Starting phenix.real_space_refine on Sat Jul 27 00:52:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wyb_37922/07_2024/8wyb_37922_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wyb_37922/07_2024/8wyb_37922.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wyb_37922/07_2024/8wyb_37922.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wyb_37922/07_2024/8wyb_37922.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wyb_37922/07_2024/8wyb_37922_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wyb_37922/07_2024/8wyb_37922_neut.cif" } resolution = 3.37 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= 0.001 sd= 0.048 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 8 5.49 5 S 132 5.16 5 C 23014 2.51 5 N 5724 2.21 5 O 6726 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 28": "OE1" <-> "OE2" Residue "A GLU 32": "OE1" <-> "OE2" Residue "A GLU 83": "OE1" <-> "OE2" Residue "A GLU 155": "OE1" <-> "OE2" Residue "A PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 341": "OE1" <-> "OE2" Residue "A GLU 379": "OE1" <-> "OE2" Residue "A TYR 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 433": "OE1" <-> "OE2" Residue "A GLU 516": "OE1" <-> "OE2" Residue "A GLU 534": "OE1" <-> "OE2" Residue "A GLU 597": "OE1" <-> "OE2" Residue "A GLU 648": "OE1" <-> "OE2" Residue "A GLU 680": "OE1" <-> "OE2" Residue "A GLU 686": "OE1" <-> "OE2" Residue "A GLU 731": "OE1" <-> "OE2" Residue "A GLU 876": "OE1" <-> "OE2" Residue "B GLU 28": "OE1" <-> "OE2" Residue "B GLU 35": "OE1" <-> "OE2" Residue "B GLU 83": "OE1" <-> "OE2" Residue "B GLU 156": "OE1" <-> "OE2" Residue "B GLU 187": "OE1" <-> "OE2" Residue "B GLU 279": "OE1" <-> "OE2" Residue "B GLU 307": "OE1" <-> "OE2" Residue "B GLU 335": "OE1" <-> "OE2" Residue "B GLU 341": "OE1" <-> "OE2" Residue "B GLU 365": "OE1" <-> "OE2" Residue "B GLU 369": "OE1" <-> "OE2" Residue "B GLU 379": "OE1" <-> "OE2" Residue "B GLU 389": "OE1" <-> "OE2" Residue "B GLU 408": "OE1" <-> "OE2" Residue "B GLU 450": "OE1" <-> "OE2" Residue "B GLU 510": "OE1" <-> "OE2" Residue "B GLU 543": "OE1" <-> "OE2" Residue "B GLU 648": "OE1" <-> "OE2" Residue "B GLU 680": "OE1" <-> "OE2" Residue "B GLU 682": "OE1" <-> "OE2" Residue "B GLU 686": "OE1" <-> "OE2" Residue "B GLU 693": "OE1" <-> "OE2" Residue "B GLU 730": "OE1" <-> "OE2" Residue "B GLU 746": "OE1" <-> "OE2" Residue "B GLU 784": "OE1" <-> "OE2" Residue "B GLU 822": "OE1" <-> "OE2" Residue "C GLU 32": "OE1" <-> "OE2" Residue "C GLU 68": "OE1" <-> "OE2" Residue "C GLU 83": "OE1" <-> "OE2" Residue "C GLU 256": "OE1" <-> "OE2" Residue "C GLU 262": "OE1" <-> "OE2" Residue "C GLU 284": "OE1" <-> "OE2" Residue "C GLU 295": "OE1" <-> "OE2" Residue "C GLU 358": "OE1" <-> "OE2" Residue "C GLU 369": "OE1" <-> "OE2" Residue "C GLU 389": "OE1" <-> "OE2" Residue "C GLU 426": "OE1" <-> "OE2" Residue "C GLU 427": "OE1" <-> "OE2" Residue "C GLU 450": "OE1" <-> "OE2" Residue "C GLU 510": "OE1" <-> "OE2" Residue "C GLU 516": "OE1" <-> "OE2" Residue "C GLU 568": "OE1" <-> "OE2" Residue "C GLU 607": "OE1" <-> "OE2" Residue "C GLU 668": "OE1" <-> "OE2" Residue "C GLU 686": "OE1" <-> "OE2" Residue "C GLU 812": "OE1" <-> "OE2" Residue "C GLU 890": "OE1" <-> "OE2" Residue "D GLU 32": "OE1" <-> "OE2" Residue "D GLU 35": "OE1" <-> "OE2" Residue "D GLU 69": "OE1" <-> "OE2" Residue "D GLU 97": "OE1" <-> "OE2" Residue "D GLU 187": "OE1" <-> "OE2" Residue "D GLU 284": "OE1" <-> "OE2" Residue "D PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 335": "OE1" <-> "OE2" Residue "D GLU 379": "OE1" <-> "OE2" Residue "D GLU 426": "OE1" <-> "OE2" Residue "D GLU 516": "OE1" <-> "OE2" Residue "D GLU 560": "OE1" <-> "OE2" Residue "D GLU 568": "OE1" <-> "OE2" Residue "D GLU 686": "OE1" <-> "OE2" Residue "D GLU 693": "OE1" <-> "OE2" Residue "D GLU 715": "OE1" <-> "OE2" Residue "D GLU 986": "OE1" <-> "OE2" Residue "E GLU 26": "OE1" <-> "OE2" Residue "E GLU 172": "OE1" <-> "OE2" Residue "E GLU 203": "OE1" <-> "OE2" Residue "E GLU 205": "OE1" <-> "OE2" Residue "E GLU 209": "OE1" <-> "OE2" Residue "E GLU 217": "OE1" <-> "OE2" Residue "E GLU 221": "OE1" <-> "OE2" Residue "E GLU 230": "OE1" <-> "OE2" Residue "F GLU 26": "OE1" <-> "OE2" Residue "F GLU 58": "OE1" <-> "OE2" Residue "F GLU 209": "OE1" <-> "OE2" Residue "F GLU 217": "OE1" <-> "OE2" Residue "F GLU 236": "OE1" <-> "OE2" Residue "G GLU 26": "OE1" <-> "OE2" Residue "G GLU 203": "OE1" <-> "OE2" Residue "H GLU 58": "OE1" <-> "OE2" Residue "H GLU 172": "OE1" <-> "OE2" Residue "H GLU 203": "OE1" <-> "OE2" Residue "H GLU 230": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 35604 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 952, 7940 Classifications: {'peptide': 952} Link IDs: {'PTRANS': 19, 'TRANS': 932} Chain breaks: 6 Chain: "B" Number of atoms: 7948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 952, 7948 Classifications: {'peptide': 952} Link IDs: {'PTRANS': 19, 'TRANS': 932} Chain breaks: 6 Chain: "C" Number of atoms: 7915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 948, 7915 Classifications: {'peptide': 948} Link IDs: {'PTRANS': 18, 'TRANS': 929} Chain breaks: 7 Chain: "D" Number of atoms: 7921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 949, 7921 Classifications: {'peptide': 949} Link IDs: {'PTRANS': 19, 'TRANS': 929} Chain breaks: 7 Chain: "E" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 939 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain breaks: 4 Chain: "F" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 913 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain breaks: 5 Chain: "G" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 939 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain breaks: 4 Chain: "H" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 913 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain breaks: 5 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 20.30, per 1000 atoms: 0.57 Number of scatterers: 35604 At special positions: 0 Unit cell: (100.067, 130.666, 258.851, 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 132 16.00 P 8 15.00 O 6726 8.00 N 5724 7.00 C 23014 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: 13.47 Conformation dependent library (CDL) restraints added in 6.1 seconds 8310 Ramachandran restraints generated. 4155 Oldfield, 0 Emsley, 4155 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8140 Finding SS restraints... Secondary structure from input PDB file: 245 helices and 14 sheets defined 65.1% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.20 Creating SS restraints... Processing helix chain 'A' and resid 23 through 39 removed outlier: 3.556A pdb=" N VAL A 27 " --> pdb=" O ASP A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 53 removed outlier: 4.035A pdb=" N SER A 51 " --> pdb=" O GLY A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 72 Processing helix chain 'A' and resid 80 through 96 Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 96 through 109 removed outlier: 3.535A pdb=" N PHE A 100 " --> pdb=" O GLY A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 124 removed outlier: 3.798A pdb=" N ASP A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N MET A 124 " --> pdb=" O LYS A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 145 Processing helix chain 'A' and resid 154 through 158 removed outlier: 3.505A pdb=" N ASP A 157 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL A 158 " --> pdb=" O GLU A 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 154 through 158' Processing helix chain 'A' and resid 186 through 192 Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 197 through 211 Processing helix chain 'A' and resid 222 through 234 removed outlier: 3.807A pdb=" N LYS A 234 " --> pdb=" O ASN A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 263 Processing helix chain 'A' and resid 271 through 275 Processing helix chain 'A' and resid 281 through 295 removed outlier: 3.668A pdb=" N VAL A 289 " --> pdb=" O ARG A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 317 removed outlier: 3.837A pdb=" N ASP A 310 " --> pdb=" O ASP A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 322 Processing helix chain 'A' and resid 326 through 334 Processing helix chain 'A' and resid 355 through 365 removed outlier: 3.501A pdb=" N ARG A 359 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU A 362 " --> pdb=" O GLU A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 373 removed outlier: 3.533A pdb=" N LYS A 372 " --> pdb=" O GLU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 391 Processing helix chain 'A' and resid 419 through 427 Processing helix chain 'A' and resid 431 through 445 removed outlier: 3.717A pdb=" N LYS A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS A 438 " --> pdb=" O ASP A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 462 Processing helix chain 'A' and resid 463 through 465 No H-bonds generated for 'chain 'A' and resid 463 through 465' Processing helix chain 'A' and resid 468 through 494 Processing helix chain 'A' and resid 494 through 499 removed outlier: 3.536A pdb=" N LEU A 498 " --> pdb=" O GLY A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 524 through 528 removed outlier: 4.153A pdb=" N PHE A 528 " --> pdb=" O ASP A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 539 Processing helix chain 'A' and resid 540 through 547 removed outlier: 4.169A pdb=" N PHE A 544 " --> pdb=" O ILE A 541 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP A 547 " --> pdb=" O PHE A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 572 Processing helix chain 'A' and resid 579 through 598 Processing helix chain 'A' and resid 600 through 604 Processing helix chain 'A' and resid 605 through 616 Processing helix chain 'A' and resid 618 through 628 Processing helix chain 'A' and resid 648 through 659 Processing helix chain 'A' and resid 660 through 671 Processing helix chain 'A' and resid 680 through 701 Processing helix chain 'A' and resid 705 through 723 removed outlier: 3.819A pdb=" N GLN A 711 " --> pdb=" O VAL A 707 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N SER A 714 " --> pdb=" O THR A 710 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLU A 715 " --> pdb=" O GLN A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 742 Processing helix chain 'A' and resid 750 through 765 removed outlier: 4.178A pdb=" N CYS A 764 " --> pdb=" O ARG A 760 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASN A 765 " --> pdb=" O LEU A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 786 Processing helix chain 'A' and resid 801 through 813 removed outlier: 3.701A pdb=" N GLY A 805 " --> pdb=" O SER A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 826 