.55 -56.70 148.25 1 2.00e+01 2.50e-03 4.44e+01 ... (remaining 18085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.014: 4458 1.014 - 2.028: 0 2.028 - 3.041: 0 3.041 - 4.055: 0 4.055 - 5.069: 14 Chirality restraints: 4472 Sorted by residual: chirality pdb=" C2 IHP F 901 " pdb=" C1 IHP F 901 " pdb=" C3 IHP F 901 " pdb=" O12 IHP F 901 " both_signs ideal model delta sigma weight residual False -2.52 2.55 -5.07 2.00e-01 2.50e+01 6.42e+02 chirality pdb=" C2 IHP G 901 " pdb=" C1 IHP G 901 " pdb=" C3 IHP G 901 " pdb=" O12 IHP G 901 " both_signs ideal model delta sigma weight residual False -2.52 2.54 -5.06 2.00e-01 2.50e+01 6.41e+02 chirality pdb=" C4 IHP F 901 " pdb=" C3 IHP F 901 " pdb=" C5 IHP F 901 " pdb=" O14 IHP F 901 " both_signs ideal model delta sigma weight residual False 2.48 -2.58 5.06 2.00e-01 2.50e+01 6.40e+02 ... (remaining 4469 not shown) Planarity restraints: 5012 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY F 257 " -0.022 2.00e-02 2.50e+03 4.23e-02 1.79e+01 pdb=" C GLY F 257 " 0.073 2.00e-02 2.50e+03 pdb=" O GLY F 257 " -0.027 2.00e-02 2.50e+03 pdb=" N GLY F 258 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 195 " 0.019 2.00e-02 2.50e+03 3.74e-02 1.40e+01 pdb=" C LYS F 195 " -0.065 2.00e-02 2.50e+03 pdb=" O LYS F 195 " 0.024 2.00e-02 2.50e+03 pdb=" N ILE F 196 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER G 805 " -0.015 2.00e-02 2.50e+03 3.14e-02 9.84e+00 pdb=" C SER G 805 " 0.054 2.00e-02 2.50e+03 pdb=" O SER G 805 " -0.020 2.00e-02 2.50e+03 pdb=" N TRP G 806 " -0.019 2.00e-02 2.50e+03 ... (remaining 5009 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1496 2.72 - 3.26: 30972 3.26 - 3.81: 46281 3.81 - 4.35: 57817 4.35 - 4.90: 94641 Nonbonded interactions: 231207 Sorted by model distance: nonbonded pdb=" N GLU A 756 " pdb=" OE1 GLU A 756 " model vdw 2.174 2.520 nonbonded pdb=" N GLU G 572 " pdb=" OE1 GLU G 572 " model vdw 2.177 2.520 nonbonded pdb=" N GLU E 767 " pdb=" OE1 GLU E 767 " model vdw 2.194 2.520 nonbonded pdb=" OH TYR E 411 " pdb=" OE2 GLU E 433 " model vdw 2.195 2.440 nonbonded pdb=" N GLU E 782 " pdb=" OE1 GLU E 782 " model vdw 2.195 2.520 ... (remaining 231202 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 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.140 Check model and map are aligned: 0.210 Set scattering table: 0.260 Process input model: 74.460 Find NCS groups from input model: 1.590 Set up NCS constraints: 0.110 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:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6720 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 : 0.004 0.060 29300 Z= 0.299 Angle : 0.889 10.424 39640 Z= 0.523 Chirality : 0.279 5.069 4472 Planarity : 0.006 0.076 5012 Dihedral : 19.140 158.968 11312 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.02 % Favored : 95.92 % Rotamer: Outliers : 1.07 % Allowed : 21.46 % Favored : 77.48 % 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: -0.83 (0.14), residues: 3532 helix: 0.37 (0.13), residues: 1476 sheet: -1.29 (0.25), residues: 440 loop : -1.13 (0.15), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP F 318 HIS 0.008 0.001 HIS E 537 PHE 0.026 0.002 PHE A 41 TYR 0.046 0.002 TYR F 101 ARG 0.019 0.001 ARG G 486 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 3188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 320 time to evaluate : 2.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 HIS cc_start: 0.4675 (p90) cc_final: 0.4466 (p90) REVERT: A 115 ARG cc_start: 0.6136 (ttt180) cc_final: 0.5926 (ttp80) REVERT: A 158 PHE cc_start: 0.7031 (m-80) cc_final: 0.6759 (m-80) REVERT: A 223 LEU cc_start: 0.7193 (OUTLIER) cc_final: 0.6934 (tp) REVERT: A 303 ASN cc_start: 0.6785 (OUTLIER) cc_final: 0.6423 (m-40) REVERT: A 523 SER cc_start: 0.7024 (p) cc_final: 0.6758 (m) REVERT: E 158 PHE cc_start: 0.6971 (m-80) cc_final: 0.6718 (m-10) REVERT: E 480 MET cc_start: 0.8307 (mmm) cc_final: 0.7915 (mmm) REVERT: E 885 LEU cc_start: 0.4546 (OUTLIER) cc_final: 0.4188 (mm) REVERT: F 747 LYS cc_start: 0.5233 (ttpp) cc_final: 0.5016 (mptt) REVERT: G 320 LEU cc_start: 0.4765 (tp) cc_final: 0.4104 (mt) REVERT: G 424 TRP cc_start: 0.6267 (p-90) cc_final: 0.5864 (p-90) REVERT: G 453 ASN cc_start: 0.6883 (t0) cc_final: 0.6540 (m-40) REVERT: G 490 MET cc_start: 0.5940 (ptt) cc_final: 0.5729 (ptm) REVERT: G 501 LEU cc_start: 0.4865 (OUTLIER) cc_final: 0.4477 (mp) REVERT: G 558 THR cc_start: 0.6008 (p) cc_final: 0.4677 (m) outliers start: 34 outliers final: 11 residues processed: 344 average time/residue: 0.4236 time to fit residues: 230.1444 Evaluate side-chains 274 residues out of total 3188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 259 time to evaluate : 3.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain E residue 229 SER Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain E residue 643 SER Chi-restraints excluded: chain E residue 879 SER Chi-restraints excluded: chain E residue 881 PHE Chi-restraints excluded: chain E residue 885 LEU Chi-restraints excluded: chain F residue 115 ARG Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 469 ASP Chi-restraints excluded: chain G residue 501 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 297 optimal weight: 0.6980 chunk 266 optimal weight: 40.0000 chunk 148 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 179 optimal weight: 20.0000 chunk 142 optimal weight: 0.7980 chunk 275 optimal weight: 7.9990 chunk 106 optimal weight: 9.9990 chunk 167 optimal weight: 6.9990 chunk 205 optimal weight: 9.9990 chunk 319 optimal weight: 0.0370 overall best weight: 1.5060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 HIS A 234 ASN A 380 HIS ** A 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 HIS ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 818 HIS E 39 ASN ** E 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 386 HIS E 453 ASN E 505 GLN E 841 GLN F 116 ASN ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 391 ASN G 451 ASN G 873 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6725 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 29300 Z= 0.239 Angle : 0.731 16.364 39640 Z= 0.350 Chirality : 0.048 0.522 4472 Planarity : 0.005 0.046 5012 Dihedral : 12.716 157.551 4041 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.92 % Allowed : 19.92 % Favored : 77.16 % 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: -0.22 (0.14), residues: 3532 helix: 0.80 (0.13), residues: 1500 sheet: -0.40 (0.26), residues: 416 loop : -0.92 (0.16), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP F 318 HIS 0.005 0.001 HIS G 638 PHE 0.015 0.002 PHE F 435 TYR 0.020 0.002 TYR F 101 ARG 0.008 0.001 ARG A 122 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 3188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 295 time to evaluate : 3.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LEU cc_start: 0.7377 (OUTLIER) cc_final: 0.7123 (mm) REVERT: A 223 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.7112 (tp) REVERT: A 241 MET cc_start: 0.5771 (OUTLIER) cc_final: 0.4614 (ptp) REVERT: A 242 CYS cc_start: 0.4730 (OUTLIER) cc_final: 0.4418 (t) REVERT: A 523 SER cc_start: 0.6982 (p) cc_final: 0.6681 (m) REVERT: A 776 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.6659 (tm-30) REVERT: E 47 GLN cc_start: 0.7258 (mm-40) cc_final: 0.7009 (mm-40) REVERT: E 159 ASP cc_start: 0.6906 (OUTLIER) cc_final: 0.6700 (m-30) REVERT: E 885 LEU cc_start: 0.4711 (OUTLIER) cc_final: 0.4400 (mm) REVERT: F 198 LYS cc_start: 0.6133 (pttp) cc_final: 0.5290 (tptp) REVERT: F 206 PHE cc_start: 0.1921 (m-80) cc_final: 0.1516 (m-80) REVERT: F 318 TRP cc_start: 0.3643 (t60) cc_final: 0.3393 (t60) REVERT: F 481 LEU cc_start: 0.5494 (mt) cc_final: 0.5163 (mt) REVERT: F 747 LYS cc_start: 0.5023 (ttpp) cc_final: 0.4804 (mmtm) REVERT: G 320 LEU cc_start: 0.4684 (tp) cc_final: 0.4210 (mt) REVERT: G 410 LEU cc_start: 0.4059 (OUTLIER) cc_final: 0.3781 (tp) REVERT: G 428 ARG cc_start: 0.3069 (mpt180) cc_final: 0.2853 (mpt-90) REVERT: G 481 LEU cc_start: 0.4904 (mt) cc_final: 0.4700 (mt) REVERT: G 501 LEU cc_start: 0.4856 (OUTLIER) cc_final: 0.4340 (mp) REVERT: G 532 LYS cc_start: 0.7559 (mmtt) cc_final: 0.6963 (mmmt) REVERT: G 558 THR cc_start: 0.5585 (p) cc_final: 0.4238 (m) REVERT: G 606 MET cc_start: 0.4342 (tmm) cc_final: 0.4136 (tmm) REVERT: G 873 ASN cc_start: 0.0623 (OUTLIER) cc_final: -0.1609 (p0) outliers start: 93 outliers final: 39 residues processed: 368 average time/residue: 0.4065 time to fit residues: 239.5479 Evaluate side-chains 306 residues out of total 3188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 257 time to evaluate : 3.