Processing helix chain 'A' and resid 831 through 841 removed outlier: 3.502A pdb=" N ILE A 835 " --> pdb=" O LYS A 831 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LYS A 840 " --> pdb=" O ASP A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 845 Processing helix chain 'A' and resid 846 through 857 removed outlier: 3.581A pdb=" N SER A 855 " --> pdb=" O SER A 851 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N PHE A 856 " --> pdb=" O HIS A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 872 Processing helix chain 'A' and resid 878 through 897 Processing helix chain 'A' and resid 911 through 922 Processing helix chain 'A' and resid 929 through 934 Processing helix chain 'A' and resid 940 through 945 removed outlier: 3.526A pdb=" N ASP A 945 " --> pdb=" O ASP A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 949 removed outlier: 3.630A pdb=" N PHE A 949 " --> pdb=" O PRO A 946 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 946 through 949' Processing helix chain 'A' and resid 950 through 954 Processing helix chain 'A' and resid 955 through 956 No H-bonds generated for 'chain 'A' and resid 955 through 956' Processing helix chain 'A' and resid 957 through 962 removed outlier: 4.163A pdb=" N ASN A 961 " --> pdb=" O SER A 957 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR A 962 " --> pdb=" O TRP A 958 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 957 through 962' Processing helix chain 'A' and resid 963 through 974 removed outlier: 4.414A pdb=" N LYS A 974 " --> pdb=" O ILE A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 991 removed outlier: 3.830A pdb=" N VAL A 980 " --> pdb=" O MET A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1003 Processing helix chain 'B' and resid 24 through 39 Processing helix chain 'B' and resid 47 through 54 removed outlier: 4.128A pdb=" N SER B 51 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER B 54 " --> pdb=" O VAL B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 72 removed outlier: 3.599A pdb=" N LEU B 62 " --> pdb=" O GLN B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 96 Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 96 through 109 Processing helix chain 'B' and resid 115 through 124 removed outlier: 3.927A pdb=" N ASP B 119 " --> pdb=" O ASN B 115 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N MET B 124 " --> pdb=" O LYS B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 146 Processing helix chain 'B' and resid 154 through 160 removed outlier: 3.855A pdb=" N VAL B 158 " --> pdb=" O ALA B 154 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN B 160 " --> pdb=" O GLU B 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 154 through 160' Processing helix chain 'B' and resid 179 through 183 removed outlier: 3.633A pdb=" N ASN B 182 " --> pdb=" O LYS B 179 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL B 183 " --> pdb=" O GLY B 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 179 through 183' Processing helix chain 'B' and resid 186 through 192 Processing helix chain 'B' and resid 192 through 197 Processing helix chain 'B' and resid 197 through 211 Processing helix chain 'B' and resid 222 through 235 removed outlier: 3.618A pdb=" N LYS B 234 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU B 235 " --> pdb=" O TRP B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 264 Processing helix chain 'B' and resid 271 through 275 Processing helix chain 'B' and resid 282 through 296 Processing helix chain 'B' and resid 297 through 301 removed outlier: 3.822A pdb=" N PHE B 301 " --> pdb=" O GLU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 317 removed outlier: 3.534A pdb=" N ASP B 310 " --> pdb=" O ASP B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 322 Processing helix chain 'B' and resid 326 through 328 No H-bonds generated for 'chain 'B' and resid 326 through 328' Processing helix chain 'B' and resid 329 through 334 removed outlier: 3.761A pdb=" N VAL B 333 " --> pdb=" O ASP B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 365 removed outlier: 3.553A pdb=" N ARG B 359 " --> pdb=" O GLY B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 373 Processing helix chain 'B' and resid 374 through 391 removed outlier: 3.612A pdb=" N ALA B 383 " --> pdb=" O GLU B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 427 Processing helix chain 'B' and resid 431 through 445 Processing helix chain 'B' and resid 447 through 462 Processing helix chain 'B' and resid 468 through 501 removed outlier: 4.679A pdb=" N LEU B 497 " --> pdb=" O ASN B 493 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEU B 498 " --> pdb=" O GLY B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 520 Processing helix chain 'B' and resid 524 through 528 removed outlier: 4.112A pdb=" N PHE B 528 " --> pdb=" O ASP B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 539 Processing helix chain 'B' and resid 542 through 547 removed outlier: 3.796A pdb=" N SER B 546 " --> pdb=" O LEU B 542 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASP B 547 " --> pdb=" O GLU B 543 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 542 through 547' Processing helix chain 'B' and resid 551 through 572 Processing helix chain 'B' and resid 579 through 598 removed outlier: 3.550A pdb=" N GLU B 597 " --> pdb=" O ARG B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 604 Processing helix chain 'B' and resid 605 through 616 Processing helix chain 'B' and resid 618 through 628 removed outlier: 3.566A pdb=" N THR B 628 " --> pdb=" O GLU B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 659 Processing helix chain 'B' and resid 660 through 671 Processing helix chain 'B' and resid 672 through 676 removed outlier: 4.107A pdb=" N LYS B 675 " --> pdb=" O SER B 672 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE B 676 " --> pdb=" O ILE B 673 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 672 through 676' Processing helix chain 'B' and resid 680 through 701 removed outlier: 4.240A pdb=" N ALA B 701 " --> pdb=" O LYS B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 723 removed outlier: 4.731A pdb=" N SER B 714 " --> pdb=" O THR B 710 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLU B 715 " --> pdb=" O GLN B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 726 No H-bonds generated for 'chain 'B' and resid 724 through 726' Processing helix chain 'B' and resid 729 through 742 Processing helix chain 'B' and resid 750 through 762 Processing helix chain 'B' and resid 768 through 786 Processing helix chain 'B' and resid 800 through 813 Processing helix chain 'B' and resid 817 through 827 Processing helix chain 'B' and resid 831 through 839 Processing helix chain 'B' and resid 840 through 845 Proline residue: B 843 - end of helix No H-bonds generated for 'chain 'B' and resid 840 through 845' Processing helix chain 'B' and resid 846 through 857 removed outlier: 3.986A pdb=" N PHE B 856 " --> pdb=" O HIS B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 871 removed outlier: 3.521A pdb=" N LEU B 865 " --> pdb=" O ASN B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 878 through 897 Processing helix chain 'B' and resid 911 through 922 Processing helix chain 'B' and resid 929 through 934 Processing helix chain 'B' and resid 940 through 945 Processing helix chain 'B' and resid 946 through 949 Processing helix chain 'B' and resid 950 through 954 Processing helix chain 'B' and resid 955 through 956 No H-bonds generated for 'chain 'B' and resid 955 through 956' Processing helix chain 'B' and resid 957 through 962 removed outlier: 3.714A pdb=" N ASN B 961 " --> pdb=" O SER B 957 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR B 962 " --> pdb=" O TRP B 958 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 957 through 962' Processing helix chain 'B' and resid 963 through 974 removed outlier: 4.524A pdb=" N LYS B 974 " --> pdb=" O ILE B 970 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 991 removed outlier: 3.577A pdb=" N VAL B 980 " --> pdb=" O MET B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 994 through 1004 removed outlier: 3.652A pdb=" N GLU B 998 " --> pdb=" O LYS B 994 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR B1003 " --> pdb=" O ILE B 999 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 39 Processing helix chain 'C' and resid 47 through 53 removed outlier: 3.794A pdb=" N SER C 51 " --> pdb=" O GLY C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 71 Processing helix chain 'C' and resid 82 through 108 Proline residue: C 88 - end of helix removed outlier: 7.152A pdb=" N GLU C 97 " --> pdb=" O ASN C 93 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N MET C 98 " --> pdb=" O VAL C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 124 removed outlier: 3.574A pdb=" N ASP C 119 " --> pdb=" O ASN C 115 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET C 124 " --> pdb=" O LYS C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 146 Processing helix chain 'C' and resid 186 through 192 Processing helix chain 'C' and resid 192 through 197 Processing helix chain 'C' and resid 197 through 211 Processing helix chain 'C' and resid 222 through 235 removed outlier: 4.133A pdb=" N LYS C 234 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU C 235 " --> pdb=" O TRP C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 263 removed outlier: 3.543A pdb=" N ASN C 263 " --> pdb=" O ILE C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 275 Processing helix chain 'C' and resid 281 through 298 Processing helix chain 'C' and resid 306 through 317 removed outlier: 3.748A pdb=" N ASP C 310 " --> pdb=" O ASP C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 322 removed outlier: 3.517A pdb=" N ALA C 321 " --> pdb=" O PRO C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 334 Processing helix chain 'C' and resid 355 through 365 removed outlier: 3.807A pdb=" N ARG C 359 " --> pdb=" O GLY C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 373 Processing helix chain 'C' and resid 374 through 392 Processing helix chain 'C' and resid 411 through 416 Processing helix chain 'C' and resid 419 through 427 Processing helix chain 'C' and resid 431 through 445 removed outlier: 3.785A pdb=" N LYS C 437 " --> pdb=" O GLU C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 462 Processing helix chain 'C' and resid 463 through 465 No H-bonds generated for 'chain 'C' and resid 463 through 465' Processing helix chain 'C' and resid 468 through 494 Processing helix chain 'C' and resid 494 through 499 removed outlier: 3.748A pdb=" N LEU C 498 " --> pdb=" O GLY C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 519 Processing helix chain 'C' and resid 523 through 528 removed outlier: 4.136A pdb=" N PHE C 528 " --> pdb=" O ILE C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 539 Processing helix chain 'C' and resid 542 through 547 removed outlier: 3.638A pdb=" N SER C 546 " --> pdb=" O LEU C 542 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASP C 547 " --> pdb=" O GLU C 543 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 542 through 547' Processing helix chain 'C' and resid 551 through 572 Processing helix chain 'C' and resid 579 through 598 Processing helix chain 'C' and resid 600 through 604 removed outlier: 3.601A pdb=" N VAL C 603 " --> pdb=" O LEU C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 616 Processing helix chain 'C' and resid 618 through 628 Processing helix chain 'C' and resid 648 through 659 Processing helix chain 'C' and resid 660 through 671 Processing helix chain 'C' and resid 680 through 700 Processing helix chain 'C' and resid 705 through 723 removed outlier: 3.914A pdb=" N GLN C 711 " --> pdb=" O VAL C 707 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N SER C 714 " --> pdb=" O THR C 710 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU C 715 " --> pdb=" O GLN C 711 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA C 718 " --> pdb=" O SER C 714 " (cutoff:3.500A) Processing helix chain 'C' and resid 729 through 742 Processing helix chain 'C' and resid 750 through 765 removed outlier: 4.281A pdb=" N CYS C 764 " --> pdb=" O ARG C 760 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ASN C 765 " --> pdb=" O LEU C 761 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 786 Processing helix chain 'C' and resid 801 through 813 removed outlier: 3.577A pdb=" N GLY C 805 " --> pdb=" O SER C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 826 Processing helix chain 'C' and resid 831 through 841 removed outlier: 3.801A pdb=" N ILE C 835 " --> pdb=" O LYS C 831 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS C 840 " --> pdb=" O ASP C 836 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU C 841 " --> pdb=" O PHE C 837 " (cutoff:3.500A) Processing helix chain 'C' and resid 842 through 845 Processing helix chain 'C' and resid 846 through 857 removed outlier: 4.279A pdb=" N PHE C 856 " --> pdb=" O HIS C 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 861 through 871 removed outlier: 3.584A pdb=" N LEU C 865 " --> pdb=" O ASN C 861 " (cutoff:3.500A) Processing helix chain 'C' and resid 878 through 897 Processing helix chain 'C' and resid 911 through 922 Processing helix chain 'C' and resid 929 through 934 Processing helix chain 'C' and resid 940 through 945 removed outlier: 3.606A pdb=" N ASP C 945 " --> pdb=" O ASP C 941 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 949 removed outlier: 3.649A pdb=" N PHE C 949 " --> pdb=" O PRO C 946 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 946 through 949' Processing helix chain 'C' and resid 950 through 954 Processing helix chain 'C' and resid 955 through 956 No H-bonds generated for 'chain 'C' and resid 955 through 956' Processing helix chain 'C' and resid 957 through 962 removed outlier: 4.173A pdb=" N ASN C 961 " --> pdb=" O SER C 957 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR C 962 " --> pdb=" O TRP C 958 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 957 through 962' Processing helix chain 'C' and resid 963 through 972 Processing helix chain 'C' and resid 976 through 991 removed outlier: 3.715A pdb=" N VAL C 980 " --> pdb=" O MET C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 994 through 1004 Processing helix chain 'D' and resid 26 through 40 Processing helix chain 'D' and resid 47 through 54 removed outlier: 3.917A pdb=" N SER D 51 " --> pdb=" O GLY D 47 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER D 54 " --> pdb=" O VAL D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 71 removed outlier: 3.606A pdb=" N LEU D 62 " --> pdb=" O GLN D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 95 Proline residue: D 88 - end of helix Processing helix chain 'D' and resid 96 through 109 removed outlier: 3.606A pdb=" N PHE D 100 " --> pdb=" O GLY D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 124 removed outlier: 3.993A pdb=" N ASP D 119 " --> pdb=" O ASN D 115 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 Processing helix chain 'D' and resid 154 through 158 Processing helix chain 'D' and resid 186 through 192 Processing helix chain 'D' and resid 192 through 197 Processing helix chain 'D' and resid 197 through 211 Processing helix chain 'D' and resid 222 through 235 Processing helix chain 'D' and resid 254 through 264 Processing helix chain 'D' and resid 271 through 275 removed outlier: 3.603A pdb=" N ILE D 275 " --> pdb=" O ALA D 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 271 through 275' Processing helix chain 'D' and resid 282 through 295 removed outlier: 3.712A pdb=" N VAL D 289 " --> pdb=" O ARG D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 317 Processing helix chain 'D' and resid 318 through 322 removed outlier: 3.552A pdb=" N ALA D 321 " --> pdb=" O PRO D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 333 removed outlier: 3.575A pdb=" N LYS D 331 " --> pdb=" O ILE D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 365 Processing helix chain 'D' and resid 369 through 373 Processing helix chain 'D' and resid 374 through 392 removed outlier: 3.750A pdb=" N ALA D 383 " --> pdb=" O GLU D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 427 removed outlier: 3.534A pdb=" N GLU D 427 " --> pdb=" O LYS D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 445 Processing helix chain 'D' and resid 447 through 462 Processing helix chain 'D' and resid 468 through 495 removed outlier: 3.623A pdb=" N TYR D 472 " --> pdb=" O GLY D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 501 Processing helix chain 'D' and resid 508 through 520 Processing helix chain 'D' and resid 525 through 530 removed outlier: 4.420A pdb=" N ASN D 529 " --> pdb=" O ASP D 525 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 539 Processing helix chain 'D' and resid 542 through 547 removed outlier: 3.571A pdb=" N SER D 546 " --> pdb=" O LEU D 542 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASP D 547 " --> pdb=" O GLU D 543 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 542 through 547' Processing helix chain 'D' and resid 551 through 572 Processing helix chain 'D' and resid 579 through 596 Processing helix chain 'D' and resid 600 through 604 removed outlier: 3.532A pdb=" N VAL D 603 " --> pdb=" O LEU D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 616 Processing helix chain 'D' and resid 618 through 628 Processing helix chain 'D' and resid 648 through 659 Processing helix chain 'D' and resid 660 through 671 Processing helix chain 'D' and resid 680 through 701 removed outlier: 4.164A pdb=" N ALA D 701 " --> pdb=" O LYS D 697 " (cutoff:3.500A) Processing helix chain 'D' and resid 705 through 723 removed outlier: 3.578A pdb=" N GLN D 711 " --> pdb=" O VAL D 707 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N SER D 714 " --> pdb=" O THR D 710 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLU D 715 " --> pdb=" O GLN D 711 " (cutoff:3.500A) Processing helix chain 'D' and resid 724 through 726 No H-bonds generated for 'chain 'D' and resid 724 through 726' Processing helix chain 'D' and resid 729 through 742 Processing helix chain 'D' and resid 750 through 765 removed outlier: 4.424A pdb=" N CYS D 764 " --> pdb=" O ARG D 760 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASN D 765 " --> pdb=" O LEU D 761 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 786 Processing helix chain 'D' and resid 800 through 813 removed outlier: 3.576A pdb=" N TYR D 804 " --> pdb=" O TYR D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 817 through 827 Processing helix chain 'D' and resid 831 through 839 Processing helix chain 'D' and resid 841 through 845 Processing helix chain 'D' and resid 846 through 857 removed outlier: 4.019A pdb=" N PHE D 856 " --> pdb=" O HIS D 852 " (cutoff:3.500A) Processing helix chain 'D' and resid 861 through 871 Processing helix chain 'D' and resid 878 through 897 Processing helix chain 'D' and resid 912 through 922 Processing helix chain 'D' and resid 929 through 934 Processing helix chain 'D' and resid 940 through 945 Processing helix chain 'D' and resid 946 through 949 Processing helix chain 'D' and resid 950 through 954 Processing helix chain 'D' and resid 955 through 961 Processing helix chain 'D' and resid 963 through 974 removed outlier: 4.405A pdb=" N LYS D 974 " --> pdb=" O ILE D 970 " (cutoff:3.500A) Processing helix chain 'D' and resid 976 through 991 removed outlier: 3.750A pdb=" N VAL D 980 " --> pdb=" O MET D 976 " (cutoff:3.500A) Processing helix chain 'D' and resid 994 through 1003 removed outlier: 3.585A pdb=" N GLU D 998 " --> pdb=" O LYS D 994 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR D1003 " --> pdb=" O ILE D 999 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 77 Processing helix chain 'F' and resid 69 through 77 Processing helix chain 'G' and resid 69 through 77 Processing helix chain 'H' and resid 69 through 77 Processing sheet with id=AA1, first strand: chain 'A' and resid 150 through 152 removed outlier: 6.287A pdb=" N SER A 150 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N LYS A 169 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE A 152 " --> pdb=" O LYS A 169 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N HIS A 128 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE A 245 " --> pdb=" O ARG A 267 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 339 through 340 Processing sheet with id=AA3, first strand: chain 'A' and resid 574 through 575 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 574 through 575 current: chain 'E' and resid 21 through 32 removed outlier: 6.788A pdb=" N THR E 62 " --> pdb=" O GLN E 28 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ALA E 30 " --> pdb=" O ASN E 60 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ASN E 60 " --> pdb=" O ALA E 30 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 59 through 63 current: chain 'E' and resid 192 through 200 Processing sheet with id=AA4, first strand: chain 'A' and resid 906 through 908 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 906 through 908 current: chain 'F' and resid 21 through 35 removed outlier: 8.716A pdb=" N VAL F 22 " --> pdb=" O PHE F 68 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N PHE F 68 " --> pdb=" O VAL F 22 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N THR F 