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 776 GLU Chi-restraints excluded: chain A residue 811 ASP Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain E residue 284 ASN Chi-restraints excluded: chain E residue 469 ASP Chi-restraints excluded: chain E residue 581 ARG Chi-restraints excluded: chain E residue 701 ASP Chi-restraints excluded: chain E residue 743 THR Chi-restraints excluded: chain E residue 881 PHE Chi-restraints excluded: chain E residue 885 LEU Chi-restraints excluded: chain F residue 115 ARG Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 360 LEU Chi-restraints excluded: chain F residue 565 LEU Chi-restraints excluded: chain F residue 573 SER Chi-restraints excluded: chain F residue 641 THR Chi-restraints excluded: chain F residue 671 ILE Chi-restraints excluded: chain F residue 676 CYS Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 189 LYS Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain G residue 381 LEU Chi-restraints excluded: chain G residue 410 LEU Chi-restraints excluded: chain G residue 501 LEU Chi-restraints excluded: chain G residue 542 LEU Chi-restraints excluded: chain G residue 565 LEU Chi-restraints excluded: chain G residue 609 LEU Chi-restraints excluded: chain G residue 641 THR Chi-restraints excluded: chain G residue 671 ILE Chi-restraints excluded: chain G residue 843 MET Chi-restraints excluded: chain G residue 864 ASP Chi-restraints excluded: chain G residue 873 ASN Chi-restraints excluded: chain G residue 878 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 177 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 266 optimal weight: 10.0000 chunk 217 optimal weight: 10.0000 chunk 88 optimal weight: 7.9990 chunk 320 optimal weight: 7.9990 chunk 345 optimal weight: 4.9990 chunk 285 optimal weight: 2.9990 chunk 317 optimal weight: 5.9990 chunk 109 optimal weight: 0.9980 chunk 256 optimal weight: 8.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 453 ASN A 710 ASN ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 HIS ** E 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 453 ASN ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 494 ASN F 497 GLN F 710 ASN G 175 HIS ** G 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 710 ASN ** G 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 846 GLN ** G 873 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6844 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 29300 Z= 0.350 Angle : 0.739 10.457 39640 Z= 0.365 Chirality : 0.048 0.628 4472 Planarity : 0.005 0.057 5012 Dihedral : 11.651 151.632 4030 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 4.23 % Allowed : 20.61 % Favored : 75.16 % 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: -0.53 (0.14), residues: 3532 helix: 0.58 (0.13), residues: 1500 sheet: -1.08 (0.24), residues: 520 loop : -0.94 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP F 430 HIS 0.007 0.001 HIS G 638 PHE 0.018 0.002 PHE G 409 TYR 0.025 0.002 TYR A 591 ARG 0.009 0.001 ARG A 122 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 3188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 285 time to evaluate : 3.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LEU cc_start: 0.7306 (OUTLIER) cc_final: 0.6965 (mm) REVERT: A 158 PHE cc_start: 0.7090 (m-80) cc_final: 0.6884 (m-80) REVERT: A 223 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.7257 (tp) REVERT: A 241 MET cc_start: 0.6112 (OUTLIER) cc_final: 0.5072 (ptp) REVERT: A 629 ASN cc_start: 0.8504 (OUTLIER) cc_final: 0.8299 (m-40) REVERT: A 754 TRP cc_start: 0.6433 (m100) cc_final: 0.6090 (m100) REVERT: A 776 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.6626 (tm-30) REVERT: E 137 LEU cc_start: -0.0224 (OUTLIER) cc_final: -0.0449 (mp) REVERT: E 159 ASP cc_start: 0.7151 (OUTLIER) cc_final: 0.6823 (m-30) REVERT: E 322 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8414 (tt0) REVERT: E 666 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.8283 (mp10) REVERT: E 776 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.6706 (tm-30) REVERT: E 885 LEU cc_start: 0.4868 (OUTLIER) cc_final: 0.4584 (mm) REVERT: F 15 GLN cc_start: 0.2550 (OUTLIER) cc_final: 0.2135 (mm-40) REVERT: F 195 LYS cc_start: 0.4859 (tttm) cc_final: 0.4402 (tttt) REVERT: F 198 LYS cc_start: 0.6138 (pttp) cc_final: 0.5295 (tptp) REVERT: F 206 PHE cc_start: 0.1520 (m-80) cc_final: 0.1276 (m-80) REVERT: F 291 LEU cc_start: 0.5802 (tt) cc_final: 0.5465 (tt) REVERT: F 354 VAL cc_start: 0.7749 (t) cc_final: 0.7526 (m) REVERT: F 398 TYR cc_start: 0.6646 (t80) cc_final: 0.6182 (t80) REVERT: F 424 TRP cc_start: 0.6615 (p-90) cc_final: 0.6397 (p-90) REVERT: F 588 HIS cc_start: 0.4666 (m90) cc_final: 0.3819 (m170) REVERT: F 819 LEU cc_start: 0.7225 (tp) cc_final: 0.5866 (mt) REVERT: G 320 LEU cc_start: 0.5196 (tp) cc_final: 0.4498 (mt) REVERT: G 381 LEU cc_start: 0.1050 (OUTLIER) cc_final: 0.0774 (mm) REVERT: G 501 LEU cc_start: 0.4727 (OUTLIER) cc_final: 0.4440 (mp) REVERT: G 532 LYS cc_start: 0.7639 (mmtt) cc_final: 0.7180 (mmmt) REVERT: G 760 MET cc_start: 0.5227 (tmm) cc_final: 0.4950 (tmm) REVERT: G 775 LYS cc_start: 0.8422 (mtmt) cc_final: 0.7968 (pttm) REVERT: G 776 GLU cc_start: 0.5659 (tm-30) cc_final: 0.5364 (tm-30) outliers start: 135 outliers final: 73 residues processed: 394 average time/residue: 0.3939 time to fit residues: 249.7884 Evaluate side-chains 332 residues out of total 3188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 245 time to evaluate : 3.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 479 ASP Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 629 ASN Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 776 GLU Chi-restraints excluded: chain A residue 811 ASP Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 87 HIS Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain E residue 284 ASN Chi-restraints excluded: chain E residue 287 ASN Chi-restraints excluded: chain E residue 322 GLU Chi-restraints excluded: chain E residue 353 ILE Chi-restraints excluded: chain E residue 469 ASP Chi-restraints excluded: chain E residue 474 THR Chi-restraints excluded: chain E residue 479 ASP Chi-restraints excluded: chain E residue 500 LYS Chi-restraints excluded: chain E residue 581 ARG Chi-restraints excluded: chain E residue 666 GLN Chi-restraints excluded: chain E residue 696 ILE Chi-restraints excluded: chain E residue 701 ASP Chi-restraints excluded: chain E residue 725 ASP Chi-restraints excluded: chain E residue 743 THR Chi-restraints excluded: chain E residue 776 GLU Chi-restraints excluded: chain E residue 804 VAL Chi-restraints excluded: chain E residue 807 LYS Chi-restraints excluded: chain E residue 811 ASP Chi-restraints excluded: chain E residue 881 PHE Chi-restraints excluded: chain E residue 885 LEU Chi-restraints excluded: chain F residue 15 GLN Chi-restraints excluded: chain F residue 115 ARG Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 431 ILE Chi-restraints excluded: chain F residue 542 LEU Chi-restraints excluded: chain F residue 573 SER Chi-restraints excluded: chain F residue 583 PHE Chi-restraints excluded: chain F residue 619 THR Chi-restraints excluded: chain F residue 641 THR Chi-restraints excluded: chain F residue 671 ILE Chi-restraints excluded: chain F residue 676 CYS Chi-restraints excluded: chain F residue 696 ILE Chi-restraints excluded: chain F residue 755 LEU Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 269 SER Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 381 LEU Chi-restraints excluded: chain G residue 460 LEU Chi-restraints excluded: chain G residue 501 LEU Chi-restraints excluded: chain G residue 523 SER Chi-restraints excluded: chain G residue 531 THR Chi-restraints excluded: chain G residue 542 LEU Chi-restraints excluded: chain G residue 551 MET Chi-restraints excluded: chain G residue 565 LEU Chi-restraints excluded: chain G residue 583 PHE Chi-restraints excluded: chain G residue 609 LEU Chi-restraints excluded: chain G residue 641 THR Chi-restraints excluded: chain G residue 660 LEU Chi-restraints excluded: chain G residue 671 ILE Chi-restraints excluded: chain G residue 843 MET Chi-restraints excluded: chain G residue 864 ASP Chi-restraints excluded: chain G residue 878 LEU Chi-restraints excluded: chain G residue 880 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 316 optimal weight: 4.9990 chunk 240 optimal weight: 7.9990 chunk 166 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 215 optimal weight: 20.0000 chunk 321 optimal weight: 0.8980 chunk 340 optimal weight: 9.9990 chunk 167 optimal weight: 3.9990 chunk 304 optimal weight: 20.0000 chunk 91 optimal weight: 5.