24 " --> pdb=" O ALA F 66 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ALA F 66 " --> pdb=" O THR F 24 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N THR F 62 " --> pdb=" O GLN F 28 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ALA F 30 " --> pdb=" O ASN F 60 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ASN F 60 " --> pdb=" O ALA F 30 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N PHE F 32 " --> pdb=" O GLU F 58 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N GLU F 58 " --> pdb=" O PHE F 32 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N GLN F 34 " --> pdb=" O GLU F 56 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLU F 56 " --> pdb=" O GLN F 34 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 56 through 68 current: chain 'F' and resid 193 through 196 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 193 through 196 current: chain 'F' and resid 218 through 222 Processing sheet with id=AA5, first strand: chain 'B' and resid 150 through 152 removed outlier: 6.932A pdb=" N LEU B 42 " --> pdb=" O HIS B 128 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N ILE B 130 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N PHE B 44 " --> pdb=" O ILE B 130 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ILE B 213 " --> pdb=" O PHE B 244 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N ILE B 246 " --> pdb=" O ILE B 213 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N PHE B 215 " --> pdb=" O ILE B 246 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N PHE B 245 " --> pdb=" O ILE B 269 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 338 through 340 Processing sheet with id=AA7, first strand: chain 'B' and resid 794 through 795 removed outlier: 3.623A pdb=" N SER B 795 " --> pdb=" O ALA E 224 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 128 through 131 removed outlier: 3.869A pdb=" N HIS C 128 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N ILE C 213 " --> pdb=" O PHE C 244 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ILE C 246 " --> pdb=" O ILE C 213 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N PHE C 215 " --> pdb=" O ILE C 246 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N PHE C 245 " --> pdb=" O ILE C 269 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 150 through 152 Processing sheet with id=AB1, first strand: chain 'C' and resid 339 through 340 Processing sheet with id=AB2, first strand: chain 'C' and resid 574 through 575 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 574 through 575 current: chain 'G' and resid 21 through 32 removed outlier: 3.509A pdb=" N THR G 29 " --> pdb=" O THR G 62 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 59 through 63 current: chain 'G' and resid 192 through 195 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 192 through 195 current: chain 'G' and resid 218 through 222 Processing sheet with id=AB3, first strand: chain 'C' and resid 906 through 908 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 906 through 908 current: chain 'H' and resid 21 through 35 removed outlier: 8.122A pdb=" N VAL H 22 " --> pdb=" O PHE H 68 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N PHE H 68 " --> pdb=" O VAL H 22 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N THR H 24 " --> pdb=" O ALA H 66 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ALA H 66 " --> pdb=" O THR H 24 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N THR H 62 " --> pdb=" O GLN H 28 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ALA H 30 " --> pdb=" O ASN H 60 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ASN H 60 " --> pdb=" O ALA H 30 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N PHE H 32 " --> pdb=" O GLU H 58 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N GLU H 58 " --> pdb=" O PHE H 32 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N GLN H 34 " --> pdb=" O GLU H 56 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLU H 56 " --> pdb=" O GLN H 34 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 56 through 68 current: chain 'H' and resid 192 through 195 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 192 through 195 current: chain 'H' and resid 218 through 222 Processing sheet with id=AB4, first strand: chain 'D' and resid 150 through 152 removed outlier: 6.337A pdb=" N SER D 150 " --> pdb=" O LEU D 167 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N LYS D 169 " --> pdb=" O SER D 150 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE D 152 " --> pdb=" O LYS D 169 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N HIS D 128 " --> pdb=" O LEU D 42 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL D 43 " --> pdb=" O VAL D 214 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ILE D 216 " --> pdb=" O VAL D 43 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N PHE D 45 " --> pdb=" O ILE D 216 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N PHE D 245 " --> pdb=" O ILE D 269 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 339 through 340 1758 hydrogen bonds defined for protein. 5076 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.91 Time building geometry restraints manager: 14.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5990 1.32 - 1.44: 10180 1.44 - 1.57: 19991 1.57 - 1.69: 8 1.69 - 1.82: 228 Bond restraints: 36397 Sorted by residual: bond pdb=" O3 NAD C1101 " pdb=" PA NAD C1101 " ideal model delta sigma weight residual 1.653 1.503 0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" O3 NAD D1101 " pdb=" PN NAD D1101 " ideal model delta sigma weight residual 1.633 1.501 0.132 2.00e-02 2.50e+03 4.33e+01 bond pdb=" O3 NAD D1101 " pdb=" PA NAD D1101 " ideal model delta sigma weight residual 1.653 1.541 0.112 2.00e-02 2.50e+03 3.16e+01 bond pdb=" O3 NAD A1101 " pdb=" PA NAD A1101 " ideal model delta sigma weight residual 1.653 1.547 0.106 2.00e-02 2.50e+03 2.81e+01 bond pdb=" O3 NAD B1101 " pdb=" PA NAD B1101 " ideal model delta sigma weight residual 1.653 1.547 0.106 2.00e-02 2.50e+03 2.79e+01 ... (remaining 36392 not shown) Histogram of bond angle deviations from ideal: 81.78 - 92.89: 5 92.89 - 104.01: 339 104.01 - 115.12: 21362 115.12 - 126.23: 26963 126.23 - 137.34: 364 Bond angle restraints: 49033 Sorted by residual: angle pdb=" CA PRO A 956 " pdb=" N PRO A 956 " pdb=" CD PRO A 956 " ideal model delta sigma weight residual 112.00 96.44 15.56 1.40e+00 5.10e-01 1.24e+02 angle pdb=" C1B NAD B1101 " pdb=" C2B NAD B1101 " pdb=" O2B NAD B1101 " ideal model delta sigma weight residual 113.98 84.70 29.28 3.00e+00 1.11e-01 9.53e+01 angle pdb=" C1B NAD A1101 " pdb=" C2B NAD A1101 " pdb=" O2B NAD A1101 " ideal model delta sigma weight residual 113.98 84.71 29.27 3.00e+00 1.11e-01 9.52e+01 angle pdb=" C1B NAD C1101 " pdb=" C2B NAD C1101 " pdb=" O2B NAD C1101 " ideal model delta sigma weight residual 113.98 89.98 24.00 3.00e+00 1.11e-01 6.40e+01 angle pdb=" CA PRO B 57 " pdb=" N PRO B 57 " pdb=" CD PRO B 57 " ideal model delta sigma weight residual 112.00 102.21 9.79 1.40e+00 5.10e-01 4.89e+01 ... (remaining 49028 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.13: 18606 20.13 - 40.26: 2558 40.26 - 60.38: 517 60.38 - 80.51: 91 80.51 - 100.64: 35 Dihedral angle restraints: 21807 sinusoidal: 9188 harmonic: 12619 Sorted by residual: dihedral pdb=" CA HIS C 349 " pdb=" C HIS C 349 " pdb=" N LYS C 350 " pdb=" CA LYS C 350 " ideal model delta harmonic sigma weight residual -180.00 -155.66 -24.34 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA SER A 615 " pdb=" C SER A 615 " pdb=" N MET A 616 " pdb=" CA MET A 616 " ideal model delta harmonic sigma weight residual 180.00 157.44 22.56 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA LEU E 208 " pdb=" C LEU E 208 " pdb=" N GLU E 209 " pdb=" CA GLU E 209 " ideal model delta harmonic sigma weight residual 180.00 157.58 22.42 0 5.00e+00 4.00e-02 2.01e+01 ... (remaining 21804 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 4910 0.084 - 0.167: 299 0.167 - 0.251: 20 0.251 - 0.335: 4 0.335 - 0.418: 2 Chirality restraints: 5235 Sorted by residual: chirality pdb=" C1B NAD A1101 " pdb=" C2B NAD A1101 " pdb=" N9A NAD A1101 " pdb=" O4B NAD A1101 " both_signs ideal model delta sigma weight residual False 2.35 1.93 0.42 2.00e-01 2.50e+01 4.38e+00 chirality pdb=" C1B NAD B1101 " pdb=" C2B NAD B1101 " pdb=" N9A NAD B1101 " pdb=" O4B NAD B1101 " both_signs ideal model delta sigma weight residual False 2.35 1.93 0.42 2.00e-01 2.50e+01 4.34e+00 chirality pdb=" C3B NAD C1101 " pdb=" C2B NAD C1101 " pdb=" C4B NAD C1101 " pdb=" O3B NAD C1101 " both_signs ideal model delta sigma weight residual False -2.71 -2.40 -0.31 2.00e-01 2.50e+01 2.47e+00 ... (remaining 5232 not shown) Planarity restraints: 6216 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 955 " 0.106 5.00e-02 4.00e+02 1.47e-01 3.44e+01 pdb=" N PRO A 956 " -0.253 5.00e-02 4.00e+02 pdb=" CA PRO A 956 " 0.072 5.00e-02 4.00e+02 pdb=" CD PRO A 956 " 0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 56 " 0.076 5.00e-02 4.00e+02 1.08e-01 1.88e+01 pdb=" N PRO B 57 " -0.187 5.00e-02 4.00e+02 pdb=" CA PRO B 57 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO B 57 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 381 " 0.018 2.00e-02 2.50e+03 2.38e-02 9.88e+00 pdb=" CG PHE C 381 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 PHE C 381 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE C 381 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE C 381 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 381 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE C 381 " -0.002 2.00e-02 2.50e+03 ... (remaining 6213 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 381 2.59 - 3.17: 31197 3.17 - 3.75: 58420 3.75 - 4.32: 80404 4.32 - 4.90: 132766 Nonbonded interactions: 303168 Sorted by model distance: nonbonded pdb=" OH TYR B 286 " pdb=" O2B NAD B1101 " model vdw 2.015 2.440 nonbonded pdb=" OD1 ASN A 78 " pdb=" N TYR A 79 " model vdw 2.068 2.520 nonbonded pdb=" OH TYR A 589 " pdb=" OD1 ASP A 651 " model vdw 2.103 2.440 nonbonded pdb=" OH TYR B 800 " pdb=" O ALA E 224 " model vdw 2.119 2.440 nonbonded pdb=" NZ LYS F 16 " pdb=" OD1 ASN F 197 " model vdw 2.158 2.520 ... (remaining 303163 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 23 through 72 or resid 79 through 463 or resid 467 through \ 633 or resid 644 through 1005 or resid 1101)) selection = (chain 'B' and (resid 23 through 72 or resid 79 through 296 or resid 304 through \ 786 or resid 789 through 1005 or resid 1101)) selection = (chain 'C' and (resid 23 through 296 or resid 304 through 463 or resid 467 throu \ gh 633 or resid 644 through 1005 or resid 1101)) selection = (chain 'D' and (resid 23 through 72 or resid 79 through 296 or resid 304 through \ 786 or resid 789 through 1005 or resid 1101)) } ncs_group { reference = (chain 'E' and (resid 8 through 36 or resid 41 through 236)) selection = (chain 'F' and (resid 8 through 176 or resid 191 through 236)) selection = (chain 'G' and (resid 8 through 36 or resid 41 through 236)) selection = (chain 'H' and (resid 8 through 176 or resid 191 through 236)) } 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: 7.280 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: 0.040 Extract box with map and model: 1.600 Check model and map are aligned: 0.290 Set scattering table: 0.370 Process input model: 93.570 Find NCS groups from input model: 3.140 Set up NCS constraints: 0.140 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.159 36397 Z= 0.299 Angle : 0.818 29.279 49033 Z= 0.406 Chirality : 0.044 0.418 5235 Planarity : 0.004 0.147 6216 Dihedral : 18.623 100.641 13667 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.51 % Allowed : 29.35 % Favored : 70.13 % 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: -0.12 (0.13), residues: 4155 helix: 0.61 (0.11), residues: 2423 sheet: -0.27 (0.34), residues: 190 loop : -1.07 (0.15), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 919 HIS 0.007 0.001 HIS C 349 PHE 0.055 0.002 PHE C 381 TYR 0.048 0.002 TYR B 282 ARG 0.011 0.001 ARG C 380 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8310 Ramachandran restraints generated. 