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 GLN A 100 HIS ** A 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 537 HIS ** E 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 846 GLN G 873 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 29300 Z= 0.357 Angle : 0.728 9.548 39640 Z= 0.361 Chirality : 0.047 0.551 4472 Planarity : 0.005 0.058 5012 Dihedral : 11.417 152.805 4030 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.38 % Favored : 94.59 % Rotamer: Outliers : 5.43 % Allowed : 20.64 % Favored : 73.93 % 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: -0.61 (0.14), residues: 3532 helix: 0.51 (0.13), residues: 1532 sheet: -1.21 (0.24), residues: 516 loop : -0.97 (0.16), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP F 430 HIS 0.006 0.001 HIS F 327 PHE 0.016 0.002 PHE E 779 TYR 0.022 0.002 TYR E 591 ARG 0.008 0.001 ARG A 122 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 3188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 283 time to evaluate : 3.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7274 (tp) REVERT: A 241 MET cc_start: 0.6477 (OUTLIER) cc_final: 0.6248 (ttp) REVERT: A 729 GLN cc_start: 0.4353 (OUTLIER) cc_final: 0.2667 (mp-120) REVERT: A 754 TRP cc_start: 0.6514 (m100) cc_final: 0.5984 (m100) REVERT: A 776 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.6564 (tm-30) REVERT: E 137 LEU cc_start: -0.0028 (OUTLIER) cc_final: -0.0295 (mp) REVERT: E 159 ASP cc_start: 0.7237 (OUTLIER) cc_final: 0.6906 (m-30) REVERT: E 322 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8423 (tt0) REVERT: E 501 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7812 (tp) REVERT: E 666 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.8259 (mp10) REVERT: E 760 MET cc_start: 0.7238 (mmm) cc_final: 0.7022 (mmm) REVERT: E 776 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.6712 (tm-30) REVERT: E 885 LEU cc_start: 0.4755 (OUTLIER) cc_final: 0.4465 (mm) REVERT: F 15 GLN cc_start: 0.2433 (OUTLIER) cc_final: 0.1973 (mm-40) REVERT: F 291 LEU cc_start: 0.6208 (OUTLIER) cc_final: 0.5935 (tt) REVERT: F 315 ASP cc_start: 0.6077 (OUTLIER) cc_final: 0.5292 (t0) REVERT: F 320 LEU cc_start: 0.4763 (OUTLIER) cc_final: 0.4556 (mt) REVERT: F 360 LEU cc_start: 0.1339 (OUTLIER) cc_final: 0.1114 (tp) REVERT: F 410 LEU cc_start: 0.4823 (mm) cc_final: 0.3944 (mt) REVERT: F 453 ASN cc_start: 0.5811 (OUTLIER) cc_final: 0.5542 (t0) REVERT: F 549 ILE cc_start: 0.6686 (mt) cc_final: 0.6462 (mt) REVERT: F 588 HIS cc_start: 0.4403 (m90) cc_final: 0.3845 (m170) REVERT: F 747 LYS cc_start: 0.5009 (ttpp) cc_final: 0.4751 (mptt) REVERT: F 755 LEU cc_start: 0.2732 (OUTLIER) cc_final: 0.2459 (mm) REVERT: F 838 ARG cc_start: 0.2871 (OUTLIER) cc_final: 0.1871 (ttt180) REVERT: G 1 MET cc_start: 0.4528 (mmp) cc_final: 0.4303 (mmm) REVERT: G 252 GLU cc_start: 0.6567 (mm-30) cc_final: 0.5616 (tt0) REVERT: G 265 ASP cc_start: 0.5788 (t0) cc_final: 0.4623 (p0) REVERT: G 320 LEU cc_start: 0.5464 (tp) cc_final: 0.4713 (mt) REVERT: G 381 LEU cc_start: 0.1323 (OUTLIER) cc_final: 0.1036 (mm) REVERT: G 532 LYS cc_start: 0.7573 (mmtt) cc_final: 0.7222 (mmmt) REVERT: G 755 LEU cc_start: 0.1326 (OUTLIER) cc_final: 0.1041 (mm) REVERT: G 775 LYS cc_start: 0.8434 (mtmt) cc_final: 0.8176 (mtmm) REVERT: G 822 ILE cc_start: 0.5562 (mm) cc_final: 0.5261 (mm) REVERT: G 846 GLN cc_start: 0.6127 (tp-100) cc_final: 0.5918 (tp40) outliers start: 173 outliers final: 92 residues processed: 426 average time/residue: 0.3800 time to fit residues: 258.6091 Evaluate side-chains 369 residues out of total 3188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 256 time to evaluate : 3.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 479 ASP Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 729 GLN Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 776 GLU Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 811 ASP Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 87 HIS Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 322 GLU Chi-restraints excluded: chain E residue 328 LYS Chi-restraints excluded: chain E residue 353 ILE Chi-restraints excluded: chain E residue 390 CYS Chi-restraints excluded: chain E residue 461 VAL Chi-restraints excluded: chain E residue 469 ASP Chi-restraints excluded: chain E residue 474 THR Chi-restraints excluded: chain E residue 479 ASP Chi-restraints excluded: chain E residue 501 LEU Chi-restraints excluded: chain E residue 558 THR Chi-restraints excluded: chain E residue 581 ARG Chi-restraints excluded: chain E residue 619 THR Chi-restraints excluded: chain E residue 649 VAL Chi-restraints excluded: chain E residue 666 GLN Chi-restraints excluded: chain E residue 701 ASP Chi-restraints excluded: chain E residue 743 THR Chi-restraints excluded: chain E residue 769 LEU Chi-restraints excluded: chain E residue 776 GLU Chi-restraints excluded: chain E residue 804 VAL Chi-restraints excluded: chain E residue 807 LYS Chi-restraints excluded: chain E residue 811 ASP Chi-restraints excluded: chain E residue 881 PHE Chi-restraints excluded: chain E residue 885 LEU Chi-restraints excluded: chain F residue 15 GLN Chi-restraints excluded: chain F residue 115 ARG Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 249 GLU Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain F residue 320 LEU Chi-restraints excluded: chain F residue 360 LEU Chi-restraints excluded: chain F residue 431 ILE Chi-restraints excluded: chain F residue 453 ASN Chi-restraints excluded: chain F residue 469 ASP Chi-restraints excluded: chain F residue 472 ILE Chi-restraints excluded: chain F residue 542 LEU Chi-restraints excluded: chain F residue 565 LEU Chi-restraints excluded: chain F residue 573 SER Chi-restraints excluded: chain F residue 583 PHE Chi-restraints excluded: chain F residue 619 THR Chi-restraints excluded: chain F residue 641 THR Chi-restraints excluded: chain F residue 671 ILE Chi-restraints excluded: chain F residue 676 CYS Chi-restraints excluded: chain F residue 696 ILE Chi-restraints excluded: chain F residue 755 LEU Chi-restraints excluded: chain F residue 772 LEU Chi-restraints excluded: chain F residue 775 LYS Chi-restraints excluded: chain F residue 838 ARG Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 189 LYS Chi-restraints excluded: chain G residue 237 GLN Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 354 VAL Chi-restraints excluded: chain G residue 381 LEU Chi-restraints excluded: chain G residue 426 LEU Chi-restraints excluded: chain G residue 460 LEU Chi-restraints excluded: chain G residue 469 ASP Chi-restraints excluded: chain G residue 501 LEU Chi-restraints excluded: chain G residue 523 SER Chi-restraints excluded: chain G residue 531 THR Chi-restraints excluded: chain G residue 542 LEU Chi-restraints excluded: chain G residue 551 MET Chi-restraints excluded: chain G residue 565 LEU Chi-restraints excluded: chain G residue 574 ILE Chi-restraints excluded: chain G residue 583 PHE Chi-restraints excluded: chain G residue 609 LEU Chi-restraints excluded: chain G residue 618 ASN Chi-restraints excluded: chain G residue 641 THR Chi-restraints excluded: chain G residue 671 ILE Chi-restraints excluded: chain G residue 755 LEU Chi-restraints excluded: chain G residue 843 MET Chi-restraints excluded: chain G residue 864 ASP Chi-restraints excluded: chain G residue 880 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 283 optimal weight: 2.9990 chunk 193 optimal weight: 10.0000 chunk 4 optimal weight: 0.9980 chunk 253 optimal weight: 10.0000 chunk 140 optimal weight: 1.9990 chunk 290 optimal weight: 1.9990 chunk 235 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 173 optimal weight: 3.9990 chunk 305 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 174 ASN ** F 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 768 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 29300 Z= 0.272 Angle : 0.680 10.903 39640 Z= 0.332 Chirality : 0.045 0.509 4472 Planarity : 0.004 0.056 5012 Dihedral : 11.056 153.069 4030 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.12 % Favored : 94.85 % Rotamer: Outliers : 4.99 % Allowed : 21.17 % Favored : 73.84 % 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: -0.50 (0.14), residues: 3532 helix: 0.61 (0.13), residues: 1536 sheet: -0.94 (0.24), residues: 488 loop : -1.03 (0.16), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP F 430 HIS 0.006 0.001 HIS G 638 PHE 0.027 0.002 PHE F 311 TYR 0.019 0.002 TYR A 591 ARG 0.006 0.001 ARG A 122 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 3188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 269 time to evaluate : 3.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7250 (tp) REVERT: A 696 ILE cc_start: 0.8575 (OUTLIER) cc_final: 0.8105 (mm) REVERT: A 729 GLN cc_start: 0.4218 (OUTLIER) cc_final: 0.2738 (mp10) REVERT: A 754 TRP cc_start: 0.6617 (m100) cc_final: 0.6212 (m100) REVERT: A 776 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.6635 (tm-30) REVERT: E 52 HIS cc_start: 0.5167 (m170) cc_final: 0.4937 (p90) REVERT: E 137 LEU cc_start: 0.0006 (OUTLIER) cc_final: -0.0263 (mp) REVERT: E 159 ASP cc_start: 0.7237 (OUTLIER) cc_final: 0.6908 (m-30) REVERT: E 322 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8471 (tt0) REVERT: E 501 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7710 (tp) REVERT: E 666 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.8319 (mp10) REVERT: E 760 MET cc_start: 0.7233 (mmm) cc_final: 0.7007 (mmm) REVERT: E 776 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.6600 (tm-30) REVERT: E 829 GLU cc_start: 0.5052 (OUTLIER) cc_final: 0.4313 (pm20) REVERT: E 885 LEU cc_start: 0.4705 (OUTLIER) cc_final: 0.4438 (mm) REVERT: F 15 GLN cc_start: 0.2444 (OUTLIER) cc_final: 0.1984 (mm-40) REVERT: F 19 ASP cc_start: 0.3242 (OUTLIER) cc_final: 0.2502 (t70) REVERT: F 315 ASP cc_start: 0.6113 (OUTLIER) cc_final: 0.5307 (t0) REVERT: F 320 LEU cc_start: 0.4825 (OUTLIER) cc_final: 0.4608 (mt) REVERT: F 532 LYS cc_start: 0.7433 (mmmt) cc_final: 0.6926 (tptp) REVERT: F 588 HIS cc_start: 0.4535 (m90) cc_final: 0.3775 (m170) REVERT: F 617 ILE cc_start: 0.7605 (mt) cc_final: 0.7353 (tp) REVERT: F 747 LYS cc_start: 0.4977 (ttpp) cc_final: 0.4766 (mptt) REVERT: F 755 LEU cc_start: 0.2674 (OUTLIER) cc_final: 0.2410 (mm) REVERT: F 838 ARG cc_start: 0.2928 (OUTLIER) cc_final: 0.1850 (ttt180) REVERT: G 1 MET cc_start: 0.4582 (mmp) cc_final: 0.4281 (mmm) REVERT: G 233 ARG cc_start: 0.7837 (mmt180) cc_final: 0.7262 (mmp-170) REVERT: G 252 GLU cc_start: 0.6704 (mm-30) cc_final: 0.5778 (tt0) REVERT: G 265 ASP cc_start: 0.6023 (t0) cc_final: 0.4844 (p0) REVERT: G 320 LEU cc_start: 0.5486 (tp) cc_final: 0.4765 (mt) REVERT: G 381 LEU cc_start: 0.1388 (OUTLIER) cc_final: 0.1124 (mm) REVERT: G 532 LYS cc_start: 0.7521 (mmtt) cc_final: 0.7174 (mmmt) REVERT: G 755 LEU cc_start: 0.1134 (OUTLIER) cc_final: 0.0845 (mm) REVERT: G 760 MET cc_start: 0.5338 (tmm) cc_final: 0.5025 (tmm) REVERT: G 799 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7462 (mt-10) outliers start: 159 outliers final: 96 residues processed: 400 average time/residue: 0.3925 time to fit residues: 251.2158 Evaluate side-chains 365 residues out of total 3188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 249 time to evaluate : 3.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 479 ASP Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 729 GLN Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 776 GLU Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 811 ASP Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 87 HIS Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain E residue 251 GLN Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 284 ASN Chi-restraints excluded: chain E residue 322 GLU Chi-restraints excluded: chain E residue 328 LYS Chi-restraints excluded: chain E residue 353 ILE Chi-restraints excluded: chain E residue 390 CYS Chi-restraints excluded: chain E residue 461 VAL Chi-restraints excluded: chain E residue 469 ASP Chi-restraints excluded: chain E residue 474 THR Chi-restraints excluded: chain E residue 479 ASP Chi-restraints excluded: chain E residue 500 LYS Chi-restraints excluded: chain E residue 501 LEU Chi-restraints excluded: chain E residue 581 ARG Chi-restraints excluded: chain E residue 619 THR Chi-restraints excluded: chain E residue 649 VAL Chi-restraints excluded: chain E residue 666 GLN Chi-restraints excluded: chain E residue 701 ASP Chi-restraints excluded: chain E residue 743 THR Chi-restraints excluded: chain E residue 769 LEU Chi-restraints excluded: chain E residue 776 GLU Chi-restraints excluded: chain E residue 804 VAL Chi-restraints excluded: chain E residue 807 LYS Chi-restraints excluded: chain E residue 811 ASP Chi-restraints excluded: chain E residue 829 GLU Chi-restraints excluded: chain E residue 881 PHE Chi-restraints excluded: chain E residue 885 LEU Chi-restraints excluded: chain F residue 15 GLN Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 115 ARG Chi-restraints excluded: chain F residue 125 ASP Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 220 ARG Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 249 GLU Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain F residue 320 LEU Chi-restraints excluded: chain F residue 431 ILE Chi-restraints excluded: chain F residue 469 ASP Chi-restraints excluded: chain F residue 515 THR Chi-restraints excluded: chain F residue 542 LEU Chi-restraints excluded: chain F residue 573 SER Chi-restraints excluded: chain F residue 583 PHE Chi-restraints excluded: chain F residue 671 ILE Chi-restraints excluded: chain F residue 676 CYS Chi-restraints excluded: chain F residue 696 ILE Chi-restraints excluded: chain F residue 751 LEU Chi-restraints excluded: chain F residue 755 LEU Chi-restraints excluded: chain F residue 772 LEU Chi-restraints excluded: chain F residue 838 ARG Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 227 ILE Chi-restraints excluded: chain G residue 228 ILE Chi-restraints excluded: chain G residue 237 GLN Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain G residue 354 VAL Chi-restraints excluded: chain G residue 381 LEU Chi-restraints excluded: chain G residue 426 LEU Chi-restraints excluded: chain G residue 431 ILE Chi-restraints excluded: chain G residue 460 LEU Chi-restraints excluded: chain G residue 469 ASP Chi-restraints excluded: chain G residue 531 THR Chi-restraints excluded: chain G residue 542 LEU Chi-restraints excluded: chain G residue 551 MET Chi-restraints excluded: chain G residue 565 LEU Chi-restraints excluded: chain G residue 583 PHE Chi-restraints excluded: chain G residue 609 LEU Chi-restraints excluded: chain G residue 641 THR Chi-restraints excluded: chain G residue 671 ILE Chi-restraints excluded: chain G residue 687 LEU Chi-restraints excluded: chain G residue 755 LEU Chi-restraints excluded: chain G residue 768 HIS Chi-restraints excluded: chain G residue 843 MET Chi-restraints excluded: chain G residue 864 ASP Chi-restraints excluded: chain G residue 878 LEU Chi-restraints excluded: chain G residue 880 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 114 optimal weight: 8.9990 chunk 306 optimal weight: 9.9990 chunk 67 optimal weight: 0.4980 chunk 199 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 chunk 340 optimal weight: 1.9990 chunk 282 optimal weight: 0.7980 chunk 157 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 112 optimal weight: 0.5980 chunk 178 optimal weight: 20.0000 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 459 ASN F 873 ASN G 237 GLN ** G 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29300 Z= 0.203 Angle : 0.633 9.643 39640 Z= 0.308 Chirality : 0.044 0.488 4472 Planarity : 0.004 0.054 5012 Dihedral : 10.728 153.249 4028 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.67 % Favored : 95.30 % Rotamer: Outliers : 3.98 % Allowed : 22.40 % Favored : 73.62 % 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: -0.26 (0.14), residues: 3532 helix: 0.80 (0.13), residues: 1536 sheet: -0.75 (0.25), residues: 488 loop : -0.91 (0.16), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 273 HIS 0.035 0.001 HIS G 768 PHE 0.023 0.001 PHE F 311 TYR 0.014 0.001 TYR E 591 ARG 0.005 0.000 ARG E 220 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 3188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 267 time to evaluate : 3.