4155 Oldfield, 0 Emsley, 4155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8310 Ramachandran restraints generated. 4155 Oldfield, 0 Emsley, 4155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 414 time to evaluate : 4.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 TYR cc_start: 0.7831 (t80) cc_final: 0.7499 (t80) REVERT: D 330 LEU cc_start: 0.8290 (tp) cc_final: 0.8085 (tt) REVERT: E 194 GLN cc_start: 0.5819 (tm-30) cc_final: 0.5587 (mp10) outliers start: 20 outliers final: 11 residues processed: 426 average time/residue: 0.4624 time to fit residues: 327.5659 Evaluate side-chains 394 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 383 time to evaluate : 4.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 759 GLU Chi-restraints excluded: chain B residue 822 GLU Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 1003 TYR Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain F residue 32 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 356 optimal weight: 4.9990 chunk 319 optimal weight: 10.0000 chunk 177 optimal weight: 7.9990 chunk 109 optimal weight: 2.9990 chunk 215 optimal weight: 0.9990 chunk 170 optimal weight: 3.9990 chunk 330 optimal weight: 30.0000 chunk 127 optimal weight: 0.2980 chunk 201 optimal weight: 0.9980 chunk 246 optimal weight: 5.9990 chunk 383 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 GLN A 698 GLN ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 765 ASN ** B 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 ASN C 58 GLN C 483 GLN ** C 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 ASN D 491 GLN D 521 ASN D 549 GLN ** D 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 36397 Z= 0.251 Angle : 0.580 9.909 49033 Z= 0.303 Chirality : 0.041 0.169 5235 Planarity : 0.004 0.067 6216 Dihedral : 8.359 89.244 4895 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.41 % Allowed : 27.04 % Favored : 70.54 % 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: -0.01 (0.13), residues: 4155 helix: 0.70 (0.10), residues: 2473 sheet: -0.53 (0.33), residues: 226 loop : -1.04 (0.15), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 601 HIS 0.008 0.001 HIS C 658 PHE 0.022 0.002 PHE E 67 TYR 0.021 0.001 TYR D 418 ARG 0.007 0.000 ARG A 760 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8310 Ramachandran restraints generated. 4155 Oldfield, 0 Emsley, 4155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8310 Ramachandran restraints generated. 4155 Oldfield, 0 Emsley, 4155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 429 time to evaluate : 4.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 PHE cc_start: 0.7888 (m-10) cc_final: 0.7631 (m-10) REVERT: A 414 TYR cc_start: 0.8138 (t80) cc_final: 0.7932 (t80) REVERT: B 134 TYR cc_start: 0.7553 (OUTLIER) cc_final: 0.6885 (p90) REVERT: B 787 ILE cc_start: 0.4995 (OUTLIER) cc_final: 0.4635 (tp) REVERT: B 930 MET cc_start: 0.5834 (mmt) cc_final: 0.4970 (ptt) REVERT: C 693 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7533 (tt0) REVERT: D 107 PHE cc_start: 0.7202 (OUTLIER) cc_final: 0.6730 (t80) REVERT: D 280 TYR cc_start: 0.7852 (OUTLIER) cc_final: 0.7546 (t80) REVERT: D 511 PHE cc_start: 0.4407 (OUTLIER) cc_final: 0.4081 (m-80) REVERT: E 15 ARG cc_start: 0.3916 (tpt170) cc_final: 0.3706 (tpt170) REVERT: E 194 GLN cc_start: 0.5944 (tm130) cc_final: 0.5704 (mp10) REVERT: H 32 PHE cc_start: 0.3072 (OUTLIER) cc_final: 0.2691 (m-80) outliers start: 94 outliers final: 32 residues processed: 500 average time/residue: 0.4677 time to fit residues: 386.8801 Evaluate side-chains 425 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 386 time to evaluate : 4.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 698 GLN Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 765 ASN Chi-restraints excluded: chain B residue 787 ILE Chi-restraints excluded: chain B residue 904 ILE Chi-restraints excluded: chain B residue 941 ASP Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 290 MET Chi-restraints excluded: chain C residue 570 SER Chi-restraints excluded: chain C residue 693 GLU Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 280 TYR Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 511 PHE Chi-restraints excluded: chain D residue 834 GLN Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 210 ASN Chi-restraints excluded: chain H residue 32 PHE Chi-restraints excluded: chain H residue 48 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 212 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 318 optimal weight: 20.0000 chunk 260 optimal weight: 10.0000 chunk 105 optimal weight: 0.1980 chunk 383 optimal weight: 0.9990 chunk 414 optimal weight: 5.9990 chunk 341 optimal weight: 9.9990 chunk 380 optimal weight: 6.9990 chunk 130 optimal weight: 0.9980 chunk 307 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 834 GLN ** B 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 491 GLN ** B 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 548 ASN ** D 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 197 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 36397 Z= 0.213 Angle : 0.550 12.377 49033 Z= 0.286 Chirality : 0.040 0.193 5235 Planarity : 0.003 0.057 6216 Dihedral : 7.241 85.113 4881 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.88 % Allowed : 26.32 % Favored : 70.80 % 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: 0.09 (0.13), residues: 4155 helix: 0.80 (0.10), residues: 2474 sheet: -0.55 (0.34), residues: 216 loop : -1.03 (0.15), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 448 HIS 0.009 0.001 HIS C 658 PHE 0.020 0.001 PHE D 722 TYR 0.022 0.001 TYR B 755 ARG 0.005 0.000 ARG C 380 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8310 Ramachandran restraints generated. 4155 Oldfield, 0 Emsley, 4155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8310 Ramachandran restraints generated. 4155 Oldfield, 0 Emsley, 4155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 423 time to evaluate : 4.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 PHE cc_start: 0.7936 (m-10) cc_final: 0.7707 (m-10) REVERT: A 414 TYR cc_start: 0.8149 (t80) cc_final: 0.7911 (t80) REVERT: A 588 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8689 (tp) REVERT: B 134 TYR cc_start: 0.7630 (OUTLIER) cc_final: 0.6918 (p90) REVERT: B 414 TYR cc_start: 0.8656 (t80) cc_final: 0.8019 (t80) REVERT: B 781 LEU cc_start: 0.8458 (tt) cc_final: 0.8186 (mp) REVERT: B 787 ILE cc_start: 0.5051 (OUTLIER) cc_final: 0.4240 (tp) REVERT: B 810 HIS cc_start: 0.7668 (t-90) cc_final: 0.7425 (t-170) REVERT: C 372 LYS cc_start: 0.4101 (OUTLIER) cc_final: 0.2686 (tptt) REVERT: C 674 ASP cc_start: 0.6506 (m-30) cc_final: 0.6147 (p0) REVERT: C 693 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7495 (tt0) REVERT: D 107 PHE cc_start: 0.7233 (OUTLIER) cc_final: 0.6705 (t80) REVERT: D 144 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8114 (mtmm) REVERT: D 280 TYR cc_start: 0.7806 (OUTLIER) cc_final: 0.7582 (t80) REVERT: D 511 PHE cc_start: 0.4540 (OUTLIER) cc_final: 0.4267 (m-80) REVERT: H 32 PHE cc_start: 0.2878 (OUTLIER) cc_final: 0.2363 (m-80) outliers start: 112 outliers final: 51 residues processed: 510 average time/residue: 0.4759 time to fit residues: 405.3628 Evaluate side-chains 449 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 388 time to evaluate : 3.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 593 ARG Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 698 GLN Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 469 CYS Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 609 HIS Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 759 GLU Chi-restraints excluded: chain B residue 787 ILE Chi-restraints excluded: chain B residue 904 ILE Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 941 ASP Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 290 MET Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 372 LYS Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 693 GLU Chi-restraints excluded: chain C residue 713 ILE Chi-restraints excluded: chain D residue 58 GLN Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 144 LYS Chi-restraints excluded: chain D residue 280 TYR Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 511 PHE Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 206 MET Chi-restraints excluded: chain F residue 13 PHE Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 210 ASN Chi-restraints excluded: chain H residue 32 PHE Chi-restraints excluded: chain H residue 48 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 379 optimal weight: 7.9990 chunk 288 optimal weight: 0.6980 chunk 199 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 183 optimal weight: 8.9990 chunk 257 optimal weight: 20.0000 chunk 385 optimal weight: 7.9990 chunk 407 optimal weight: 4.9990 chunk 201 optimal weight: 0.9980 chunk 365 optimal weight: 6.9990 chunk 109 optimal weight: 1.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN B 475 GLN B 765 ASN ** B 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 GLN ** C 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 GLN D 548 ASN ** D 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 36397 Z= 0.320 Angle : 0.583 12.260 49033 Z= 0.305 Chirality : 0.042 0.198 5235 Planarity : 0.004 0.052 6216 Dihedral : 6.833 78.019 4881 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.88 % Allowed : 25.68 % Favored : 70.44 % 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: 0.01 (0.13), residues: 4155 helix: 0.74 (0.10), residues: 2474 sheet: -0.50 (0.35), residues: 216 loop : -1.08 (0.15), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 72 HIS 0.007 0.001 HIS C 658 PHE 0.024 0.002 PHE E 67 TYR 0.032 0.002 TYR B 755 ARG 0.005 0.000 ARG C 247 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8310 Ramachandran restraints generated. 4155 Oldfield, 0 Emsley, 4155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8310 Ramachandran restraints generated. 4155 Oldfield, 0 Emsley, 4155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 414 time to evaluate : 3.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 744 PHE cc_start: 0.8983 (OUTLIER) cc_final: 0.8636 (t80) REVERT: B 134 TYR cc_start: 0.7932 (OUTLIER) cc_final: 0.6826 (p90) REVERT: B 531 MET cc_start: 0.8961 (mmp) cc_final: 0.8527 (mmt) REVERT: B 781 LEU cc_start: 0.8460 (tt) cc_final: 0.8212 (mp) REVERT: B 930 MET cc_start: 0.5696 (mmt) cc_final: 0.4768 (ptp) REVERT: C 101 ASP cc_start: 0.7766 (m-30) cc_final: 0.7479 (m-30) REVERT: D 107 PHE cc_start: 0.7336 (OUTLIER) cc_final: 0.6759 (t80) REVERT: D 144 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8239 (mtmm) REVERT: D 280 TYR cc_start: 0.7867 (OUTLIER) cc_final: 0.7585 (t80) REVERT: D 511 PHE cc_start: 0.4672 (OUTLIER) cc_final: 0.4428 (m-80) REVERT: G 50 LEU cc_start: -0.0691 (OUTLIER) cc_final: -0.0917 (mm) REVERT: H 32 PHE cc_start: 0.2631 (OUTLIER) cc_final: 0.1914 (m-80) outliers start: 151 outliers final: 78 residues processed: 529 average time/residue: 0.4600 time to fit residues: 405.3588 Evaluate side-chains 463 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 377 time to evaluate : 3.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 593 ARG Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 698 GLN Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 469 CYS Chi-restraints excluded: chain B residue 475 GLN Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 554 ASP Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 609 HIS Chi-restraints excluded: chain B residue 661 ILE Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 759 GLU Chi-restraints excluded: chain B residue 826 CYS Chi-restraints excluded: chain B residue 904 ILE Chi-restraints excluded: chain B residue 911 ASP Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 941 ASP Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 290 MET Chi-restraints excluded: chain C residue 356 TYR Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 570 SER Chi-restraints excluded: chain C residue 713 ILE Chi-restraints excluded: chain D residue 58 GLN Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 144 LYS Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 280 TYR Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 419 ASP Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 511 PHE Chi-restraints excluded: chain D residue 651 ASP Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 206 MET Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 13 PHE Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 210 ASN Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain H residue 32 PHE Chi-restraints excluded: chain H residue 48 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 339 optimal weight: 10.0000 chunk 231 optimal weight: 1.9990 chunk 5 optimal weight: 0.3980 chunk 303 optimal weight: 0.5980 chunk 168 optimal weight: 0.9990 chunk 348 optimal weight: 5.9990 chunk 281 optimal weight: 20.0000 chunk 0 optimal weight: 5.9990 chunk 208 optimal weight: 1.9990 chunk 366 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 698 GLN B 475 GLN ** B 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 483 GLN ** C 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 782 GLN ** D 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 548 ASN D 549 GLN ** D 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 GLN E 210 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 36397 Z= 0.234 Angle : 0.546 12.752 49033 Z= 0.284 Chirality : 0.040 0.168 5235 Planarity : 0.003 0.048 6216 Dihedral : 6.588 71.088 4881 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.16 % Allowed : 26.14 % Favored : 70.70 % 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: 0.13 (0.13), residues: 4155 helix: 0.83 (0.10), residues: 2472 sheet: -0.42 (0.36), residues: 216 loop : -1.04 (0.15), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 72 HIS 0.006 0.001 HIS C 658 PHE 0.020 0.001 PHE C 511 TYR 0.029 0.001 TYR B 755 ARG 0.005 0.000 ARG C 247 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8310 Ramachandran restraints generated. 4155 Oldfield, 0 Emsley, 4155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8310 Ramachandran restraints generated. 4155 Oldfield, 0 Emsley, 4155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 399 time to evaluate : 4.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 744 PHE cc_start: 0.9012 (OUTLIER) cc_final: 0.8670 (t80) REVERT: A 930 MET cc_start: 0.4603 (OUTLIER) cc_final: 0.4056 (mmm) REVERT: B 287 SER cc_start: 0.8140 (OUTLIER) cc_final: 0.7532 (m) REVERT: B 357 MET cc_start: 0.8250 (tpt) cc_final: 0.8033 (mmt) REVERT: B 531 MET cc_start: 0.8951 (mmp) cc_final: 0.8490 (mmt) REVERT: B 781 LEU cc_start: 0.8384 (tt) cc_final: 0.8173 (mp) REVERT: B 930 MET cc_start: 0.5755 (mmt) cc_final: 0.4762 (ptp) REVERT: C 101 ASP cc_start: 0.7820 (m-30) cc_final: 0.7602 (m-30) REVERT: C 620 ILE cc_start: 0.6316 (OUTLIER) cc_final: 0.6094 (mt) REVERT: C 674 ASP cc_start: 0.6418 (m-30) cc_final: 0.6216 (p0) REVERT: C 693 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7566 (tt0) REVERT: D 107 PHE cc_start: 0.7315 (OUTLIER) cc_final: 0.6811 (t80) REVERT: D 144 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8190 (mtmm) REVERT: D 280 TYR cc_start: 0.7867 (OUTLIER) cc_final: 0.7579 (t80) REVERT: D 511 PHE cc_start: 0.4771 (OUTLIER) cc_final: 0.4568 (m-80) REVERT: H 32 PHE cc_start: 0.2698 (OUTLIER) cc_final: 0.1916 (m-80) outliers start: 123 outliers final: 69 residues processed: 490 average time/residue: 0.4786 time to fit residues: 389.7826 Evaluate side-chains 449 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 370 time to evaluate : 4.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 698 GLN Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 930 MET Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 469 CYS Chi-restraints excluded: chain B residue 475 GLN Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 554 ASP Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 661 ILE Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 759 GLU Chi-restraints excluded: chain B residue 904 ILE Chi-restraints excluded: chain B residue 911 ASP Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 290 MET Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 570 SER Chi-restraints excluded: chain C residue 620 ILE Chi-restraints excluded: chain C residue 693 GLU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 713 ILE Chi-restraints excluded: chain D residue 58 GLN Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 144 LYS Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 280 TYR Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 419 ASP Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 511 PHE Chi-restraints excluded: chain D residue 667 LEU Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 206 MET Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 13 PHE Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 210 ASN Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain H residue 32 PHE Chi-restraints excluded: chain H residue 48 LYS Chi-restraints excluded: chain H residue 173 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 137 optimal weight: 2.9990 chunk 367 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 239 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 408 optimal weight: 10.0000 chunk 338 optimal weight: 0.0470 chunk 189 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 135 optimal weight: 2.9990 chunk 214 optimal weight: 1.9990 overall best weight: 1.1284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN ** A 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 698 GLN B 475 GLN ** B 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 548 ASN ** D 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 979 HIS E 60 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 36397 Z= 0.225 Angle : 0.544 13.191 49033 Z= 0.282 Chirality : 0.040 0.351 5235 Planarity : 0.003 0.046 6216 Dihedral : 6.399 64.443 4881 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.11 % Allowed : 26.32 % Favored : 70.57 % 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: 0.18 (0.13), residues: 4155 helix: 0.89 (0.11), residues: 2470 sheet: -0.47 (0.36), residues: 224 loop : -1.03 (0.15), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 601 HIS 0.006 0.001 HIS C 658 PHE 0.030 0.001 PHE F 204 TYR 0.019 0.001 TYR B 755 ARG 0.008 0.000 ARG B 760 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8310 Ramachandran restraints generated. 4155 Oldfield, 0 Emsley, 4155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8310 Ramachandran restraints generated. 4155 Oldfield, 0 Emsley, 4155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 392 time to evaluate : 4.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 TYR cc_start: 0.8415 (t80) cc_final: 0.8196 (t80) REVERT: A 694 GLU cc_start: 0.6929 (mm-30) cc_final: 0.6683 (mm-30) REVERT: A 698 GLN cc_start: 0.7549 (OUTLIER) cc_final: 0.6405 (mt0) REVERT: A 744 PHE cc_start: 0.9034 (OUTLIER) cc_final: 0.8481 (m-80) REVERT: A 930 MET cc_start: 0.4719 (OUTLIER) cc_final: 0.4161 (mmm) REVERT: B 270 ASP cc_start: 0.8058 (t70) cc_final: 0.7598 (t0) REVERT: B 287 SER cc_start: 0.8149 (OUTLIER) cc_final: 0.7549 (m) REVERT: B 357 MET cc_start: 0.8251 (tpt) cc_final: 0.8026 (mmt) REVERT: B 448 TRP cc_start: 0.8805 (m-10) cc_final: 0.8202 (m-10) REVERT: B 781 LEU cc_start: 0.8342 (tt) cc_final: 0.8139 (mp) REVERT: B 930 MET cc_start: 0.5687 (mmt) cc_final: 0.4766 (ptp) REVERT: C 101 ASP cc_start: 0.7822 (m-30) cc_final: 0.7607 (m-30) REVERT: C 421 MET cc_start: 0.5612 (ptp) cc_final: 0.5378 (ptp) REVERT: C 693 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7593 (tt0) REVERT: D 107 PHE cc_start: 0.7312 (OUTLIER) cc_final: 0.6818 (t80) REVERT: D 134 TYR cc_start: 0.9041 (OUTLIER) cc_final: 0.8385 (m-80) REVERT: D 144 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8198 (mtmm) REVERT: D 280 TYR cc_start: 0.7900 (OUTLIER) cc_final: 0.7565 (t80) REVERT: D 877 PHE cc_start: 0.0818 (OUTLIER) cc_final: -0.0112 (m-80) outliers start: 121 outliers final: 75 residues processed: 484 average time/residue: 0.4640 time to fit residues: 375.5691 Evaluate side-chains 452 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 367 time to evaluate : 3.