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.7191 (tp) REVERT: A 523 SER cc_start: 0.7064 (p) cc_final: 0.6835 (m) REVERT: A 696 ILE cc_start: 0.8551 (OUTLIER) cc_final: 0.8089 (mm) REVERT: A 729 GLN cc_start: 0.4093 (OUTLIER) cc_final: 0.2769 (mp10) REVERT: A 754 TRP cc_start: 0.6556 (m100) cc_final: 0.6158 (m100) REVERT: A 776 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.6654 (tm-30) REVERT: E 14 MET cc_start: 0.7493 (ttt) cc_final: 0.7069 (ttm) REVERT: E 159 ASP cc_start: 0.7241 (OUTLIER) cc_final: 0.6949 (m-30) REVERT: E 322 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.8476 (tt0) REVERT: E 501 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7705 (tp) REVERT: E 776 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.6574 (tm-30) REVERT: E 885 LEU cc_start: 0.4829 (OUTLIER) cc_final: 0.4596 (mm) REVERT: F 15 GLN cc_start: 0.2500 (OUTLIER) cc_final: 0.2129 (mm-40) REVERT: F 19 ASP cc_start: 0.3356 (OUTLIER) cc_final: 0.2494 (t70) REVERT: F 320 LEU cc_start: 0.4830 (OUTLIER) cc_final: 0.4617 (mt) REVERT: F 504 GLU cc_start: 0.7910 (pp20) cc_final: 0.7685 (pm20) REVERT: F 532 LYS cc_start: 0.7336 (mmmt) cc_final: 0.6847 (tptp) REVERT: F 588 HIS cc_start: 0.4574 (m90) cc_final: 0.3847 (m170) REVERT: F 617 ILE cc_start: 0.7694 (mt) cc_final: 0.7309 (tp) REVERT: F 747 LYS cc_start: 0.5056 (ttpp) cc_final: 0.4808 (mptt) REVERT: F 755 LEU cc_start: 0.2219 (OUTLIER) cc_final: 0.1991 (mm) REVERT: F 838 ARG cc_start: 0.2999 (OUTLIER) cc_final: 0.1911 (ttt180) REVERT: G 1 MET cc_start: 0.4446 (mmp) cc_final: 0.4079 (mmm) REVERT: G 233 ARG cc_start: 0.7861 (mmt180) cc_final: 0.7276 (mmp-170) REVERT: G 252 GLU cc_start: 0.6707 (mm-30) cc_final: 0.5780 (tt0) REVERT: G 265 ASP cc_start: 0.6022 (t0) cc_final: 0.4826 (p0) REVERT: G 271 GLU cc_start: 0.7357 (mt-10) cc_final: 0.7112 (mt-10) REVERT: G 320 LEU cc_start: 0.5384 (tp) cc_final: 0.4696 (mt) REVERT: G 381 LEU cc_start: 0.1244 (OUTLIER) cc_final: 0.0988 (mm) REVERT: G 428 ARG cc_start: 0.3044 (mpt180) cc_final: 0.2844 (mpt-90) REVERT: G 532 LYS cc_start: 0.7471 (mmtt) cc_final: 0.7155 (mmmt) REVERT: G 755 LEU cc_start: 0.0772 (OUTLIER) cc_final: 0.0488 (mm) REVERT: G 760 MET cc_start: 0.5307 (tmm) cc_final: 0.5020 (tmm) REVERT: G 775 LYS cc_start: 0.8449 (mtmt) cc_final: 0.8225 (mtmm) REVERT: G 799 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7479 (mt-10) outliers start: 127 outliers final: 87 residues processed: 373 average time/residue: 0.4032 time to fit residues: 239.9474 Evaluate side-chains 347 residues out of total 3188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 244 time to evaluate : 3.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 389 ASN Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 729 GLN Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 776 GLU Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 811 ASP Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 87 HIS Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 322 GLU Chi-restraints excluded: chain E residue 328 LYS Chi-restraints excluded: chain E residue 353 ILE Chi-restraints excluded: chain E residue 461 VAL Chi-restraints excluded: chain E residue 479 ASP Chi-restraints excluded: chain E residue 501 LEU Chi-restraints excluded: chain E residue 558 THR Chi-restraints excluded: chain E residue 581 ARG Chi-restraints excluded: chain E residue 619 THR Chi-restraints excluded: chain E residue 649 VAL Chi-restraints excluded: chain E residue 701 ASP Chi-restraints excluded: chain E residue 743 THR Chi-restraints excluded: chain E residue 769 LEU Chi-restraints excluded: chain E residue 776 GLU Chi-restraints excluded: chain E residue 807 LYS Chi-restraints excluded: chain E residue 811 ASP Chi-restraints excluded: chain E residue 885 LEU Chi-restraints excluded: chain F residue 15 GLN Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 115 ARG Chi-restraints excluded: chain F residue 125 ASP Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 220 ARG Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 249 GLU Chi-restraints excluded: chain F residue 320 LEU Chi-restraints excluded: chain F residue 431 ILE Chi-restraints excluded: chain F residue 469 ASP Chi-restraints excluded: chain F residue 472 ILE Chi-restraints excluded: chain F residue 515 THR Chi-restraints excluded: chain F residue 542 LEU Chi-restraints excluded: chain F residue 573 SER Chi-restraints excluded: chain F residue 583 PHE Chi-restraints excluded: chain F residue 671 ILE Chi-restraints excluded: chain F residue 676 CYS Chi-restraints excluded: chain F residue 740 ILE Chi-restraints excluded: chain F residue 751 LEU Chi-restraints excluded: chain F residue 755 LEU Chi-restraints excluded: chain F residue 838 ARG Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 228 ILE Chi-restraints excluded: chain G residue 237 GLN Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 354 VAL Chi-restraints excluded: chain G residue 381 LEU Chi-restraints excluded: chain G residue 431 ILE Chi-restraints excluded: chain G residue 469 ASP Chi-restraints excluded: chain G residue 531 THR Chi-restraints excluded: chain G residue 542 LEU Chi-restraints excluded: chain G residue 551 MET Chi-restraints excluded: chain G residue 583 PHE Chi-restraints excluded: chain G residue 592 VAL Chi-restraints excluded: chain G residue 609 LEU Chi-restraints excluded: chain G residue 641 THR Chi-restraints excluded: chain G residue 671 ILE Chi-restraints excluded: chain G residue 687 LEU Chi-restraints excluded: chain G residue 755 LEU Chi-restraints excluded: chain G residue 819 LEU Chi-restraints excluded: chain G residue 843 MET Chi-restraints excluded: chain G residue 864 ASP Chi-restraints excluded: chain G residue 880 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 328 optimal weight: 7.9990 chunk 38 optimal weight: 10.0000 chunk 194 optimal weight: 3.9990 chunk 248 optimal weight: 7.9990 chunk 192 optimal weight: 1.9990 chunk 286 optimal weight: 2.9990 chunk 190 optimal weight: 20.0000 chunk 339 optimal weight: 5.9990 chunk 212 optimal weight: 9.9990 chunk 206 optimal weight: 0.0980 chunk 156 optimal weight: 2.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 133 GLN ** F 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 459 ASN G 237 GLN ** G 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 588 HIS ** G 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 moved from start: 0.4159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 29300 Z= 0.274 Angle : 0.675 9.957 39640 Z= 0.331 Chirality : 0.046 0.547 4472 Planarity : 0.004 0.056 5012 Dihedral : 10.639 154.729 4026 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.55 % Favored : 94.42 % Rotamer: Outliers : 4.36 % Allowed : 22.40 % Favored : 73.24 % 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: -0.32 (0.14), residues: 3532 helix: 0.76 (0.14), residues: 1537 sheet: -0.86 (0.25), residues: 490 loop : -0.93 (0.16), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 273 HIS 0.012 0.001 HIS E 52 PHE 0.020 0.002 PHE F 311 TYR 0.021 0.002 TYR A 591 ARG 0.005 0.000 ARG A 122 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 3188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 268 time to evaluate : 3.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 LEU cc_start: 0.7491 (OUTLIER) cc_final: 0.7249 (tp) REVERT: A 347 LYS cc_start: 0.8154 (tttt) cc_final: 0.7844 (tptm) REVERT: A 696 ILE cc_start: 0.8623 (OUTLIER) cc_final: 0.8189 (mm) REVERT: A 729 GLN cc_start: 0.4222 (OUTLIER) cc_final: 0.3012 (mp10) REVERT: A 776 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.6620 (tm-30) REVERT: E 14 MET cc_start: 0.7599 (ttt) cc_final: 0.7194 (ttm) REVERT: E 137 LEU cc_start: 0.0125 (OUTLIER) cc_final: -0.0152 (mp) REVERT: E 159 ASP cc_start: 0.7301 (OUTLIER) cc_final: 0.6983 (m-30) REVERT: E 501 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7805 (tp) REVERT: E 760 MET cc_start: 0.7247 (mmm) cc_final: 0.7018 (mmm) REVERT: E 776 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.6596 (tm-30) REVERT: E 829 GLU cc_start: 0.5283 (OUTLIER) cc_final: 0.4362 (pm20) REVERT: E 860 GLN cc_start: 0.7537 (tm-30) cc_final: 0.7273 (tt0) REVERT: E 885 LEU cc_start: 0.4615 (OUTLIER) cc_final: 0.4395 (mm) REVERT: F 15 GLN cc_start: 0.2492 (OUTLIER) cc_final: 0.2039 (mm-40) REVERT: F 19 ASP cc_start: 0.3148 (OUTLIER) cc_final: 0.2371 (t70) REVERT: F 315 ASP cc_start: 0.6220 (OUTLIER) cc_final: 0.5438 (t0) REVERT: F 320 LEU cc_start: 0.4984 (OUTLIER) cc_final: 0.4765 (mt) REVERT: F 487 GLN cc_start: 0.5861 (OUTLIER) cc_final: 0.4822 (tm130) REVERT: F 504 GLU cc_start: 0.7946 (pp20) cc_final: 0.7720 (pm20) REVERT: F 532 LYS cc_start: 0.7345 (mmmt) cc_final: 0.6900 (tptp) REVERT: F 588 HIS cc_start: 0.4451 (m90) cc_final: 0.3791 (m170) REVERT: F 617 ILE cc_start: 0.7789 (mt) cc_final: 0.7401 (tp) REVERT: F 639 LEU cc_start: 0.6903 (tt) cc_final: 0.6260 (mt) REVERT: F 689 LYS cc_start: 0.3874 (tttm) cc_final: 0.2914 (mmtm) REVERT: F 747 LYS cc_start: 0.5075 (ttpp) cc_final: 0.4804 (mptt) REVERT: F 755 LEU cc_start: 0.2465 (OUTLIER) cc_final: 0.2235 (mm) REVERT: F 838 ARG cc_start: 0.3062 (OUTLIER) cc_final: 0.1940 (ttt180) REVERT: G 1 MET cc_start: 0.4527 (mmp) cc_final: 0.4171 (mmm) REVERT: G 210 ILE cc_start: 0.7736 (mt) cc_final: 0.7312 (mm) REVERT: G 233 ARG cc_start: 0.7795 (mmt180) cc_final: 0.7183 (mmp-170) REVERT: G 252 GLU cc_start: 0.6868 (mm-30) cc_final: 0.6003 (tt0) REVERT: G 265 ASP cc_start: 0.6180 (t0) cc_final: 0.5014 (p0) REVERT: G 271 GLU cc_start: 0.7422 (mt-10) cc_final: 0.7173 (mt-10) REVERT: G 301 GLN cc_start: 0.5968 (mm-40) cc_final: 0.5601 (tp40) REVERT: G 320 LEU cc_start: 0.5512 (tp) cc_final: 0.4881 (mt) REVERT: G 532 LYS cc_start: 0.7423 (mmtt) cc_final: 0.7123 (mmmt) REVERT: G 755 LEU cc_start: 0.0707 (OUTLIER) cc_final: 0.0417 (mm) REVERT: G 760 MET cc_start: 0.5559 (tmm) cc_final: 0.5295 (tmm) REVERT: G 775 LYS cc_start: 0.8467 (mtmt) cc_final: 0.8236 (mmtp) REVERT: G 799 GLU cc_start: 0.7658 (mt-10) cc_final: 0.6978 (mt-10) outliers start: 139 outliers final: 101 residues processed: 387 average time/residue: 0.3995 time to fit residues: 246.8400 Evaluate side-chains 365 residues out of total 3188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 246 time to evaluate : 3.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 389 ASN Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 479 ASP Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 729 GLN Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 776 GLU Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 811 ASP Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 222 GLU Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 284 ASN Chi-restraints excluded: chain E residue 328 LYS Chi-restraints excluded: chain E residue 353 ILE Chi-restraints excluded: chain E residue 390 CYS Chi-restraints excluded: chain E residue 461 VAL Chi-restraints excluded: chain E residue 469 ASP Chi-restraints excluded: chain E residue 479 ASP Chi-restraints excluded: chain E residue 501 LEU Chi-restraints excluded: chain E residue 558 THR Chi-restraints excluded: chain E residue 581 ARG Chi-restraints excluded: chain E residue 619 THR Chi-restraints excluded: chain E residue 649 VAL Chi-restraints excluded: chain E residue 701 ASP Chi-restraints excluded: chain E residue 743 THR Chi-restraints excluded: chain E residue 769 LEU Chi-restraints excluded: chain E residue 776 GLU Chi-restraints excluded: chain E residue 807 LYS Chi-restraints excluded: chain E residue 811 ASP Chi-restraints excluded: chain E residue 829 GLU Chi-restraints excluded: chain E residue 885 LEU Chi-restraints excluded: chain F residue 15 GLN Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 115 ARG Chi-restraints excluded: chain F residue 125 ASP Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 220 ARG Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain F residue 320 LEU Chi-restraints excluded: chain F residue 431 ILE Chi-restraints excluded: chain F residue 469 ASP Chi-restraints excluded: chain F residue 472 ILE Chi-restraints excluded: chain F residue 487 GLN Chi-restraints excluded: chain F residue 515 THR Chi-restraints excluded: chain F residue 542 LEU Chi-restraints excluded: chain F residue 573 SER Chi-restraints excluded: chain F residue 583 PHE Chi-restraints excluded: chain F residue 671 ILE Chi-restraints excluded: chain F residue 676 CYS Chi-restraints excluded: chain F residue 719 ASN Chi-restraints excluded: chain F residue 740 ILE Chi-restraints excluded: chain F residue 751 LEU Chi-restraints excluded: chain F residue 755 LEU Chi-restraints excluded: chain F residue 838 ARG Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 227 ILE Chi-restraints excluded: chain G residue 228 ILE Chi-restraints excluded: chain G residue 237 GLN Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 431 ILE Chi-restraints excluded: chain G residue 531 THR Chi-restraints excluded: chain G residue 542 LEU Chi-restraints excluded: chain G residue 551 MET Chi-restraints excluded: chain G residue 583 PHE Chi-restraints excluded: chain G residue 592 VAL Chi-restraints excluded: chain G residue 609 LEU Chi-restraints excluded: chain G residue 641 THR Chi-restraints excluded: chain G residue 671 ILE Chi-restraints excluded: chain G residue 687 LEU Chi-restraints excluded: chain G residue 743 THR Chi-restraints excluded: chain G residue 745 LEU Chi-restraints excluded: chain G residue 755 LEU Chi-restraints excluded: chain G residue 819 LEU Chi-restraints excluded: chain G residue 864 ASP Chi-restraints excluded: chain G residue 878 LEU Chi-restraints excluded: chain G residue 880 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 209 optimal weight: 8.9990 chunk 135 optimal weight: 0.8980 chunk 202 optimal weight: 0.2980 chunk 102 optimal weight: 0.0870 chunk 66 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 215 optimal weight: 8.9990 chunk 231 optimal weight: 0.7980 chunk 167 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 266 optimal weight: 10.0000 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 ASN E 380 HIS ** E 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 133 GLN F 284 ASN F 451 ASN F 459 ASN G 237 GLN ** G 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 moved from start: 0.4360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 29300 Z= 0.160 Angle : 0.614 10.066 39640 Z= 0.295 Chirality : 0.044 0.565 4472 Planarity : 0.004 0.051 5012 Dihedral : 10.264 154.227 4024 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.60 % Favored : 96.38 % Rotamer: Outliers : 3.14 % Allowed : 23.71 % Favored : 73.15 % 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: -0.03 (0.15), residues: 3532 helix: 0.90 (0.13), residues: 1564 sheet: -0.54 (0.25), residues: 488 loop : -0.76 (0.17), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A 273 HIS 0.013 0.001 HIS E 87 PHE 0.020 0.001 PHE F 311 TYR 0.010 0.001 TYR G 238 ARG 0.004 0.000 ARG A 122 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 3188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 278 time to evaluate : 3.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.7053 (tp) REVERT: A 290 LEU cc_start: 0.7308 (tp) cc_final: 0.7035 (tt) REVERT: A 347 LYS cc_start: 0.8090 (tttt) cc_final: 0.7846 (tptm) REVERT: A 696 ILE cc_start: 0.8560 (OUTLIER) cc_final: 0.8125 (mm) REVERT: A 729 GLN cc_start: 0.4271 (OUTLIER) cc_final: 0.3462 (mp-120) REVERT: E 14 MET cc_start: 0.7450 (ttt) cc_final: 0.7033 (ttm) REVERT: E 159 ASP cc_start: 0.7307 (OUTLIER) cc_final: 0.7081 (m-30) REVERT: E 319 ILE cc_start: 0.8392 (mt) cc_final: 0.8162 (tp) REVERT: E 501 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7703 (tp) REVERT: E 776 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.6561 (tm-30) REVERT: E 829 GLU cc_start: 0.5300 (OUTLIER) cc_final: 0.4425 (pm20) REVERT: E 860 GLN cc_start: 0.7506 (tm-30) cc_final: 0.7213 (tt0) REVERT: F 15 GLN cc_start: 0.2719 (OUTLIER) cc_final: 0.2268 (mm-40) REVERT: F 19 ASP cc_start: 0.3280 (OUTLIER) cc_final: 0.2409 (t70) REVERT: F 291 LEU cc_start: 0.6371 (OUTLIER) cc_final: 0.5834 (tt) REVERT: F 320 LEU cc_start: 0.4761 (OUTLIER) cc_final: 0.4544 (mt) REVERT: F 383 ASN cc_start: 0.4200 (m-40) cc_final: 0.3890 (m-40) REVERT: F 481 LEU cc_start: 0.6022 (mt) cc_final: 0.5693 (mt) REVERT: F 532 LYS cc_start: 0.7147 (mmmt) cc_final: 0.6761 (tptp) REVERT: F 588 HIS cc_start: 0.4511 (m90) cc_final: 0.3834 (m170) REVERT: F 617 ILE cc_start: 0.7822 (mt) cc_final: 0.7419 (tp) REVERT: F 747 LYS cc_start: 0.4945 (ttpp) cc_final: 0.4711 (mptt) REVERT: F 755 LEU cc_start: 0.2161 (OUTLIER) cc_final: 0.1953 (mm) REVERT: F 838 ARG cc_start: 0.3038 (OUTLIER) cc_final: 0.1934 (ttt180) REVERT: G 1 MET cc_start: 0.4501 (mmp) cc_final: 0.4236 (mmt) REVERT: G 210 ILE cc_start: 0.7638 (mt) cc_final: 0.7236 (mm) REVERT: G 233 ARG cc_start: 0.7766 (mmt180) cc_final: 0.6894 (mmp80) REVERT: G 252 GLU cc_start: 0.6837 (mm-30) cc_final: 0.5947 (tt0) REVERT: G 265 ASP cc_start: 0.6121 (t0) cc_final: 0.4914 (p0) REVERT: G 271 GLU cc_start: 0.7334 (mt-10) cc_final: 0.7082 (mt-10) REVERT: G 292 THR cc_start: 0.6542 (p) cc_final: 0.6195 (p) REVERT: G 320 LEU cc_start: 0.5403 (tp) cc_final: 0.4779 (mt) REVERT: G 481 LEU cc_start: 0.5701 (mt) cc_final: 0.5352 (mt) REVERT: G 532 LYS cc_start: 0.7286 (mmtt) cc_final: 0.7054 (mmmt) REVERT: G 633 MET cc_start: 0.4907 (ptp) cc_final: 0.4406 (mmp) REVERT: G 755 LEU cc_start: 0.0293 (OUTLIER) cc_final: 0.0027 (mm) REVERT: G 799 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7238 (tt0) outliers start: 100 outliers final: 62 residues processed: 358 average time/residue: 0.3874 time to fit residues: 223.2969 Evaluate side-chains 322 residues out of total 3188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 246 time to evaluate : 3.