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 356 TYR Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 698 GLN Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 930 MET Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 469 CYS Chi-restraints excluded: chain B residue 475 GLN Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 661 ILE Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 759 GLU Chi-restraints excluded: chain B residue 765 ASN Chi-restraints excluded: chain B residue 904 ILE Chi-restraints excluded: chain B residue 911 ASP Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 941 ASP Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 693 GLU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 713 ILE Chi-restraints excluded: chain D residue 58 GLN Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 144 LYS Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 280 TYR Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 419 ASP Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 548 ASN Chi-restraints excluded: chain D residue 553 ASP Chi-restraints excluded: chain D residue 651 ASP Chi-restraints excluded: chain D residue 667 LEU Chi-restraints excluded: chain D residue 877 PHE Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 206 MET Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 13 PHE Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 210 ASN Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 231 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 393 optimal weight: 0.9990 chunk 46 optimal weight: 0.3980 chunk 232 optimal weight: 0.0270 chunk 298 optimal weight: 1.9990 chunk 231 optimal weight: 5.9990 chunk 343 optimal weight: 6.9990 chunk 227 optimal weight: 9.9990 chunk 406 optimal weight: 20.0000 chunk 254 optimal weight: 5.9990 chunk 247 optimal weight: 0.9980 chunk 187 optimal weight: 1.9990 overall best weight: 0.8842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 GLN ** B 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 483 GLN ** C 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 548 ASN ** D 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 36397 Z= 0.196 Angle : 0.534 13.551 49033 Z= 0.276 Chirality : 0.040 0.347 5235 Planarity : 0.003 0.047 6216 Dihedral : 6.232 59.862 4881 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.93 % Allowed : 26.66 % Favored : 70.42 % 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 (0.13), residues: 4155 helix: 0.95 (0.11), residues: 2474 sheet: -0.40 (0.36), residues: 224 loop : -1.01 (0.15), residues: 1457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 601 HIS 0.006 0.001 HIS C 658 PHE 0.028 0.001 PHE C 544 TYR 0.021 0.001 TYR B 755 ARG 0.007 0.000 ARG B 760 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8310 Ramachandran restraints generated. 4155 Oldfield, 0 Emsley, 4155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8310 Ramachandran restraints generated. 4155 Oldfield, 0 Emsley, 4155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 395 time to evaluate : 3.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 744 PHE cc_start: 0.9025 (OUTLIER) cc_final: 0.8505 (m-80) REVERT: A 930 MET cc_start: 0.4694 (OUTLIER) cc_final: 0.4131 (mmm) REVERT: B 270 ASP cc_start: 0.8052 (t70) cc_final: 0.7611 (t0) REVERT: B 287 SER cc_start: 0.8150 (OUTLIER) cc_final: 0.7561 (m) REVERT: B 357 MET cc_start: 0.8240 (tpt) cc_final: 0.7996 (mmt) REVERT: B 448 TRP cc_start: 0.8801 (m-10) cc_final: 0.8198 (m-10) REVERT: B 495 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7734 (tp) REVERT: B 930 MET cc_start: 0.5626 (mmt) cc_final: 0.4715 (ptp) REVERT: C 101 ASP cc_start: 0.7807 (m-30) cc_final: 0.7585 (m-30) REVERT: C 518 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7127 (pm20) REVERT: C 693 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7577 (tt0) REVERT: D 107 PHE cc_start: 0.7306 (OUTLIER) cc_final: 0.6826 (t80) REVERT: D 134 TYR cc_start: 0.9033 (OUTLIER) cc_final: 0.8376 (m-80) REVERT: D 144 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8139 (mtmm) REVERT: D 280 TYR cc_start: 0.7917 (OUTLIER) cc_final: 0.7587 (t80) REVERT: D 877 PHE cc_start: 0.0833 (OUTLIER) cc_final: -0.0119 (m-80) REVERT: E 194 GLN cc_start: 0.4841 (mp10) cc_final: 0.4446 (mp10) outliers start: 114 outliers final: 74 residues processed: 480 average time/residue: 0.4557 time to fit residues: 364.0892 Evaluate side-chains 456 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 371 time to evaluate : 4.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 356 TYR Chi-restraints excluded: chain A residue 378 TYR Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 930 MET Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 469 CYS Chi-restraints excluded: chain B residue 475 GLN Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 554 ASP Chi-restraints excluded: chain B residue 661 ILE Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 759 GLU Chi-restraints excluded: chain B residue 765 ASN Chi-restraints excluded: chain B residue 904 ILE Chi-restraints excluded: chain B residue 911 ASP Chi-restraints excluded: chain B residue 925 ILE Chi-restraints excluded: chain B residue 941 ASP Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 518 GLU Chi-restraints excluded: chain C residue 570 SER Chi-restraints excluded: chain C residue 693 GLU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 713 ILE Chi-restraints excluded: chain D residue 58 GLN Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 144 LYS Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 280 TYR Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 419 ASP Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 432 ILE Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 553 ASP Chi-restraints excluded: chain D residue 651 ASP Chi-restraints excluded: chain D residue 667 LEU Chi-restraints excluded: chain D residue 877 PHE Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 206 MET Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 13 PHE Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 210 ASN Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 231 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 251 optimal weight: 5.9990 chunk 162 optimal weight: 4.9990 chunk 242 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 78 optimal weight: 0.0040 chunk 258 optimal weight: 10.0000 chunk 277 optimal weight: 8.9990 chunk 201 optimal weight: 0.6980 chunk 37 optimal weight: 0.2980 chunk 319 optimal weight: 3.9990 overall best weight: 0.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 93 ASN A 226 ASN ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 GLN ** B 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 349 HIS C 483 GLN ** C 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN ** D 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 36397 Z= 0.205 Angle : 0.543 13.162 49033 Z= 0.280 Chirality : 0.040 0.300 5235 Planarity : 0.003 0.048 6216 Dihedral : 6.098 59.829 4881 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.80 % Allowed : 26.76 % Favored : 70.44 % 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: 0.29 (0.13), residues: 4155 helix: 0.96 (0.11), residues: 2475 sheet: -0.34 (0.36), residues: 224 loop : -0.99 (0.15), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 601 HIS 0.009 0.001 HIS C 658 PHE 0.024 0.001 PHE E 67 TYR 0.023 0.001 TYR A 223 ARG 0.006 0.000 ARG B 760 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8310 Ramachandran restraints generated. 4155 Oldfield, 0 Emsley, 4155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8310 Ramachandran restraints generated. 4155 Oldfield, 0 Emsley, 4155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 385 time to evaluate : 3.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 TYR cc_start: 0.8133 (t80) cc_final: 0.7497 (t80) REVERT: A 744 PHE cc_start: 0.9050 (OUTLIER) cc_final: 0.8459 (m-80) REVERT: A 930 MET cc_start: 0.4672 (OUTLIER) cc_final: 0.4181 (mmm) REVERT: B 270 ASP cc_start: 0.8077 (t70) cc_final: 0.7648 (t0) REVERT: B 287 SER cc_start: 0.8128 (OUTLIER) cc_final: 0.7547 (m) REVERT: B 357 MET cc_start: 0.8262 (tpt) cc_final: 0.8016 (mmt) REVERT: B 448 TRP cc_start: 0.8801 (m-10) cc_final: 0.8224 (m-10) REVERT: B 495 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7717 (tp) REVERT: B 930 MET cc_start: 0.5598 (mmt) cc_final: 0.4782 (ptp) REVERT: C 101 ASP cc_start: 0.7783 (m-30) cc_final: 0.7577 (m-30) REVERT: C 518 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7076 (pm20) REVERT: C 611 TYR cc_start: 0.7400 (t80) cc_final: 0.7178 (t80) REVERT: C 693 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7609 (tt0) REVERT: C 722 PHE cc_start: 0.6004 (OUTLIER) cc_final: 0.4373 (m-80) REVERT: D 107 PHE cc_start: 0.7316 (OUTLIER) cc_final: 0.6840 (t80) REVERT: D 134 TYR cc_start: 0.9021 (OUTLIER) cc_final: 0.8345 (m-80) REVERT: D 144 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8180 (mtmm) REVERT: D 280 TYR cc_start: 0.7952 (OUTLIER) cc_final: 0.7583 (t80) REVERT: D 877 PHE cc_start: 0.0814 (OUTLIER) cc_final: -0.0161 (m-80) REVERT: E 33 SER cc_start: 0.6600 (m) cc_final: 0.6394 (m) REVERT: E 194 GLN cc_start: 0.5026 (mp10) cc_final: 0.4677 (mp10) outliers start: 109 outliers final: 76 residues processed: 467 average time/residue: 0.4598 time to fit residues: 358.3798 Evaluate side-chains 464 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 376 time to evaluate : 3.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 356 TYR Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 930 MET Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 469 CYS Chi-restraints excluded: chain B residue 475 GLN Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 554 ASP Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 661 ILE Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 759 GLU Chi-restraints excluded: chain B residue 765 ASN Chi-restraints excluded: chain B residue 904 ILE Chi-restraints excluded: chain B residue 911 ASP Chi-restraints excluded: chain B residue 925 ILE Chi-restraints excluded: chain B residue 941 ASP Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 518 GLU Chi-restraints excluded: chain C residue 693 GLU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 713 ILE Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain D residue 58 GLN Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 144 LYS Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 280 TYR Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 419 ASP Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 432 ILE Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 553 ASP Chi-restraints excluded: chain D residue 651 ASP Chi-restraints excluded: chain D residue 667 LEU Chi-restraints excluded: chain D residue 877 PHE Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 206 MET Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 13 PHE Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 231 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 369 optimal weight: 0.0670 chunk 389 optimal weight: 1.9990 chunk 355 optimal weight: 20.0000 chunk 379 optimal weight: 0.9990 chunk 228 optimal weight: 9.9990 chunk 165 optimal weight: 0.6980 chunk 297 optimal weight: 1.9990 chunk 116 optimal weight: 0.0020 chunk 342 optimal weight: 8.9990 chunk 358 optimal weight: 10.0000 chunk 377 optimal weight: 0.7980 overall best weight: 0.5128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN B 475 GLN ** B 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 681 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 36397 Z= 0.165 Angle : 0.540 13.691 49033 Z= 0.277 Chirality : 0.039 0.291 5235 Planarity : 0.003 0.045 6216 Dihedral : 5.970 59.143 4881 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.13 % Allowed : 27.66 % Favored : 70.21 % 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: 0.37 (0.13), residues: 4155 helix: 1.04 (0.11), residues: 2463 sheet: -0.31 (0.36), residues: 224 loop : -0.95 (0.15), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP E 72 HIS 0.008 0.001 HIS C 658 PHE 0.023 0.001 PHE C 544 TYR 0.026 0.001 TYR C 709 ARG 0.005 0.000 ARG B 760 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8310 Ramachandran restraints generated. 4155 Oldfield, 0 Emsley, 4155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8310 Ramachandran restraints generated. 4155 Oldfield, 0 Emsley, 4155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 405 time to evaluate : 3.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 TYR cc_start: 0.7961 (t80) cc_final: 0.7325 (t80) REVERT: A 744 PHE cc_start: 0.9038 (OUTLIER) cc_final: 0.8471 (m-80) REVERT: A 930 MET cc_start: 0.4604 (OUTLIER) cc_final: 0.4127 (mmm) REVERT: B 270 ASP cc_start: 0.8063 (t70) cc_final: 0.7647 (t0) REVERT: B 357 MET cc_start: 0.8226 (tpt) cc_final: 0.7970 (mmt) REVERT: B 425 ILE cc_start: 0.7650 (mm) cc_final: 0.7433 (mt) REVERT: B 448 TRP cc_start: 0.8771 (m-10) cc_final: 0.8170 (m-10) REVERT: B 495 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7718 (tp) REVERT: B 930 MET cc_start: 0.5497 (mmt) cc_final: 0.4747 (ptp) REVERT: C 518 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.6862 (pm20) REVERT: C 611 TYR cc_start: 0.7402 (t80) cc_final: 0.7165 (t80) REVERT: C 693 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7646 (tt0) REVERT: C 722 PHE cc_start: 0.6052 (OUTLIER) cc_final: 0.4361 (m-80) REVERT: D 107 PHE cc_start: 0.7271 (OUTLIER) cc_final: 0.6824 (t80) REVERT: D 144 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8097 (mtmm) REVERT: D 280 TYR cc_start: 0.7915 (OUTLIER) cc_final: 0.7565 (t80) REVERT: D 1001 MET cc_start: 0.3454 (tpp) cc_final: 0.3160 (tpp) REVERT: E 33 SER cc_start: 0.6809 (m) cc_final: 0.6593 (m) REVERT: E 194 GLN cc_start: 0.5049 (mp10) cc_final: 0.4717 (mp10) outliers start: 83 outliers final: 57 residues processed: 466 average time/residue: 0.4690 time to fit residues: 364.6568 Evaluate side-chains 445 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 379 time to evaluate : 4.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 930 MET Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 469 CYS Chi-restraints excluded: chain B residue 475 GLN Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 661 ILE Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 759 GLU Chi-restraints excluded: chain B residue 802 ARG Chi-restraints excluded: chain B residue 904 ILE Chi-restraints excluded: chain B residue 925 ILE Chi-restraints excluded: chain B residue 941 ASP Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 518 GLU Chi-restraints excluded: chain C residue 570 SER Chi-restraints excluded: chain C residue 693 GLU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 713 ILE Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain D residue 58 GLN Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 144 LYS Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 280 TYR Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 419 ASP Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 432 ILE Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 651 ASP Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 206 MET Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 13 PHE Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain H residue 173 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 248 optimal weight: 10.0000 chunk 400 optimal weight: 7.9990 chunk 244 optimal weight: 6.9990 chunk 190 optimal weight: 5.9990 chunk 278 optimal weight: 7.9990 chunk 420 optimal weight: 8.9990 chunk 386 optimal weight: 7.9990 chunk 334 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 258 optimal weight: 5.9990 chunk 205 optimal weight: 0.8980 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 HIS ** A 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 GLN ** B 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 606 HIS ** B 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 810 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 910 ASN ** D 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 867 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 36397 Z= 0.454 Angle : 0.681 14.235 49033 Z= 0.351 Chirality : 0.045 0.252 5235 Planarity : 0.004 0.047 6216 Dihedral : 6.181 58.696 4879 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.31 % Favored : 95.67 % Rotamer: Outliers : 2.44 % Allowed : 27.40 % Favored : 70.16 % 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: -0.03 (0.13), residues: 4155 helix: 0.70 (0.10), residues: 2466 sheet: -0.27 (0.39), residues: 198 loop : -1.11 (0.15), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP D 601 HIS 0.008 0.001 HIS C 658 PHE 0.026 0.002 PHE A 942 TYR 0.026 0.002 TYR A 650 ARG 0.010 0.001 ARG C 247 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8310 Ramachandran restraints generated. 4155 Oldfield, 0 Emsley, 4155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8310 Ramachandran restraints generated. 4155 Oldfield, 0 Emsley, 4155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 388 time to evaluate : 3.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 744 PHE cc_start: 0.9142 (OUTLIER) cc_final: 0.8539 (m-80) REVERT: A 930 MET cc_start: 0.4835 (OUTLIER) cc_final: 0.4295 (mmm) REVERT: B 425 ILE cc_start: 0.7967 (mm) cc_final: 0.7761 (mt) REVERT: B 495 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7745 (tp) REVERT: B 826 CYS cc_start: 0.7546 (t) cc_final: 0.7277 (t) REVERT: B 930 MET cc_start: 0.5674 (mmt) cc_final: 0.4929 (ptp) REVERT: C 518 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.6991 (pm20) REVERT: C 693 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7627 (tt0) REVERT: D 107 PHE cc_start: 0.7445 (OUTLIER) cc_final: 0.6843 (t80) REVERT: D 280 TYR cc_start: 0.8043 (OUTLIER) cc_final: 0.7678 (t80) REVERT: D 877 PHE cc_start: 0.1072 (OUTLIER) cc_final: 0.0566 (m-80) REVERT: D 1001 MET cc_start: 0.3595 (tpp) cc_final: 0.3329 (tpp) REVERT: E 194 GLN cc_start: 0.5179 (mp10) cc_final: 0.4821 (mp10) outliers start: 95 outliers final: 66 residues processed: 461 average time/residue: 0.4624 time to fit residues: 352.4592 Evaluate side-chains 442 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 368 time to evaluate : 6.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 930 MET Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 469 CYS Chi-restraints excluded: chain B residue 475 GLN Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 554 ASP Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 661 ILE Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 759 GLU Chi-restraints excluded: chain B residue 925 ILE Chi-restraints excluded: chain B residue 941 ASP Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 518 GLU Chi-restraints excluded: chain C residue 570 SER Chi-restraints excluded: chain C residue 693 GLU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 713 ILE Chi-restraints excluded: chain D residue 58 GLN Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 280 TYR Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 432 ILE Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 651 ASP Chi-restraints excluded: chain D residue 877 PHE Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 206 MET Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 13 PHE Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain H residue 173 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 265 optimal weight: 10.0000 chunk 356 optimal weight: 5.9990 chunk 102 optimal weight: 0.6980 chunk 308 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 chunk 335 optimal weight: 7.9990 chunk 140 optimal weight: 4.9990 chunk 344 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 GLN ** B 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 910 ASN D 867 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.214639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.150240 restraints weight = 50979.908| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 3.49 r_work: 0.3528 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 36397 Z= 0.211 Angle : 0.593 14.732 49033 Z= 0.302 Chirality : 0.041 0.271 5235 Planarity : 0.003 0.048 6216 Dihedral : 5.994 58.722 4879 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.35 % Favored : 96.63 % Rotamer: Outliers : 1.93 % Allowed : 28.07 % Favored : 70.01 % 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 (0.13), residues: 4155 helix: 0.81 (0.10), residues: 2483 sheet: -0.43 (0.35), residues: 238 loop : -1.05 (0.16), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP D 601 HIS 0.009 0.001 HIS C 658 PHE 0.047 0.001 PHE C 381 TYR 0.029 0.001 TYR C 709 ARG 0.008 0.000 ARG C 247 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9489.88 seconds wall clock time: 169 minutes 50.20 seconds (10190.20 seconds total)