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 52 HIS Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 389 ASN Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 729 GLN Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 811 ASP Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 353 ILE Chi-restraints excluded: chain E residue 461 VAL Chi-restraints excluded: chain E residue 463 VAL Chi-restraints excluded: chain E residue 469 ASP Chi-restraints excluded: chain E residue 501 LEU Chi-restraints excluded: chain E residue 776 GLU Chi-restraints excluded: chain E residue 807 LYS Chi-restraints excluded: chain E residue 811 ASP Chi-restraints excluded: chain E residue 829 GLU Chi-restraints excluded: chain F residue 15 GLN Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 115 ARG Chi-restraints excluded: chain F residue 125 ASP Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 220 ARG Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 320 LEU Chi-restraints excluded: chain F residue 431 ILE Chi-restraints excluded: chain F residue 469 ASP Chi-restraints excluded: chain F residue 472 ILE Chi-restraints excluded: chain F residue 583 PHE Chi-restraints excluded: chain F residue 671 ILE Chi-restraints excluded: chain F residue 676 CYS Chi-restraints excluded: chain F residue 751 LEU Chi-restraints excluded: chain F residue 755 LEU Chi-restraints excluded: chain F residue 838 ARG Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 228 ILE Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain G residue 431 ILE Chi-restraints excluded: chain G residue 542 LEU Chi-restraints excluded: chain G residue 592 VAL Chi-restraints excluded: chain G residue 609 LEU Chi-restraints excluded: chain G residue 671 ILE Chi-restraints excluded: chain G residue 687 LEU Chi-restraints excluded: chain G residue 745 LEU Chi-restraints excluded: chain G residue 755 LEU Chi-restraints excluded: chain G residue 793 LEU Chi-restraints excluded: chain G residue 819 LEU Chi-restraints excluded: chain G residue 843 MET Chi-restraints excluded: chain G residue 878 LEU Chi-restraints excluded: chain G residue 880 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 308 optimal weight: 8.9990 chunk 325 optimal weight: 5.9990 chunk 296 optimal weight: 0.9990 chunk 316 optimal weight: 0.7980 chunk 324 optimal weight: 0.6980 chunk 190 optimal weight: 6.9990 chunk 137 optimal weight: 3.9990 chunk 248 optimal weight: 20.0000 chunk 97 optimal weight: 6.9990 chunk 285 optimal weight: 0.5980 chunk 299 optimal weight: 6.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 478 HIS ** E 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 87 HIS G 234 ASN ** G 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.4537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 29300 Z= 0.203 Angle : 0.628 9.950 39640 Z= 0.302 Chirality : 0.044 0.461 4472 Planarity : 0.004 0.055 5012 Dihedral : 10.130 155.182 4022 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.47 % Favored : 95.50 % Rotamer: Outliers : 3.23 % Allowed : 24.06 % Favored : 72.71 % 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: 0.14 (0.15), residues: 3532 helix: 0.98 (0.14), residues: 1558 sheet: -0.32 (0.25), residues: 486 loop : -0.63 (0.17), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 273 HIS 0.005 0.001 HIS F 818 PHE 0.018 0.001 PHE F 311 TYR 0.017 0.001 TYR A 591 ARG 0.005 0.000 ARG G 578 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 3188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 259 time to evaluate : 3.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 LEU cc_start: 0.7496 (OUTLIER) cc_final: 0.7264 (tp) REVERT: A 290 LEU cc_start: 0.7382 (tp) cc_final: 0.7104 (tt) REVERT: A 347 LYS cc_start: 0.8087 (tttt) cc_final: 0.7832 (tptm) REVERT: A 696 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.8154 (mm) REVERT: A 729 GLN cc_start: 0.4599 (OUTLIER) cc_final: 0.3304 (mp10) REVERT: E 14 MET cc_start: 0.7494 (ttt) cc_final: 0.7094 (ttm) REVERT: E 159 ASP cc_start: 0.7353 (OUTLIER) cc_final: 0.7113 (m-30) REVERT: E 501 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7683 (tp) REVERT: E 776 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.6528 (tm-30) REVERT: E 829 GLU cc_start: 0.5424 (OUTLIER) cc_final: 0.4483 (pm20) REVERT: E 860 GLN cc_start: 0.7529 (tm-30) cc_final: 0.7254 (tt0) REVERT: F 15 GLN cc_start: 0.2744 (OUTLIER) cc_final: 0.2237 (mm-40) REVERT: F 19 ASP cc_start: 0.3139 (OUTLIER) cc_final: 0.2367 (t70) REVERT: F 291 LEU cc_start: 0.6444 (tt) cc_final: 0.5925 (tt) REVERT: F 320 LEU cc_start: 0.4770 (OUTLIER) cc_final: 0.4541 (mt) REVERT: F 383 ASN cc_start: 0.4104 (m-40) cc_final: 0.3821 (m-40) REVERT: F 481 LEU cc_start: 0.6079 (mt) cc_final: 0.5751 (mt) REVERT: F 588 HIS cc_start: 0.4531 (m90) cc_final: 0.3831 (m170) REVERT: F 617 ILE cc_start: 0.7795 (mt) cc_final: 0.7353 (tp) REVERT: F 747 LYS cc_start: 0.4984 (ttpp) cc_final: 0.4735 (mptt) REVERT: F 755 LEU cc_start: 0.2283 (OUTLIER) cc_final: 0.2067 (mm) REVERT: F 776 GLU cc_start: 0.4733 (tt0) cc_final: 0.4367 (tm-30) REVERT: F 838 ARG cc_start: 0.3157 (OUTLIER) cc_final: 0.2007 (ttt180) REVERT: G 67 ARG cc_start: -0.0550 (OUTLIER) cc_final: -0.2034 (mtm180) REVERT: G 233 ARG cc_start: 0.7772 (mmt180) cc_final: 0.6927 (mmp80) REVERT: G 252 GLU cc_start: 0.6892 (mm-30) cc_final: 0.6026 (tt0) REVERT: G 271 GLU cc_start: 0.7399 (mt-10) cc_final: 0.7166 (tt0) REVERT: G 320 LEU cc_start: 0.5488 (tp) cc_final: 0.4858 (mt) REVERT: G 481 LEU cc_start: 0.5641 (mt) cc_final: 0.5280 (mt) REVERT: G 532 LYS cc_start: 0.7259 (mmtt) cc_final: 0.7028 (mmmt) REVERT: G 633 MET cc_start: 0.4938 (ptp) cc_final: 0.4382 (mmp) REVERT: G 755 LEU cc_start: 0.0371 (OUTLIER) cc_final: 0.0064 (mm) REVERT: G 775 LYS cc_start: 0.8448 (mtmt) cc_final: 0.8147 (mmtp) REVERT: G 799 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7004 (tt0) outliers start: 103 outliers final: 69 residues processed: 344 average time/residue: 0.4104 time to fit residues: 226.6017 Evaluate side-chains 332 residues out of total 3188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 249 time to evaluate : 3.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 52 HIS Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 389 ASN Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 729 GLN Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 222 GLU Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 461 VAL Chi-restraints excluded: chain E residue 463 VAL Chi-restraints excluded: chain E residue 469 ASP Chi-restraints excluded: chain E residue 501 LEU Chi-restraints excluded: chain E residue 649 VAL Chi-restraints excluded: chain E residue 776 GLU Chi-restraints excluded: chain E residue 807 LYS Chi-restraints excluded: chain E residue 829 GLU Chi-restraints excluded: chain F residue 15 GLN Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 115 ARG Chi-restraints excluded: chain F residue 125 ASP Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 220 ARG Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 284 ASN Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 320 LEU Chi-restraints excluded: chain F residue 431 ILE Chi-restraints excluded: chain F residue 472 ILE Chi-restraints excluded: chain F residue 515 THR Chi-restraints excluded: chain F residue 676 CYS Chi-restraints excluded: chain F residue 751 LEU Chi-restraints excluded: chain F residue 755 LEU Chi-restraints excluded: chain F residue 838 ARG Chi-restraints excluded: chain G residue 67 ARG Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain G residue 531 THR Chi-restraints excluded: chain G residue 542 LEU Chi-restraints excluded: chain G residue 592 VAL Chi-restraints excluded: chain G residue 609 LEU Chi-restraints excluded: chain G residue 671 ILE Chi-restraints excluded: chain G residue 687 LEU Chi-restraints excluded: chain G residue 743 THR Chi-restraints excluded: chain G residue 745 LEU Chi-restraints excluded: chain G residue 755 LEU Chi-restraints excluded: chain G residue 772 LEU Chi-restraints excluded: chain G residue 843 MET Chi-restraints excluded: chain G residue 878 LEU Chi-restraints excluded: chain G residue 880 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 315 optimal weight: 8.9990 chunk 207 optimal weight: 3.9990 chunk 334 optimal weight: 7.9990 chunk 204 optimal weight: 7.9990 chunk 158 optimal weight: 0.8980 chunk 232 optimal weight: 0.8980 chunk 350 optimal weight: 3.9990 chunk 322 optimal weight: 6.9990 chunk 279 optimal weight: 0.4980 chunk 28 optimal weight: 1.9990 chunk 215 optimal weight: 9.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6873 moved from start: 0.4787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29300 Z= 0.214 Angle : 0.632 9.432 39640 Z= 0.306 Chirality : 0.044 0.457 4472 Planarity : 0.004 0.056 5012 Dihedral : 10.050 155.902 4022 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.61 % Favored : 95.36 % Rotamer: Outliers : 2.82 % Allowed : 24.72 % Favored : 72.46 % 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: 0.11 (0.15), residues: 3532 helix: 0.95 (0.13), residues: 1558 sheet: -0.44 (0.25), residues: 478 loop : -0.60 (0.17), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 273 HIS 0.008 0.001 HIS G 537 PHE 0.023 0.001 PHE E 158 TYR 0.016 0.001 TYR E 591 ARG 0.004 0.000 ARG A 122 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 274 time to evaluate : 3.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.7275 (tp) REVERT: A 290 LEU cc_start: 0.7478 (tp) cc_final: 0.7220 (tt) REVERT: A 297 LYS cc_start: 0.8307 (tttm) cc_final: 0.7976 (mmtp) REVERT: A 347 LYS cc_start: 0.8080 (tttt) cc_final: 0.7874 (tptm) REVERT: A 696 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.8203 (mm) REVERT: A 729 GLN cc_start: 0.4534 (OUTLIER) cc_final: 0.3330 (mp10) REVERT: E 14 MET cc_start: 0.7546 (ttt) cc_final: 0.7160 (ttm) REVERT: E 322 GLU cc_start: 0.8254 (tt0) cc_final: 0.7983 (pt0) REVERT: E 501 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7666 (tp) REVERT: E 776 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.6491 (tm-30) REVERT: E 829 GLU cc_start: 0.5404 (OUTLIER) cc_final: 0.4441 (pm20) REVERT: E 860 GLN cc_start: 0.7630 (tm-30) cc_final: 0.7362 (tt0) REVERT: F 15 GLN cc_start: 0.2630 (OUTLIER) cc_final: 0.2155 (mm-40) REVERT: F 19 ASP cc_start: 0.3107 (OUTLIER) cc_final: 0.2332 (t70) REVERT: F 198 LYS cc_start: 0.6864 (pttt) cc_final: 0.5487 (tptp) REVERT: F 320 LEU cc_start: 0.4747 (OUTLIER) cc_final: 0.4525 (mt) REVERT: F 383 ASN cc_start: 0.4111 (m-40) cc_final: 0.3823 (m-40) REVERT: F 460 LEU cc_start: 0.5566 (mt) cc_final: 0.5256 (mp) REVERT: F 487 GLN cc_start: 0.6006 (OUTLIER) cc_final: 0.5046 (tm130) REVERT: F 588 HIS cc_start: 0.4456 (m90) cc_final: 0.3760 (m170) REVERT: F 617 ILE cc_start: 0.7782 (mt) cc_final: 0.7285 (tp) REVERT: F 747 LYS cc_start: 0.4951 (ttpp) cc_final: 0.4714 (mptt) REVERT: F 755 LEU cc_start: 0.2348 (OUTLIER) cc_final: 0.2135 (mm) REVERT: F 776 GLU cc_start: 0.5153 (tt0) cc_final: 0.4774 (tm-30) REVERT: F 838 ARG cc_start: 0.3213 (OUTLIER) cc_final: 0.2058 (ttt180) REVERT: G 1 MET cc_start: 0.3966 (mmt) cc_final: 0.3702 (mmm) REVERT: G 233 ARG cc_start: 0.7740 (mmt180) cc_final: 0.6938 (mmp80) REVERT: G 252 GLU cc_start: 0.6978 (mm-30) cc_final: 0.6117 (tt0) REVERT: G 271 GLU cc_start: 0.7402 (mt-10) cc_final: 0.7185 (tt0) REVERT: G 320 LEU cc_start: 0.5580 (tp) cc_final: 0.4931 (mt) REVERT: G 481 LEU cc_start: 0.5912 (mt) cc_final: 0.5539 (mt) REVERT: G 532 LYS cc_start: 0.7297 (mmtt) cc_final: 0.7059 (mmmt) REVERT: G 633 MET cc_start: 0.4919 (ptp) cc_final: 0.4293 (mmp) REVERT: G 639 LEU cc_start: 0.6457 (tt) cc_final: 0.5981 (mt) REVERT: G 755 LEU cc_start: 0.0341 (OUTLIER) cc_final: 0.0073 (mm) REVERT: G 775 LYS cc_start: 0.8415 (mtmt) cc_final: 0.8159 (mmtt) REVERT: G 799 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7076 (tt0) outliers start: 90 outliers final: 66 residues processed: 347 average time/residue: 0.3996 time to fit residues: 221.6874 Evaluate side-chains 336 residues out of total 3188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 257 time to evaluate : 2.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 52 HIS Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 389 ASN Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 729 GLN Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 222 GLU Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 461 VAL Chi-restraints excluded: chain E residue 463 VAL Chi-restraints excluded: chain E residue 469 ASP Chi-restraints excluded: chain E residue 501 LEU Chi-restraints excluded: chain E residue 649 VAL Chi-restraints excluded: chain E residue 776 GLU Chi-restraints excluded: chain E residue 807 LYS Chi-restraints excluded: chain E residue 829 GLU Chi-restraints excluded: chain F residue 15 GLN Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 115 ARG Chi-restraints excluded: chain F residue 125 ASP Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 220 ARG Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 284 ASN Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 320 LEU Chi-restraints excluded: chain F residue 431 ILE Chi-restraints excluded: chain F residue 472 ILE Chi-restraints excluded: chain F residue 487 GLN Chi-restraints excluded: chain F residue 515 THR Chi-restraints excluded: chain F residue 676 CYS Chi-restraints excluded: chain F residue 751 LEU Chi-restraints excluded: chain F residue 755 LEU Chi-restraints excluded: chain F residue 838 ARG Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain G residue 531 THR Chi-restraints excluded: chain G residue 542 LEU Chi-restraints excluded: chain G residue 592 VAL Chi-restraints excluded: chain G residue 609 LEU Chi-restraints excluded: chain G residue 671 ILE Chi-restraints excluded: chain G residue 687 LEU Chi-restraints excluded: chain G residue 743 THR Chi-restraints excluded: chain G residue 755 LEU Chi-restraints excluded: chain G residue 772 LEU Chi-restraints excluded: chain G residue 843 MET Chi-restraints excluded: chain G residue 880 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 171 optimal weight: 0.8980 chunk 221 optimal weight: 6.9990 chunk 297 optimal weight: 0.0010 chunk 85 optimal weight: 1.9990 chunk 257 optimal weight: 6.9990 chunk 41 optimal weight: 0.0570 chunk 77 optimal weight: 6.9990 chunk 279 optimal weight: 7.9990 chunk 117 optimal weight: 6.9990 chunk 287 optimal weight: 8.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.7908 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 ASN ** E 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4851 r_free = 0.4851 target = 0.241724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.193451 restraints weight = 50162.767| |-----------------------------------------------------------------------------| r_work (start): 0.4339 rms_B_bonded: 3.87 r_work: 0.4037 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.4962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 29300 Z= 0.166 Angle : 0.609 9.231 39640 Z= 0.293 Chirality : 0.043 0.452 4472 Planarity : 0.004 0.054 5012 Dihedral : 9.754 155.404 4022 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.02 % Favored : 95.95 % Rotamer: Outliers : 2.42 % Allowed : 25.47 % Favored : 72.11 % 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: 0.35 (0.15), residues: 3532 helix: 1.16 (0.14), residues: 1544 sheet: -0.27 (0.26), residues: 470 loop : -0.49 (0.17), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP A 273 HIS 0.005 0.001 HIS E 307 PHE 0.018 0.001 PHE F 311 TYR 0.011 0.001 TYR A 197 ARG 0.004 0.000 ARG G 578 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6573.48 seconds wall clock time: 118 minutes 19.39 seconds (7099.39 seconds total)